[ { "templateType" : "single", "fileName" : "adverseEvents.txt", "schemaVersion" : "3.37", "jsonFileName" : "adverseEvents.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The adverse event user defined ID is an identifier chosen by the data provider to refer to a adverse event. The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject for the reported adverse event.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject for the reported adverse event.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "An adverse event may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession for the study in which the reported adverse event occurred.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The adverse event name is a display name that is available when the data is shared, but it is not referenced by other data..", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The adverse event name is an alternate identifier that is visible when the adverse event is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The preferred adverse event name is a term from the MedDRA (www.meddra.org) adverse event classification dictionary. This is an optional term and often updated by ImmPort staff by mapping AE reported names to MedDRA terms.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "name_preferred", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "namePreferred", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The preferred adverse event name is a term from the MedDRA (www.meddra.org) adverse event classification dictionary.", "templateColumn" : "Name Preferred", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_adverse_event_severity", "pv" : true, "conditionalRequired" : false, "description" : "The severity value is chosen from a list of preferred terms.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "severity_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "severityReported", "columnType" : "varchar(60)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The severity value is chosen from a list of preferred terms.", "templateColumn" : "Severity Reported", "foreignKey" : false, "pvPreferredTableColumn" : "severity_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe the outcome of the adverse event.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "outcome_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "outcomeReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The outcome of the adverse event.", "templateColumn" : "Outcome Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study day in which the adverse event was initially reported.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "start_study_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startStudyDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study day in which the adverse event was initially reported.", "templateColumn" : "Start Study Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study day in which the adverse event ceased.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "end_study_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endStudyDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study day in which the adverse event ceased.", "templateColumn" : "End Study Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Was the adverse event believed to be related to a study intervention.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "relation_to_study_treatment", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "relationToStudyTreatment", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Was the adverse event believed to be related to a study intervention.", "templateColumn" : "Relation To Study Treatment", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Which portion(s) of the subject was affected by the adverse event.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "organ_or_body_system_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "organOrBodySystemReported", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Which portion(s) of the subject was affected by the adverse event.", "templateColumn" : "Organ Or Body System Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A lengthier description of the adverse event.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A lengthier description of the adverse event.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Where on/in the subject was the adverse event reported.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "location_of_reaction_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "locationOfReactionReported", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Where on/in the subject was the adverse event reported.", "templateColumn" : "Location Of Reaction Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "What was done to address the adverse event.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "study_treatment_action_taken", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTreatmentActionTaken", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "What was done to address the adverse event.", "templateColumn" : "Study Treatment Action Taken", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Was the adverse event related to some non-study intervention.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "relation_to_nonstudy_treatment", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "relationToNonstudyTreatment", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Was the adverse event related to some non-study intervention.", "templateColumn" : "Relation To Nonstudy Treatment", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Was the adverse event believed to be casued by a study intervention.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "causality", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "causality", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Was the adverse event believed to be caused by a study intervention.", "templateColumn" : "Causality", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Allows for describing the time during a study day in which an adverse event was reported.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "start_time", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startTime", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Allows for describing the time during a study day in which an adverse event was reported.", "templateColumn" : "Start Time", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Allows for describing the time during a study day in which an adverse event was reported.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "adverse_event", "ppvPreferredTableColumn" : null, "tableColumn" : "end_time", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endTime", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Allows for describing the time during a study day in which an adverse event was reported.", "templateColumn" : "End Time", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "adverseevents", "description" : "The Adverse Event Template reports adverse events that are recorded for subjects in a study." }, { "templateType" : "single", "fileName" : "assessmentcomponent.txt", "schemaVersion" : "3.37", "jsonFileName" : "assessmentcomponent.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component user defined ID is an identifier chosen by the data provider to refer to an assessment. The user defined ID is not shared", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an assessment component user defined ID or ImmPort accession.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a assessment panel user defined ID or ImmPort accession for the assessment panel.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "assessment_panel", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "assessment_panel_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assessmentPanelId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a assessment panel user defined ID or ImmPort accession for the assessment_panel.", "templateColumn" : "Assessment Panel ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The link to a study's planned visit provides temporal context for a subjects assessment during the course of a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "planned_visit", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assessment component name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Study time collected describes the time value for when the assessment was completed.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "study_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component value is often the response to a question in a CRF.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueReported", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assessment component value is often the response to a question in a CRF.", "templateColumn" : "Result Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_unit_of_measure", "pv" : true, "conditionalRequired" : false, "description" : "The unit for the assessment value.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultUnitReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit for the assessment value.", "templateColumn" : "Result Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "unit_of_measure_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suggested terms include Mild, Moderate, and Severe.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_category", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueCategory", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A categorical representation of the assessment value.", "templateColumn" : "Result Value Category", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please indicate the age at which a condition reported in the assessment occurred. This column is optional unless units (Age At Onset Unit Reported) is provided.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "age_at_onset_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageAtOnsetReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Age At Onset Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_preferred_time_unit", "pv" : true, "conditionalRequired" : false, "description" : "The time unit for the age of onset value. This column is optional unless value (Age At Onset Reported) is provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "age_at_onset_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageAtOnsetUnitReported", "columnType" : "varchar(25)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Suggested values include Days, Months, Years.", "templateColumn" : "Age At Onset Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "time_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Is the condition reported in the assessment significant for the study analysis?", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "is_clinically_significant", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "isClinicallySignificant", "columnType" : "varchar(1)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a 'Y' or 'N.'", "templateColumn" : "Is Clinically Significant", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please use SnoMED CT terms if possible.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "location_of_finding_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "locationOfFindingReported", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Where on the subject's body does the condition reported in the assessment occur?", "templateColumn" : "Location Of Finding Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please use SnoMED CT terms if possible.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "organ_or_body_system_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "organOrBodySystemReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "What is the organ or body system affected by the condition reported in the assessment?", "templateColumn" : "Organ Or Body System Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suggested terms include prone, supine, seated, and standing.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_position_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectPositionReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The position the subject was in when the assessment was completed.", "templateColumn" : "Subject Position Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "There are no preferrred response values.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "time_of_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "timeOfDay", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "When during the day was the assessment completed.", "templateColumn" : "Time Of Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "What is the wording of the question to elicit the assessment result?", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "verbatim_question", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "verbatimQuestion", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "What is the actual question in the CRF?", "templateColumn" : "Verbatim Question", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Assessments can include study subject medical history and/or family history.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "who_is_assessed", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "whoIsAssessed", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Is the study subject assessed or a member of the study subject's family?", "templateColumn" : "Who Is Assessed", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "assessmentcomponent", "description" : "The assessment an be either new or pre-defined in this template. Any combination is acceptable. The only restriction is that the assessment panel id is the key to the template and must be unique within the template." }, { "templateType" : "combined", "fileName" : "assessmentpanel.txt", "schemaVersion" : "3.37", "jsonFileName" : "assessmentpanel.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment panel user defined ID is an identifier chosen by the data provider to refer to a set of assessments, often organized into a Case Report Form. This ID may be referenced by other data records (e.g. assessment). The user defined ID is not shared", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter either an assessment panel user defined ID or ImmPort accession.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "An assessment panel may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the assessment panel is new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment panel name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "The assessment panel name is an alternate identifier that is visible when the assessment panel is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment type is not a constrained list of terms and suggested values include Physical Exam, Questionnaire, Medical History, Family History.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "assessment_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assessmentType", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Suggested values include Physical Exam, Questionnaire, Medical History, Family History.", "templateColumn" : "Assessment Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment status is not a constrained list of terms and suggested values include Completed, Partial, and Not Completed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "status", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "status", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "The assessment status is not a constrained list of terms and suggested values include Completed, Partial, and Not Completed.", "templateColumn" : "Status", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "crfFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter CRF file(s) to link to the assessment panel. Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "templateColumn" : "CRF File Names", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "assessmentpanel", "description" : "The assessment panel can be either new or pre-defined in this template. Any combination is acceptable. The only restriction is that the assessment panel id is the key to the template and must be unique within the template." }, { "templateType" : "combined-result", "fileName" : "assessments.txt", "schemaVersion" : "3.37", "jsonFileName" : "assessments.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject for the subject from which the assessment was completed. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the assessment was completed.", "templateColumn" : "Subject ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment panel user defined ID is an identifier chosen by the data provider to refer to a set of assessments, often organized into a Case Report Form. This ID may be referenced by other data records (e.g. assessment). The user defined ID is not shared", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assessmentPanelId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter either an assessment panel user defined ID or ImmPort accession.", "templateColumn" : "Assessment Panel ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An assessment panel may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "assessment_panel_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Assessment Panel in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the assessment panel is new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The assessment panel name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "assessment_panel_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : "you are defining a new Assessment Panel in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "The assessment panel name is an alternate identifier that is visible when the assessment panel is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment type is not a constrained list of terms and suggested values include Physical Exam, Questionnaire, Medical History, Family History.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "assessment_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assessmentType", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Suggested values include Physical Exam, Questionnaire, Medical History, Family History.", "templateColumn" : "Assessment Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment status is not a constrained list of terms and suggested values include Completed, Partial, and Not Completed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "assessment_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "status", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "status", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "The assessment status is not a constrained list of terms and suggested values include Completed, Partial, and Not Completed.", "templateColumn" : "Status", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "crfFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "assessment_panel", "ppv" : false, "comment" : "Please enter CRF file(s) to link to the assessment panel. Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "templateColumn" : "CRF File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "This pseudo column separates the results (assessment components) from the assessment panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component user defined ID is an identifier chosen by the data provider to refer to this assessment result. An assessment component is a portion of an assessment panel. The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assessment component identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The link to a study's planned visit provides temporal context for a subjects assessment during the course of a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "planned_visit", "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assessment component name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Study time collected describes the time value for when the assessment was completed.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "study_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please indicate the age at which a condition reported in the assessment occurred. This column is optional unless units (Age At Onset Unit Reported) is provided.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Age At Onset Unit Reported", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "age_at_onset_reported", "conditionalRequiredWhenText" : "Age At Onset Unit Reported is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageAtOnsetReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Age At Onset Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_preferred_time_unit", "pv" : true, "conditionalRequired" : true, "description" : "The time unit for the age of onset value. This column is optional unless value (Age At Onset Reported) is provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Age At Onset Reported", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "age_at_onset_unit_reported", "conditionalRequiredWhenText" : "Age At Onset Reported is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageAtOnsetUnitReported", "columnType" : "varchar(25)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Suggested values include Days, Months, Years.", "templateColumn" : "Age At Onset Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "time_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Is the condition reported in the assessment significant for the study analysis?", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "is_clinically_significant", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "isClinicallySignificant", "columnType" : "varchar(1)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a 'Y' or 'N.'", "templateColumn" : "Is Clinically Significant", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please use SnoMED CT terms if possible.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "location_of_finding_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "locationOfFindingReported", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Where on the subject's body does the condition reported in the assessment occur?", "templateColumn" : "Location Of Finding Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please use SnoMED CT terms if possible.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "organ_or_body_system_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "organOrBodySystemReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "What is the organ or body system affected by the condition reported in the assessment?", "templateColumn" : "Organ Or Body System Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assessment component value is often the response to a question in a CRF.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueReported", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assessment component value is often the response to a question in a CRF.", "templateColumn" : "Result Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_unit_of_measure", "pv" : true, "conditionalRequired" : false, "description" : "The unit for the assessment value.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultUnitReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit for the assessment value.", "templateColumn" : "Result Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "unit_of_measure_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suggested terms include Mild, Moderate, and Severe.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_category", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueCategory", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A categorical representation of the assessment value.", "templateColumn" : "Result Value Category", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suggested terms include prone, supine, seated, and standing.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_position_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectPositionReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The position the subject was in when the assessment was completed.", "templateColumn" : "Subject Position Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "There are no preferrred response values.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "time_of_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "timeOfDay", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "When during the day was the assessment completed.", "templateColumn" : "Time Of Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "What is the wording of the question to elicit the assessment result?", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "verbatim_question", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "verbatimQuestion", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "What is the actual question in the CRF?", "templateColumn" : "Verbatim Question", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Assessments can include study subject medical history and/or family history.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "assessment_component", "ppvPreferredTableColumn" : null, "tableColumn" : "who_is_assessed", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "whoIsAssessed", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Is the study subject assessed or a member of the study subject's family?", "templateColumn" : "Who Is Assessed", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "assessments", "description" : "The assessment panels template defines and annotates the assessment panels and the assessment components (results) defines and annotates the assessment for the panel. Assessment panels are often encoded in Case Report Forms (CRFs) and these are linked to a study. Assessment components are the answers to questions or assessments recorded in a CRF for a given subject within a study. The assessment template enables you to define the panel and its components in a single form. The assessment panel can be either new or pre-defined in this template. Any combination is acceptable. The only restriction is that the assessment panel id is the key to the template and must be unique within the template." }, { "templateType" : "compound", "fileName" : "basic_study_design.txt", "schemaVersion" : "3.37", "jsonFileName" : "basic_study_design.json", "validationLevel" : "", "templates" : [ { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study user defined ID is an identifier chosen by the data provider to refer to a study design. This ID may be referenced by other data records (e.g. arm). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The brief title will be displayed on ImmPort wherever the study is described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "brief_title", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "briefTitle", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The brief title serves as a working title for a study.", "templateColumn" : "Brief Title", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The official study title is displayed on the ImmPort study detail page.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "official_title", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "officialTitle", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The official study title may be the same as the brief title, but is often more descriptive.", "templateColumn" : "Official Title", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A brief study description highlights the essential features of a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "brief_description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "briefDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Summarize the goals, methods and results of the study.", "templateColumn" : "Brief Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The detailed description can be formatted with html tags to improve legibility. Embedded new line characters should be removed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "clob", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The detailed description supports a lengthy description of the goals and methods of the study.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If a study is interventional or has an interventional component, a short descriptive name of the intervention agent is requested.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "intervention_agent", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "interventionAgent", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "IA brief description of the study's interventional component (e.g. influenza vaccine).", "templateColumn" : "Intervention Agent", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The endpoints can be formatted with html tags to improve legibility. Embedded new line characters should be removed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "endpoints", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endpoints", "columnType" : "clob", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Endpoints include assessments, lab tests and assays that are part of a study design.", "templateColumn" : "Endpoints", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The organization that provides funding and support for the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "sponsoring_organization", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "sponsoringOrganization", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The organization that provides funding and support for the study.", "templateColumn" : "Sponsoring Organization", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The unit of time used to describe the subject's age in the study. The unit of time for a subject must conform to this unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "age_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit of time used to describe the subject's age in the study. The unit of time for a subject must conform to this unit.", "templateColumn" : "Age Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The date format is either dd-MMM-yy or dd-MMM-yyyy where day (dd) is one or two digits 1..31 appropriate to the month, month (MMM) is case-insensitive value (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec), and year is either (yy) two digits, for example 05 means 2005, and 96 means 1996, or (yyyy) is four digit year, for example 2005.", "jsonDataType" : "date", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "actual_start_date", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "actualStartDate", "columnType" : "date", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The commencement time point of the study. The date format is either dd-MMM-yy or dd-MMM-yyyy. ", "templateColumn" : "Actual Start Date", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The date format is either dd-MMM-yy or dd-MMM-yyyy where day (dd) is one or two digits 1..31 appropriate to the month, month (MMM) is case-insensitive value (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec), and year is either (yy) two digits, for example 05 means 2005, and 96 means 1996, or (yyyy) is four digit year, for example 2005.", "jsonDataType" : "date", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_public_release_date", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedPublicReleaseDate", "columnType" : "date", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Projected date for the release of the study to the public. The date format is either dd-MMM-yy or dd-MMM-yyyy. ", "templateColumn" : "Planned Public Release Date", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The hypothesis can be formatted with html tags to improve legibility. Embedded new line characters should be removed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "hypothesis", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hypothesis", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The explanatory proposition(s) being tested by the research study.", "templateColumn" : "Hypothesis", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The objectives can be formatted with html tags to improve legibility. Embedded new line characters should be removed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "objectives", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "objectives", "columnType" : "clob", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The goals of the research study.", "templateColumn" : "Objectives", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The number of subjects proposed to be enrolled in the study.", "jsonDataType" : "positive", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "target_enrollment", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "targetEnrollment", "columnType" : "integer", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The number of subjects proposed to be enrolled in the study.", "templateColumn" : "Target Enrollment", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The minimum age of subjects enrolled in the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "minimum_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minimumAge", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The minimum age of subjects enrolled in the study.", "templateColumn" : "Minimum Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum age of subjects enrolled in the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study", "ppvPreferredTableColumn" : null, "tableColumn" : "maximum_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maximumAge", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The maximum age of subjects enrolled in the study.", "templateColumn" : "Maximum Age", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study", "jsonCompoundAttribute" : "study", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A research focus for the study from the drop down list", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_categorization", "ppvPreferredTableColumn" : null, "tableColumn" : "research_focus", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "researchFocus", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_research_focus", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please use the drop down list", "templateColumn" : "Research Focus", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_categorization", "jsonCompoundAttribute" : "studyCategorization", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : "lk_disease_condition", "pv" : true, "conditionalRequired" : false, "description" : "The condition(s)/disease(s) that is (are) being researched or evaluated in the study. Please select condition or disease from the list provided if the condition or disease matches yours or enter a condition or disease if there is not an appropriate one provided. Values provided by the user are further checked against the pref mapping table lk_study_condition_pref_mappng.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_condition_or_disease", "ppvPreferredTableColumn" : "condition_preferred", "tableColumn" : "condition_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_study_condition_pref_mappng", "jsonAttribute" : "conditionReported", "columnType" : "varchar(550)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The condition(s)/disease(s) that is (are) being researched or evaluated in the study. Please select condition or disease from the list provided if the condition or disease matches yours or enter a condition or disease if there is not an appropriate one provided. Values provided by the user are further checked against the pref mapping table lk_study_condition_pref_mappng.", "templateColumn" : "Condition Reported", "foreignKey" : false, "pvPreferredTableColumn" : "condition_preferred" } ], "name" : "study_2_condition_or_disease", "jsonCompoundAttribute" : "study2ConditionOrDisease", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study's arm(s) or cohort(s) group subjects by criteria relevant to the study (e.g. age, condition) and/or treatments or interventions. Insert rows in the template to define additional arms or cohorts linked to the study. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The arm or cohort user defined ID is an identifier chosen by the data provider to refer to a subject grouping in the study document. This ID may be referenced by other data records (e.g. subjects). The user defined ID is not shared.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The arm or cohort name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The arm or cohort name is an alternate identifier that is visible when the study is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The description should expand any abbreviations used in the arm or cohort name. For example for an observational study with a cohort whose name was \"ADEH+\", the description would be \"Atopic dermatitis with eczema herpeticum\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The description should expand any abbreviations used in the arm or cohort name.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_arm_type", "pv" : true, "conditionalRequired" : false, "description" : "The drop down list provides the list of preferred study arm types derived from the National Cancer Institute Thesaurus (NCIT). For an interventional study, the type defines the treatment/control attributes of the arms. The attributes are selected from the values listed below (a study may have more than one arm of a given value). Clinical studies often use the following terms. Experimental - Arm for procedure or drug being evaluated. Active Comparator - arm receiving \"standard of care\" treatment. Placebo Comparator - arm receiving placebo treatment. Sham Comparator - arm receiving a sham procedure such as a urgery or a sham device. No Intervention - arm receiving neither \"standard of care\" treatment a placebo, or sham procedure or device. For an observational study, the type should be Observational - All arms are observing differences in cohorts", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : "type_preferred", "tableColumn" : "type_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_arm_type_pref_mapping", "jsonAttribute" : "typeReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "Please select a preferred arm study type from the the drop down list. Terms are derived from the National Cancer Institute Thesaurus (NCIT). The study arm type is a preferred value and the table lk_arm_type_pref_mapping is also used to map the reported type to the drop down list (lk_arm_type).", "templateColumn" : "Type Reported", "foreignKey" : false, "pvPreferredTableColumn" : "type_preferred" } ], "name" : "arm_or_cohort", "jsonCompoundAttribute" : "armOrCohort", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The personnel user defined ID is an identifier chosen by the data provider to refer to personnel who may be contacted for more details about the study document. If more than one study personnel record is to be defined, copy the block of rows from Study_Personnel_ID to Site_Name for each additional study personnel record. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Usually, the education achievement level of the person.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "honorific", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "honorific", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Usually, the education achievement level of the person.", "templateColumn" : "Honorific", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The last name of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "last_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lastName", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The last name of the study personnel being described.", "templateColumn" : "Last Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The first name of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "first_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "firstName", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The first name of the study personnel being described.", "templateColumn" : "First Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suffixes that are part of the study personnel's name being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "suffixes", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "suffixes", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Suffixes that are part of the study personnel's name being described.", "templateColumn" : "Suffixes", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The organization with whom the study personnel being described is affiliated.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "organization", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "organization", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The organization with whom the study personnel being described is affiliated.", "templateColumn" : "Organization", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "ORCID (Open Researcher and Contributor Identification), a non-profit organization that promotes the use of its unique digital identifier to connect researchers with their science contributions over time and across changes of name, location and institutional affiliation. The NIH encourages use of this ID. See the link https://nexus.od.nih.gov/all/2019/08/05/linking-orcid-identifiers-to-era-profiles-to-streamline-application-processes-and-to-enhance-tracking-of-career-outcomes/.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "orcid", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "orcidId", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "ORCID (Open Researcher and Contributor Identification), a non-profit organization that promotes the use of its unique digital identifier to connect researchers with their science contributions over time and across changes of name, location and institutional affiliation. The NIH encourages use of this ID.", "templateColumn" : "ORCID ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Contact information of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "email", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "email", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Contact information of the study personnel being described.", "templateColumn" : "Email", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The role the personnel play in the study as defined by the research team.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "title_in_study", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "titleInStudy", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The role the personnel play in the study as defined by the research team.", "templateColumn" : "Title In Study", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The ImmPort display will show the personnel listed as 'PI' in the study.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "role_in_study", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "roleInStudy", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_personnel_role", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please use the drop down list.", "templateColumn" : "Role In Study", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter the site name if there is a need to further differentiate the affiliation of the study personnel form the Organization.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "site_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "siteName", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter the site name if there is a need to further differentiate the affiliation of the study personnel from the Organization.", "templateColumn" : "Site Name", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_personnel", "jsonCompoundAttribute" : "studyPersonnel", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The planned visit user defined ID is an identifier chosen by the data provider to refer to a planned visit. This ID may be referenced by other data records (e.g. biological samples). The user defined ID is not shared. Insert rows in the template to define additional planned visits linked to the study. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "the visit name should indicate the purpose of the visit (e.g. screening, assessment, inoculation, sample drawn). The visit name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The visit name is an alternate identifier that is visible when the protocol is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive whole number value.", "jsonDataType" : "positive", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "order_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "orderNumber", "columnType" : "integer", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The order of the visit within the study design schedule.", "templateColumn" : "Order Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive or negative numeric value.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "min_start_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minStartDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The minimum start day for a visit as defined in the study schedule.", "templateColumn" : "Min Start Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive or negative numeric value. If no value is entered, the maximum start day will be set equal to the minimum start day.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "max_start_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maxStartDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The maximum start day for a visit as defined in the study schedule.", "templateColumn" : "Max Start Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter a start rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "start_rule", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startRule", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter a start rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "templateColumn" : "Start Rule", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter an end rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "end_rule", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endRule", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter an end rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "templateColumn" : "End Rule", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "planned_visit", "jsonCompoundAttribute" : "plannedVisit", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The inclusion or exclusion user defined ID is an identifier chosen by the data provider to refer to a criterion used to determine whether a subject may be enrolled in a study. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "One or more criterion must be described to decide whether a subject may be enrolled in a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "criterion", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "criterion", "columnType" : "varchar(750)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The criterion describes the parameter used to decide if a subject may be enrolled in a study.", "templateColumn" : "Criterion", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The criterion category is selected form a preferred list of terms.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "criterion_category", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "criterionCategory", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_criterion_category", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "There are two values to choose from: inclusion or exclusion.", "templateColumn" : "Criterion Category", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "inclusion_exclusion", "jsonCompoundAttribute" : "inclusionExclusion", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol ID for the study. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "protocol", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The protocol ID for the study.", "templateColumn" : "Protocol ID", "foreignKey" : true, "pvPreferredTableColumn" : null } ], "name" : "study_2_protocol", "jsonCompoundAttribute" : "study2Protocol", "templateRequired" : "yes" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If there are additional files (e.g. as data dictionaries, CRFs, custom formatted lab tests or assessments) that should be linked to the study please indicate them in this block. Insert rows in the template to link additional files to the study. Use the study_design_edit template to add additional records after a study is defined in ImmPort. The file size name limit is 250 characters. For a given study, all file names for study_file must be unique.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "file_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "fileName", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the file, including file extension, that is to be linked to the study. The file size name limit is 250 characters. For a given study, all file names for study_file must be unique.", "templateColumn" : "File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A brief description of the file.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A brief description of the file.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Additional study data or study descriptions are current preferred terms.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "study_file_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyFileType", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_study_file_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study File Type", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_file", "jsonCompoundAttribute" : "studyFile", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The name of the website to which the link refers. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_link", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the website to which the link refers.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If this is a clinical trial, please include the clinicalTrial.gov URL.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_link", "ppvPreferredTableColumn" : null, "tableColumn" : "value", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "value", "columnType" : "varchar(2000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Define websites that are linked to the study. Insert rows in the template to define additional websites linked to the study.", "templateColumn" : "Value", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_link", "jsonCompoundAttribute" : "studyLink", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Pubmed or PubMedCentral identifier of an article that includes data from this study. Use the study_design_edit template to add additional records after a study is defined in ImmPort.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "pubmed_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "pubmedId", "columnType" : "varchar(16)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Pubmed or PubMedCentral identifier of an article that includes data from this study.", "templateColumn" : "Pubmed ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Digital Object Identifier is a persistent identifier or handle used to uniquely identify an object. ImmPort DOIs are generated by DataCite (https://www.datacite.org/)", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "doi", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "doi", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Digital Object Identifier is a persistent identifier or handle used to uniquely identify an object.", "templateColumn" : "DOI", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The title of an article that includes data from this study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "title", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "title", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The title of an article that includes data from this study.", "templateColumn" : "Title", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The journal name that publishes an article that includes data from this study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "journal", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "journal", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The journal name that publishes an article that includes data from this study.", "templateColumn" : "Journal", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The article publication year.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "year", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "year", "columnType" : "varchar(4)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The article publication year.", "templateColumn" : "Year", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The article publication month.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "month", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "month", "columnType" : "varchar(12)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The article publication month.", "templateColumn" : "Month", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The journal's issue number.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "issue", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "issue", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The journal's issue number.", "templateColumn" : "Issue", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The journal's page number.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "pages", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "pages", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The journal's page number.", "templateColumn" : "Pages", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The article's authors.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "authors", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "authors", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The article's authors.", "templateColumn" : "Authors", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_pubmed", "jsonCompoundAttribute" : "studyPubmed", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The ID assigned to this contract by the sponsoring organizaton. If it is a NIH Contract, please enter the project number assigned and available from NIH Reporter. Example: 1P01AI165072-01.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "contract_grant", "ppvPreferredTableColumn" : null, "tableColumn" : "external_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "externalId", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The ID assigned to this contract by the sponsoring organizaton. If it is a NIH Contract, please enter the project number assigned and available from NIH Reporter. Example: 1P01AI165072-01.", "templateColumn" : "External ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Category choices are NIH or Other", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "contract_grant", "ppvPreferredTableColumn" : null, "tableColumn" : "category", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "category", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_contract_category", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Category choices are NIH or Other", "templateColumn" : "Category", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Name of the contract", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "contract_grant", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Name of the contract", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Add the URL for the link to the contract details. For example the link for a NIH contract 1K23HL125663-01, Metabolic derangements in ARDS is https://reporter.nih.gov/project-details/8804164", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "contract_grant", "ppvPreferredTableColumn" : null, "tableColumn" : "link", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "link", "columnType" : "varchar(2000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Add the URL for the link to the contract details. For example the link for a NIH contract 1K23HL125663-01, Metabolic derangements in ARDS is https://reporter.nih.gov/project-details/8804164", "templateColumn" : "Link", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "contract_grant", "jsonCompoundAttribute" : "contractGrant", "templateRequired" : "no" } ], "name" : "basic_study_design", "description" : "The basic study design template defines and annotates key elements of a study including the purpose, subject grouping, schedule of events, personnel, and references (weblinks, publications). Use the study_design_edit template to add additional information for a study after a study is defined in ImmPort. The basic study design template consists of several sections or compound templates. Some compound templates are required: study, arm_or_cohort, inclusion_exclusion, planned_visit, study_2_condition_or_disease, study_2_protocol, study_categorization, study_personnel. Other compound templates are optional: study_file, study_link, and study_pubmed." }, { "templateType" : "single", "fileName" : "bioSamples.txt", "schemaVersion" : "3.37", "jsonFileName" : "bioSamples.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "planned_visit", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a treatment user defined ID or ImmPort accession if the sample was manipulated in a manner significant to the assay prior to the assay being conducted. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "biosamples", "description" : "The biological sample template is a legacy template that defines and annotates the types of samples derived from study subjects and when during the study schedule the sample was derived. The function of this template is also captured in the experiment samples template. This template will continue to be supported for the foreseeable future to support backward compatibility." }, { "templateType" : "combined", "fileName" : "controlSamples.txt", "schemaVersion" : "3.37", "jsonFileName" : "controlSamples.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The control sample user defined ID is an identifier chosen by the data provider. This ID may be referenced by other data records (e.g. MBAA results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "controlSampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Control Sample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The manufacturer or lab where the control sample was obtained.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "control_sample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "source", "conditionalRequiredWhenText" : "you are defining a new Control Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "source", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The manufacturer or lab where the control sample was obtained.", "templateColumn" : "Source", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The manufacturer or source lab's identifier.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "control_sample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_id", "conditionalRequiredWhenText" : "you are defining a new Control Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The manufacturer or source lab's identifier.", "templateColumn" : "Catalog ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The dilution factor indicates how much a sample was diluted before it was assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "control_sample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "dilution_factor", "conditionalRequiredWhenText" : "you are defining a new Control Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dilutionFactor", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Dilution Factor", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "control_sample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_id", "conditionalRequiredWhenText" : "you are defining a new Control Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_group_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayGroupId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay Group ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The format of the result file depends on the assay type. ImmPort supports results templates (MBAA_Results.txt) for some of the commonly used immunological assay methods. These template facilitate the sharing and re-use of results data in a standard format. If the result file is the ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "control_sample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Control Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The format of the result file depends on the assay type. ImmPort supports results templates (MBAA_Results.txt) for some of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. If the result file is the ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is expected to be the MBAA_Results.txt ImmPort template. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "Enter the file name (including file extension) that contains assay results for the control sample. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "control_sample", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "HIPC recommends including bead level result files if they are available. Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "control_sample", "ppv" : false, "comment" : "HIPC recommends including bead level result files if they are available. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either an experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "controlsamples", "description" : "The control sample template defines and annotates the control samples included in MBAA assays. Control samples are not assumed to be of biologic origin. This template requires that the control sample be always new, while the experiment can be new or pre-defined. The control sample is the key to the templates and must be unique within the template." }, { "templateType" : "multiple", "fileName" : "CyTOF_Derived_data.txt", "schemaVersion" : "3.37", "jsonFileName" : "CyTOF_Derived_data.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_cell_population", "pv" : true, "conditionalRequired" : false, "description" : "The drop down list provides a list of cell population names. Please select a name if it matches your cell population name or enter a population name if there is not an appropriate one provided. The population name has a limit of 150 characters. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Population Name Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : "population_name_preferred", "tableColumn" : "population_name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_cell_population_pref_map", "jsonAttribute" : "populationNameReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The population name is the type of cells whose count is reported. Please select a population name from the drop down list if it matches your cell population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Population Name Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "templateColumn" : "Population Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_prefix_preferred and population_name_preferred" }, { "pvTableName" : "lk_cell_population_definition", "pv" : true, "conditionalRequired" : false, "description" : "he gating definition is the set of markers and their expression profile that describes a cell population name. Please select a gating definition from the drop down list if it matches your gating definition or enter a gating definition if there is not an appropriate one provided. The marker names should conform to standard names as described in the LK_ANALYTE table. Note that a comma, forward slash or pipe may be used as marker delimiter. The expression values are '-', '+', '+-', '+~', '++', or ''. The gating definition has a limit of 150 characters.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_defnition_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "gatingDefinitionReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The gating definition is the set of markers and their expression profile. Please select a gating definition from the drop down list or enter a gating definition. Please see the ImmPort Upload Templates for details on representing marker names, delimiters and expression values. ", "templateColumn" : "Gating Definition Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_defnition_preferred" }, { "pvTableName" : "lk_cell_population", "pv" : true, "conditionalRequired" : false, "description" : "The drop down provides the base parent population. Please select a name if it matches your base parent population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Parent Population Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : "parent_population_preferred", "tableColumn" : "parent_population_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_cell_population_pref_map", "jsonAttribute" : "parentPopulationReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The base parent population name. Please select a population name from the drop down list if it matches your base parent population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\" . Also, if the Parent Population eported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "templateColumn" : "Parent Population Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_prefix_preferred and population_name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The count of the cell type defined by the marker gating definition.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_statistic_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "populationStatisticCountPercentileEtc", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Population Statistic (count, percentile, etc)", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_cell_pop_statistic_unit", "pv" : true, "conditionalRequired" : false, "description" : "The unit used to describe the cell count. Please select a unit from the drop down list if the definition matches your unit name or enter a unit if there is not an appropriate one provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_stat_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "populationStatUnitReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit used to describe the cell count. Please select a unit from the list provided if the definition matches your unit name or enter a unit if there is not an appropriate one provided.", "templateColumn" : "Population Stat Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "statistic_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "An XML formatted export of the analysis program is expected (e.g. an xml format of a FlowJo .jo or .wsp file). The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "workspaceFile", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the file that stores the interpreted CyTOF results from the analysis program. The file size name limit is 240 characters.", "templateColumn" : "Workspace File", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "cytof_derived_data", "description" : "The CYTOF derived data template captures and annotates the assay results for a sample by linking sample, experiment, and interpreted results together." }, { "templateType" : "multiple", "fileName" : "ELISA_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "ELISA_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elisa_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The analyte's concentration value.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte's concentration value.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_concentration_unit", "pv" : true, "conditionalRequired" : false, "description" : "The analyte's concentration unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte's concentration unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "concentration_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Unstructured text to further describe the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Unstructured text to further describe the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elisa_results", "description" : "The ELISA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Analyte', 'Calculated Concentration Value', and 'Calculated Concentration Unit' needed to describe each assay result." }, { "templateType" : "multiple", "fileName" : "ELISPOT_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "ELISPOT_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elispot_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The number of spots generated by the reporting assay reagent.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "spot_number_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "spotNumberReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Spot Number Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The number of live cells assayed per well.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "cell_number_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "cellNumberReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Cell Number Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Unstructured text to further describe the result", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Unstructured text to further describe the result", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elispot_results", "description" : "The ELISPOT experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Analyte', 'Number Of Spots Per Well', and 'Cell number per well Value', 'Cell number per well Unit' needed to describe each assay result." }, { "templateType" : "single", "fileName" : "experiments.txt", "schemaVersion" : "3.37", "jsonFileName" : "experiments.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment user defined ID is an identifier chosen by the data provider to refer to an experiment. This ID may be referenced by other data records (e.g. experiment sample, control sample, standard curve). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "An experiment may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession for the study in which the experiment occurs.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a protocol user defined ID or ImmPort accession. One or more identifiers can be entered per subject. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "protocol", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null } ], "name" : "experiments", "description" : "The experiments template is a legacy template that defines and annotates the mechanistic assays performed on samples. The function of this template is also captured in the experiment samples template. This template will continue to be supported for the foreseeable future to support backward compatibility." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.CYTOF.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.CYTOF.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The primary output for CYTOF assays is a file in .fcs format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The primary output for CYTOF assays is a file in .fcs format. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "cytof", "description" : "The CYTOF experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.ELISA.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.ELISA.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : " This COLUMN must appear as the FIRST COLUMN for a repeating result column group. The list of values displays common immunology gene symbol and the gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The analyte's concentration value.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte's concentration value.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_concentration_unit", "pv" : true, "conditionalRequired" : false, "description" : "The analyte's concentration unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte's concentration unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "concentration_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elisa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elisa", "description" : "The ELISA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Analyte', 'Calculated Concentration Value', and 'Calculated Concentration Unit' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.ELISPOT.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.ELISPOT.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The molecule or entity being measured. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The molecule or entity being measured. This COLUMN must appear as the FIRST COLUMN for a repeating result column group. The list of values displays common immunology gene symbol and the gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The number of spots generated by the reporting assay reagent.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "spot_number_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "spotNumberReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Spot Number Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The number of live cells assayed per well.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "cell_number_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "cellNumberReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Cell Number Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "elispot_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elispot", "description" : "The ELISPOT experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Analyte', 'Number Of Spots Per Well', and 'Cell number per well Value', 'Cell number per well Unit' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Flow_Cytometry.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Flow_Cytometry.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The primary output for flow cytometry assays is a file in .fcs format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "fcsResultFile", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The primary output for flow cytometry assays is a file in .fcs format. The file size name limit is 240 characters.", "templateColumn" : ".Fcs Result File", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "compensationOrControlFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Flow cytometry assay runs include compensation and/or control files. The set of compensation/control files from an assay run should be linked to the experiment sample that is linked to the assayed sample's fcs file. The file size name limit is 240 characters.", "templateColumn" : "Compensation Or Control File Name(s)", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "flow_cytometry", "description" : "The flow cytometry experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Gene_Expression_Array.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Gene_Expression_Array.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "ImmPort expects array gene expression results to be deposited in NCBI GEO since this is a prerequisite for publication. Please choose this repository name from the list.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Accession", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Accession is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Array gene expression results are expected to be deposited in NCBI GEO Please choose this repository name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Name", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Name is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s).", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "gene_expression_array", "description" : "The gene expression experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Genotyping_Array.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Genotyping_Array.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "ImmPort expects genotyping results to be deposited in dbGAP since this is a prerequisite for publication. In order to avoid duplication of data upload by requiring the same data be sent to ImmPort as well as dbGAP, ImmPort requires only the dbGAP accession.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Accession", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Accession is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Genotyping results are expected to be deposited in dbGAP. Please choose this repository name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Name", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Name is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s).", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "genotyping_array", "description" : "The genotyping experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.HAI.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.HAI.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_virus_strain", "pv" : true, "conditionalRequired" : false, "description" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "virus_strain_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "virusStrainReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared. This COLUMN must appear as the FIRST COLUMN for a repeating result column group.", "templateColumn" : "Virus Strain Reported", "foreignKey" : false, "pvPreferredTableColumn" : "virus_strain_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum sample dilution factor that continues to demonstrate inhibition of hemagglutination.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_titer_unit", "pv" : true, "conditionalRequired" : false, "description" : "The dilution factor unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dilution factor unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "titer_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hai", "description" : "The HAI experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Virus Strain'and 'Titration Dilution Value' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.HLA.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.HLA.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you do not use the ImmPort template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hla", "description" : "The HLA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Image_Histology.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Image_Histology.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter the file name for this assay result. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the file name for this assay result. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "image_histology", "description" : "The image histology experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.KIR.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.KIR.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you do not use the ImmPort template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "kir", "description" : "The KIR experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Mass_Spectrometry_Metabolomics.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Mass_Spectrometry_Metabolomics.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The standard parsable template file for this template is Mass_Spectrometry_Metabolomic_Results.txt. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you DO NOT use the ImmPort template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The standard parsable template file for this template is Mass_Spectrometry_Metabolomic_Results.txt. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Metabolite Mass spectrometry results are expected to be deposited in an external repository. Please choose one these repositorys name from the list.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Accession", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Accession is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Metabolite Mass spectrometry results are expected to be deposited in an external repository. Please choose one these repositorys name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Name", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Name is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s).", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mass_spec_metabolomics", "description" : "The Mass Spectrometry experiment sample template for Metabolomics defines and annotates the assay results for a sample by linking sample, experiment, and resultstogether. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Mass_Spectrometry_Proteomics.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Mass_Spectrometry_Proteomics.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The standard parsable template file for this template is Mass_Spectrometry_Proteomic_Results.txt. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you DO NOT use the ImmPort template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The standard parsable template file for this template is Mass_Spectrometry_Proteomic_Results.txt. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Protein sequence file in fasta sequence format.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "proteinSequenceDatabaseFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Protein sequence file in fasta sequence format.", "templateColumn" : "Protein Sequence Database File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "ImmPort expects Protein Mass spectrometry results are expected to be deposited in PRIDE or MassIVE. Please choose one these repositorys name from the list.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Accession", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Accession is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Protein Mass spectrometry results are expected to be deposited in PRIDE or MassIVE. Please choose one these repositorys name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Repository Name", "operator" : "not-empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and Repository Name is provided", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s).", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mass_spec_proteomics", "description" : "The Mass Spectrometry experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and resultstogether. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.MBAA.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.MBAA.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you do not use the ImmPort template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_mbaa_detail", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_id", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The dilution factor indicates how much a sample was diluted before it was assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_mbaa_detail", "ppvPreferredTableColumn" : null, "tableColumn" : "dilution_factor", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dilutionFactor", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Dilution Factor", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_mbaa_detail", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_group_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayGroupId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay Group ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe the MBAA plate type used in the assay.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_mbaa_detail", "ppvPreferredTableColumn" : null, "tableColumn" : "plate_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plateType", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_plate_type", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe the MBAA plate type used in the assay.", "templateColumn" : "Plate Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mbaa", "description" : "The MBAA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.Neutralizing_Antibody_Titer.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Neutralizing_Antibody_Titer.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_virus_strain", "pv" : true, "conditionalRequired" : false, "description" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "virus_strain_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "virusStrainReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared. This COLUMN must appear as the FIRST COLUMN for a repeating result column group.", "templateColumn" : "Virus Strain Reported", "foreignKey" : false, "pvPreferredTableColumn" : "virus_strain_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum sample dilution factor that continues to demonstrate virus neutralization.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_titer_unit", "pv" : true, "conditionalRequired" : false, "description" : "The dilution factor unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dilution factor unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "titer_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "neutralizing_antibody_titer", "description" : "The neutralizing antibody experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Virus Strain'and 'Titration Dilution Value' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.Other.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Other.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter the file name for this assay result. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the file name for this assay result. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "other", "description" : "This experiment sample template is used when no other experiment sample template is available to define and annotate the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.QRT-PCR.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.QRT-PCR.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The NCBI Gene symbol for the gene being assayed. Please select a gene symbol from the list provided if the gene symbol matches your symbol or enter a symbol if there is not an appropriate one provided. This symbol is visible when the result is shared. If the gene sybmol is a NCBI Gene Symbol that is provided in the list, then the columns 'Gene Name' and 'Gene ID' will also be overwritten by the gene name and Entrez Gene ID provided by NCBI.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneSymbolName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Gene symbol for the gene being assayed. Please select a gene symbol from the list provided if the gene symbol matches your symbol or enter a symbol if there is not an appropriate one provided. This symbol is visible when the result is shared.", "templateColumn" : "Gene Symbol Name", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This value could be absolute or relative. For example, an absolute expression value could be 6 ng RNA/mg intestine. In this case, 6 should be entered in the 'Expression value of target RNA' column, while ng RNA/ mg intestine is in the 'Expression unit of target RNA' column. A relative expression value, like signal versus GAPDH, could be 2.07. In this case, 2.07 should be in the 'Expression value of target RNA' column, while relative to GAPDH is in the 'Expression unit of target RNA' column.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_pcr_expression_unit", "pv" : true, "conditionalRequired" : false, "description" : "The unit for the Expression Value Of Target Nucleic ACID. Please select a unit from the list provided if the unit matches your unit or enter a unit if there is not an appropriate one provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit for the Expression Value Of Target Nucleic ACID. Please select a unit from the list provided if the unit matches your unit or enter a unit if there is not an appropriate one provided.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "expression_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The NCBI Gene ID for the gene being assayed. A number is expected.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "gene_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneId", "columnType" : "varchar(10)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Gene ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The NCBI Gene name for the gene being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "gene_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneName", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Gene name for the gene being assayed.", "templateColumn" : "Gene Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Additional identifier(s) for the gene being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "other_gene_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "otherGeneAccession", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Additional identifier(s) for the gene being assayed.", "templateColumn" : "Other Gene Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "qrt-pcr", "description" : "The qRT-PCR experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying at least the group of columns 'Entrez Gene ID' and 'Threshold Cycles(ct)' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-multiple", "fileName" : "experimentSamples.RNA_Sequencing.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.RNA_Sequencing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column. If NO RESULT FILE is provided, then leave this column blank.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "If the result file is an ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column. If NO RESULT FILE is provided, then leave this column blank.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Completing this column is conditional upon whether the \"ImmPort Template?\" column value is set to \"Yes\" or \"No\". If the value is not set, DO NOT PROVIDE a result file (it will be ignored). If the \"ImmPort Template?\" column value is set to \"Yes\", do not enter a file name in the \"Result File Name\" column. If the \"ImmPort Template?\" column value is set to \"No\", enter a file name in the \"Result File Name\" column. ImmPort supports results templates for many of the commonly used immunological assay methods. These templates facilitate the sharing and re-use of results data in a standard format. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please use the ImmPort template for this assay result (as opposed to custom file formats) to standardize the format of the data when it is shared. If you use the ImmPort template (strongly recommended by NIAID DAIT), do not enter the template name in this column and set the \"ImmPort Template?\" column value to \"Yes\". If you do not use the ImmPort template and are providing a result template, enter the file name (including file extension) that contains assay results for the experiment sample and set the \"ImmPort Template?\" column value to \"No\". The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "ImmPort expects RNA sequencing results to be deposited into a public repository since this is a prerequisite for publication. In order to avoid duplication of data upload by requiring the same data be sent to ImmPort as well as the public repository, ImmPort requires public repository name and accession.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "ImmPort Template?", "operator" : "empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and ImmPort Template? is blank", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "RNA sequencing results are expected to be deposited into a public repository. If you provide NO RESULTS FILE, please choose the repository name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "ImmPort Template?", "operator" : "empty-value", "value" : "" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one) and ImmPort Template? is blank", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s). You need to provide the repository accession if you do NOT PROVIDE A RESULTS FILE.", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "rna_sequencing", "description" : "The RNA sequencing Transcripts results experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment are new, then you must complete the required columns to describe them. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "combined-result", "fileName" : "experimentSamples.Virus_Neutralization.txt", "schemaVersion" : "3.37", "jsonFileName" : "experimentSamples.Virus_Neutralization.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment and biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment and biosample", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.", "templateColumn" : "Expsample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Describe important characteristics of the sample being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Describe important characteristics of the sample being assayed.", "templateColumn" : "Expsample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "reagent", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either an assay reagent user defined ID or ImmPort accession.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template.", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "expsample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "treatment", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample_2_treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "treatment_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "treatmentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter either a treatment user defined ID or ImmPort accession.", "templateColumn" : "Treatment ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Biosample Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Biosample Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is a display name that is available when the data is shared, but it is not referenced by other data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentName", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Experiment Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "expsample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentDescription", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Experiment Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "expsample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_virus_strain", "pv" : true, "conditionalRequired" : false, "description" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "virus_strain_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "virusStrainReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared. This COLUMN must appear as the FIRST COLUMN for a repeating result column group.", "templateColumn" : "Virus Strain Reported", "foreignKey" : false, "pvPreferredTableColumn" : "virus_strain_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum sample dilution factor that continues to demonstrate virus neutralization.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_titer_unit", "pv" : true, "conditionalRequired" : false, "description" : "The dilution factor unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dilution factor unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "titer_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "virus_neutralization", "description" : "The virus neutralization experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Virus Strain'and 'Titration Dilution Value' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described." }, { "templateType" : "multiple", "fileName" : "FCM_Derived_data.txt", "schemaVersion" : "3.37", "jsonFileName" : "FCM_Derived_data.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_cell_population", "pv" : true, "conditionalRequired" : false, "description" : "The drop down list provides a list of cell population names. Please select a name if it matches your cell population name or enter a population name if there is not an appropriate one provided. The population name has a limit of 150 characters. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Population Name Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : "population_name_preferred", "tableColumn" : "population_name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_cell_population_pref_map", "jsonAttribute" : "populationNameReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The population name is the type of cells whose count is reported. Please select a population name from the drop down list if it matches your cell population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Population Name Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "templateColumn" : "Population Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_prefix_preferred and population_name_preferred" }, { "pvTableName" : "lk_cell_population_definition", "pv" : true, "conditionalRequired" : false, "description" : "he gating definition is the set of markers and their expression profile that describes a cell population name. Please select a gating definition from the drop down list if it matches your gating definition or enter a gating definition if there is not an appropriate one provided. The marker names should conform to standard names as described in the LK_ANALYTE table. Note that a comma, forward slash or pipe may be used as marker delimiter. The expression values are '-', '+', '+-', '+~', '++', or ''. The gating definition has a limit of 150 characters.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_defnition_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "gatingDefinitionReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The gating definition is the set of markers and their expression profile. Please select a gating definition from the drop down list or enter a gating definition. Please see the ImmPort Upload Templates for details on representing marker names, delimiters and expression values. ", "templateColumn" : "Gating Definition Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_defnition_preferred" }, { "pvTableName" : "lk_cell_population", "pv" : true, "conditionalRequired" : false, "description" : "The drop down provides the base parent population. Please select a name if it matches your base parent population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\". Also, if the Parent Population Reported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : "parent_population_preferred", "tableColumn" : "parent_population_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_cell_population_pref_map", "jsonAttribute" : "parentPopulationReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The base parent population name. Please select a population name from the drop down list if it matches your base parent population name or enter a name if there is not an appropriate one provided. This column can also have the format: \"lineage_prefix ; population name\", \"population_name&modifiers\", or \"lineage_prefix ; population_name&modifiers\" . Also, if the Parent Population eported does not occur in the drop down, it will be tested against the lk_cell_population_pref_map to determine a preferred name.", "templateColumn" : "Parent Population Reported", "foreignKey" : false, "pvPreferredTableColumn" : "population_prefix_preferred and population_name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The count of the cell type defined by the marker gating definition.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_statistic_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "populationStatisticCountPercentileEtc", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Population Statistic (count, percentile, etc)", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_cell_pop_statistic_unit", "pv" : true, "conditionalRequired" : false, "description" : "The unit used to describe the cell count. Please select a unit from the drop down list if the definition matches your unit name or enter a unit if there is not an appropriate one provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "population_stat_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "populationStatUnitReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit used to describe the cell count. Please select a unit from the list provided if the definition matches your unit name or enter a unit if there is not an appropriate one provided.", "templateColumn" : "Population Stat Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "statistic_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "An XML formatted export of the analysis program is expected (e.g. an xml format of a FlowJo .jo or .wsp file). The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "workspaceFile", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the file that stores the interpreted flow cytometry results from the analysis program. The file size name limit is 240 characters.", "templateColumn" : "Workspace File", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "fcs_analyzed_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "fcm_derived_data", "description" : "The flow cytometry derived data template captures and annotates the assay results for a sample by linking sample, experiment, and interpreted results together." }, { "templateType" : "multiple", "fileName" : "HAI_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "HAI_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hai_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_virus_strain", "pv" : true, "conditionalRequired" : false, "description" : "The name of the virus strain used in the assay. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "virus_strain_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "virusStrainReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the virus strain used in the assay. The list of values displays common immunology terms on the left and their preferred term on the right, separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Virus Strain Reported", "foreignKey" : false, "pvPreferredTableColumn" : "virus_strain_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum sample dilution factor that continues to demonstrate inhibition of hemagglutination.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_titer_unit", "pv" : true, "conditionalRequired" : false, "description" : "The dilution factor unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dilution factor unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "titer_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hai_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hai_results", "description" : "The HAI experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Virus Strain'and 'Titration Dilution Value' needed to describe each assay result." }, { "templateType" : "multiple", "fileName" : "HLA_Typing.txt", "schemaVersion" : "3.37", "jsonFileName" : "HLA_Typing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "ImmPort recommends using population names as defined by the http://www.allelefrequencies.net site.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "ancestral_population", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ancestralPopulation", "columnType" : "varchar(250)", "cv" : true, "cvTableName" : "lk_ancestral_population", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "ImmPort recommends using population names as defined by the http://www.allelefrequencies.net site.", "templateColumn" : "Ancestral Population", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaAAllele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-A Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaAAllele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-A Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaBAllele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-B Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaBAllele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-B Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaCAllele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-C Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaCAllele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-C Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDpa1Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DPA1 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDpa1Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DPA1 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDpb1Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DPB1 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDpb1Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DPB1 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDqa1Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DQA1 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDqa1Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DQA1 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDqb1Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DQB1 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDqb1Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DQB1 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb1Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB1 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb1Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB1 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb3Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB3 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb3Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB3 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb4Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB4 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb4Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB4 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb5Allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB5 Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "At least one of HLA-A Allele 1, HLA-A Allele 2, HLA-B Allele 1, HLA-B Allele 2, HLA-C Allele 1, HLA-C Allele 2, HLA-DPA1 Allele 1, HLA-DPA1 Allele 2, HLA-DPB1 Allele 1, HLA-DPB1 Allele 2, HLA-DQA1 Allele 1, HLA-DQA1 Allele 2, HLA-DQB1 Allele 1, HLA-DQB1 Allele 2, HLA-DRB1 Allele 1, HLA-DRB1 Allele 2, HLA-DRB3 Allele 1, HLA-DRB3 Allele 2, HLA-DRB4 Allele 1, HLA-DRB4 Allele 2, HLA-DRB5 Allele 1, HLA-DRB5 Allele 2 is required when Expsample ID is provided." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "hlaDrb5Allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "HLA-DRB5 Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "hla_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hla_typing", "description" : "The HLA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together." }, { "templateType" : "single", "fileName" : "immuneExposure.txt", "schemaVersion" : "3.37", "jsonFileName" : "immuneExposure.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject for the reported immune exposure.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject for the reported immune exposure.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A subject may be assigned to a single arm within a study. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "arm_or_cohort", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "arm_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "armOrCohortId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study arm or cohort user defined ID or ImmPort accession. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "templateColumn" : "Arm Or Cohort ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_exposure_process", "pv" : true, "conditionalRequired" : false, "description" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_process_preferred", "tableColumn" : "exposure_process_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_process_pref_map", "jsonAttribute" : "exposureProcessReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "templateColumn" : "Exposure Process Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_process_preferred" }, { "pvTableName" : "lk_exposure_material", "pv" : true, "conditionalRequired" : true, "description" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_material_preferred", "tableColumn" : "exposure_material_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_material_pref_map", "jsonAttribute" : "exposureMaterialReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "templateColumn" : "Exposure Material Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_material_preferred and exposure_material_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Exposure Material Reported", "operator" : "not-preferred-value", "value" : "lk_exposure_material" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "exposure_material_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\" and Exposure Material Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "exposureMaterialId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "templateColumn" : "Exposure Material ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease", "pv" : true, "conditionalRequired" : true, "description" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "disease_preferred", "tableColumn" : "disease_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_study_condition_pref_mappng", "jsonAttribute" : "diseaseReported", "columnType" : "varchar(550)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The Value provide by the user is further checked against the pref mapping table lk_study_condition_pref_mappng.", "templateColumn" : "Disease Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_preferred and disease_ontology_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "infectious challenge" }, { "field" : "Disease Reported", "operator" : "not-empty-value", "value" : "" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] }, { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_ontology_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"infectious challenge\" and Disease Reported is provided and Disease Reported does not match a recognized preferred term OR Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\" and Disease Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseOntologyId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "templateColumn" : "Disease Ontology ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease_stage", "pv" : true, "conditionalRequired" : true, "description" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_stage_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseStageReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "templateColumn" : "Disease Stage Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_stage_preferred" } ], "name" : "immuneexposure", "description" : "The subjectHuman and subjectAnimals templates define and annotate the subjects in studies with respect to immune exposure. The Immune Exposure template updates the subjects previously defined in studies with respect to immune exposure." }, { "templateType" : "single", "fileName" : "interventions.txt", "schemaVersion" : "3.37", "jsonFileName" : "interventions.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The intervention user defined ID is an identifier chosen by the data provider to refer to a adverse event. The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A biological sample may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The intervention name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The intervention name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The compound name describes what substance entered the subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "compound_name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "compoundNameReported", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The compound name describes what substance entered the subject.", "templateColumn" : "Compound Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Compound role indicates the purpose or category of the substance.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "compound_role", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "compoundRole", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_compound_role", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Compound role indicates the purpose or category of the substance.", "templateColumn" : "Compound Role", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The amount of a substance.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "dose_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "doseReported", "columnType" : "varchar(150)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The amount of a substance.", "templateColumn" : "Dose Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study day in which the substance was initially encountered.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "start_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startDay", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study day in which the substance was initially encountered.", "templateColumn" : "Start Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study day in which the substance was encounter ended.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "end_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endDay", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study day in which the substance was encounter ended.", "templateColumn" : "End Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Did the substance encounter complete or was ended.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "status", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "status", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Did the substance encounter complete or was ended.", "templateColumn" : "Status", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The purpose the substance was encountered.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "reported_indication", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reportedIndication", "columnType" : "varchar(255)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The purpose the substance was encountered.", "templateColumn" : "Reported Indication", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The packaging or delivery of the substance.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "formulation", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "formulation", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The packaging or delivery of the substance.", "templateColumn" : "Formulation", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The dose value.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "dose", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dose", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dose value.", "templateColumn" : "Dose", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The dose unit.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "dose_units", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "doseUnits", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dose unit.", "templateColumn" : "Dose Units", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "How often the substance was encountered.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "dose_freq_per_interval", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "doseFreqPerInterval", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "How often the substance was encountered.", "templateColumn" : "Dose Freq Per Interval", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "How the substance was administered.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "route_of_admin_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "routeOfAdminReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "How the substance was administered.", "templateColumn" : "Route Of Admin Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Is the substance encounter continuing.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "is_ongoing", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "isOngoing", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Is the substance encounter continuing.", "templateColumn" : "Is Ongoing", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Time within a study day the substance is initially encountered.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "start_time", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startTime", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Time within a study day the substance is initially encountered.", "templateColumn" : "Start Time", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Time within a study day the substance encounter ended.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "end_time", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endTime", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Time within a study day the substance encounter ended.", "templateColumn" : "End Time", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Length of time for the encounter.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "duration", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "duration", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Length of time for the encounter.", "templateColumn" : "Duration", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Time unit for the duration.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "intervention", "ppvPreferredTableColumn" : null, "tableColumn" : "duration_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "durationUnit", "columnType" : "varchar(10)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Time unit for the duration.", "templateColumn" : "Duration Unit", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "interventions", "description" : "The Intervention Template records the study interventions, concomitant medications, and anything else that was reported as entering a subject." }, { "templateType" : "multiple", "fileName" : "KIR_Typing.txt", "schemaVersion" : "3.37", "jsonFileName" : "KIR_Typing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "kir_typing_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "kir_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "kir_haplotype", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "kirHaplotype", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "KIR Haplotype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "kir_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_1", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "allele1", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "Allele 1", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "kir_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "allele_2", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "allele2", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "Allele 2", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "kir_typing_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "kir_typing", "description" : "The KIR experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together." }, { "templateType" : "single", "fileName" : "labTest_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "labTest_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test user defined ID is an identifier chosen by the data provider to refer the lab test. The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test panel identifier must be stored in ImmPort or in the labTestPanels.txt template. The lab test panel serves as the parent entity to bind lab test results of a similar type together.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "lab_test_panel", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "lab_test_panel_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "labTestPanelId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a lab test panel user defined ID or ImmPort accession.", "templateColumn" : "Lab Test Panel ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biosample identifier must be stored in ImmPort or in the biosamples.txt template. A single biosample identifier is expected.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "biosample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "biosample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.", "templateColumn" : "Biosample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_lab_test_name", "pv" : true, "conditionalRequired" : false, "description" : "The lab test name describes lab test. Please select a unit from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please select a unit from the list provided if the name matches your name or enter a name if there is not an appropriate one provided.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test result captures the assayed value for a sample and can include letters, numbers and greater than or less than symbols.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueReported", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab test result captures the assayed value.", "templateColumn" : "Result Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_unit_of_measure", "pv" : true, "conditionalRequired" : false, "description" : "The lab test result unit describes the unit for the lab test value.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "result_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultUnitReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab test result unit describes the unit for the lab test value.", "templateColumn" : "Result Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "unit_of_measure_preferred" } ], "name" : "labtest_results", "description" : "The lab test results template is a legacy template that supports reporting the lab test results (but does not support defining the lab test panel which is the parent of a lab test). The function of this template is also captured in the lab tests template. This template will continue to be supported for the foreseeable future to support backward compatibility." }, { "templateType" : "single", "fileName" : "labTestPanels.txt", "schemaVersion" : "3.37", "jsonFileName" : "labTestPanels.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test panel user defined ID is an identifier chosen by the data provider to refer to lab panel. This ID may be referenced by other data records (e.g. lab test). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_lab_test_panel_name", "pv" : true, "conditionalRequired" : false, "description" : "The lab panel name describes a lab test panel. Please select a preferred value from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab panel name describes a lab test panel. Please select a preferred value from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A lab test panel may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession for the study in which the lab test panel occurs.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Please enter either a protocol user defined ID or ImmPort accession. One or more identifiers can be entered per subject. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "protocol", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "lab_test_panel_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null } ], "name" : "labtestpanels", "description" : "The lab test panels template is a legacy template that defines and annotates the collection of lab tests applied to a sample (but not the lab test results). The function of this template is also captured in the lab tests template. This template will continue to be supported for the foreseeable future to support backward compatibility." }, { "templateType" : "combined-result", "fileName" : "labTests.txt", "schemaVersion" : "3.37", "jsonFileName" : "labTests.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A lab test panel may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "lab_test_panel_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample And lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Lab Test Panel in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample and lab_test_panel", "ppv" : false, "comment" : "Please enter a study user defined ID or ImmPort accession for the study in which the lab test panel occurs. The Study ID is only required when both the lab test panel and biological sample are new.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "biosampleId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to a lab test.", "templateColumn" : "Biosample ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "subject", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The link to a study's planned visit provides temporal context for a sample's derivation from a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "planned_visit", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "planned_visit_accession", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "plannedVisitId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter either a study's planned visit user defined ID or ImmPort accession.", "templateColumn" : "Planned Visit ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The sample types are adopted from Uberon, Cell and CHEBI ontologies.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_sample_type", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose a biological sample type from the drop down list.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Type", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "subtype", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subtype", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.", "templateColumn" : "Subtype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The biological sample description is used to describe details of the sample not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "The biological sample description is used to describe details of the sample not captured in other columns.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Study time collected describes the time value for when a sample was derived from a subject.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollected", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Study Time Collected", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time units are standard terms recommended by the HIPC Standards group.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_collected_unit", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeCollectedUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time Collected Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The time zero event refers to the study milestone upon which time is based.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0Event", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_t0_event", "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study Time T0 Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "biosample_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Study Time T0 Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "biosample", "ppvPreferredTableColumn" : null, "tableColumn" : "study_time_t0_event_specify", "conditionalRequiredWhenText" : "you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyTimeT0EventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.", "templateColumn" : "Study Time T0 Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test panel user defined ID is an identifier chosen by the data provider to refer to lab panel. This ID may be referenced by other data records (e.g. lab test). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "labTestPanelId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "lab_test_panel", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Lab Test Panel ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession. One or more identifiers can be entered per subject. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "lab_test_panel_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "lab_test_panel_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Lab Test Panel in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "lab_test_panel", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession. The Protocol ID(s) is required when either the lab test panel or the biological sample are new.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_lab_test_panel_name", "pv" : true, "conditionalRequired" : true, "description" : "The lab panel name describe lab test panel. Please select a lab panel name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "lab_test_panel_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "lab_test_panel", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : "you are defining a new Lab Test Panel in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "lab_test_panel", "ppv" : false, "comment" : "The lab panel name describes the lab test panel. Please select a lab panel name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "biosample", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test user defined ID is an identifier chosen by the data provider to refer the lab test. The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab test identifier should be unique to the ImmPort workspace to which the data will be uploaded. This COLUMN must appear as the FIRST COLUMN for a repeating result column group.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_lab_test_name", "pv" : true, "conditionalRequired" : false, "description" : "The lab test name describes lab test. Please select a lab test name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the panel is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "nameReported", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please select a lab test name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided.", "templateColumn" : "Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lab test result captures the assayed value for a sample and can include letters, numbers and greater than or less than symbols.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "result_value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultValueReported", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab test result captures the assayed value.", "templateColumn" : "Result Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_unit_of_measure", "pv" : true, "conditionalRequired" : false, "description" : "The lab test result unit describes the unit for the lab test value.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "lab_test", "ppvPreferredTableColumn" : null, "tableColumn" : "result_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultUnitReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lab test result unit describes the unit for the lab test value.", "templateColumn" : "Result Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "unit_of_measure_preferred" } ], "name" : "labtests", "description" : "The lab tests template defines and annotates the lab test panels, the lab tests and results. This template combines the functions of the legacy lab test panels and lab test results templates into a single template. The biological sample and the lab test panel can be either new or pre-defined in this template. Any combination is acceptable. The only restriction is that the biological sample is the key to template and must be unique within the template." }, { "templateType" : "multiple", "fileName" : "Mass_Spectrometry_Metabolomic_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "Mass_Spectrometry_Metabolomic_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The intensity of the mass spectrometry result.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "intensity", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "intensity", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The intensity of the mass spectrometry result.", "templateColumn" : "Intensity", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The retention time of the mass spectrometry result.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "retention_time", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "retentionTime", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The retention time of the mass spectrometry result.", "templateColumn" : "Retention Time", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The unit of time for the the retention time of the mass spectrometry result. Please select a time unit name from the list provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "retention_time_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "retentionTimeUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit of time for the the retention time of the mass spectrometry result. Please select a time unit name from the list provided.", "templateColumn" : "Retention Time Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The ratio of mass to Z charge.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "m_z_ratio", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "mZRatio", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The ratio of mass to Z charge.", "templateColumn" : "M/Z Ratio", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Z charge of the mass spectrometry result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "z_charge", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "zCharge", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Z charge of the mass spectrometry result.", "templateColumn" : "Z (Charge)", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_hmdb", "pv" : true, "conditionalRequired" : false, "description" : "The Optional HMDB, PubChem, or RefMet ID associated with the result. Pick a value from the list if it fits the result.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "database_id_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "databaseIdReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Optional Database ID (Human Metabalone Database (HMDB), PubChem, or RefMet ID) associated with the result. Pick a value from the list if it fits the result.", "templateColumn" : "Database ID Reported", "foreignKey" : false, "pvPreferredTableColumn" : "metabolite_name and hmdb_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Optional name of the reported metabolite used in the mass spectrometry.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "metabolite_name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "metaboliteName", "columnType" : "varchar(255)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Optional name of the reported metabolite used in the mass spectrometry.", "templateColumn" : "Metabolite Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mass_spec_metabolomic_results", "description" : "The Metabolite Mass Spectrometry experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one intensity results per assayed sample." }, { "templateType" : "multiple", "fileName" : "Mass_Spectrometry_Proteomic_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "Mass_Spectrometry_Proteomic_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The intensity of the mass spectrometry result.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "intensity", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "intensity", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The intensity of the mass spectrometry result.", "templateColumn" : "Intensity", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_protein_name", "pv" : true, "conditionalRequired" : false, "description" : "The Name of the protein reported. Choose from a pick list of triples: (Gene Name, UniProt ID, Primary Protein Accession) as defined by UNIPROT if it matches your protein, otherwise provide your own Protein Accession Name.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "protein_name_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "proteinNameReported", "columnType" : "varchar(255)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Name of the protein reported. Choose from a pick list of triples: (Gene Name, UniProt ID, Primary Protein Accession) as defined by UNIPROT if it matches your protein, otherwise provide your own Protein Accession Name.", "templateColumn" : "Protein Name Reported", "foreignKey" : false, "pvPreferredTableColumn" : "uniprot_gene_name and uniprot_id and protein_name_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mass_spectrometry_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mass_spec_proteomic_results", "description" : "The Protein Mass Spectrometry experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one intensity results per assayed sample." }, { "templateType" : "single", "fileName" : "MBAA_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "MBAA_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source ID is defined in the corresponding ImmPort template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "sourceId", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The source ID for the assay result is either an experiment sample, a control sample, or a standard curve.", "templateColumn" : "Source ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source type is either an experiment sample, control sample or standard curve.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "source_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "sourceType", "columnType" : "varchar(30)", "cv" : true, "cvTableName" : "lk_source_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Source Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_group_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayGroupId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay Group ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Mean Fluorescence Intensity", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "mfi", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "mfi", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Mean Fluorescence Intensity", "templateColumn" : "MFI", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reported concentration value of the standard curve sample or calculated from the MFI using the standard curve.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "concentration_value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "concentrationValueReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Concentration Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_concentration_unit", "pv" : true, "conditionalRequired" : false, "description" : "The concentration unit of the standard curve sample or calculated from the MFI using the standard curve", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "concentration_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "concentrationUnitReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The concentration unit of the standard curve sample or calculated from the MFI using the standard curve.", "templateColumn" : "Concentration Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "concentration_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The position on the assay plate.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "mfi_coordinate", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "mfiCoordinate", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The position on the assay plate.", "templateColumn" : "MFI Coordinate", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "mbaa_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "mbaa_results", "description" : "The MBAA experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together." }, { "templateType" : "multiple", "fileName" : "PCR_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "PCR_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The NCBI Gene symbol for the gene being assayed. Please select a gene symbol from the list provided if the gene symbol matches your symbol or enter a symbol if there is not an appropriate one provided. This symbol is visible when the result is shared. If the gene symbol is a NCBI Gene Symbol that is provided in the list, then the columns 'Gene Name' and 'Gene ID' will also be overwritten by the gene name and Entrez Gene ID provided by NCBI.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneSymbolName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Gene symbol for the gene being assayed. Please select a gene symbol from the list provided if the gene symbol matches your symbol or enter a symbol if there is not an appropriate one provided. This symbol is visible when the result is shared.", "templateColumn" : "Gene Symbol Name", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This value could be absolute or relative. For example, an absolute expression value could be 6 ng RNA/mg intestine. In this case, 6 should be entered in the 'Expression value of target RNA' column, while ng RNA/ mg intestine is in the 'Expression unit of target RNA' column. A relative expression value, like signal versus GAPDH, could be 2.07. In this case, 2.07 should be in the 'Expression value of target RNA' column, while relative to GAPDH is in the 'Expression unit of target RNA' column.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_pcr_expression_unit", "pv" : true, "conditionalRequired" : false, "description" : "The unit for the Expression Value Of Target Nucleic ACID. Please select a unit from the list provided if the unit matches your unit or enter a unit if there is not an appropriate one provided.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit for the Expression Value Of Target Nucleic ACID. Please select a unit from the list provided if the unit matches your unit or enter a unit if there is not an appropriate one provided.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "expression_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The NCBI Gene ID for the gene being assayed. A number is expected.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "gene_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneId", "columnType" : "varchar(10)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Gene ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The NCBI Gene name for the gene being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "gene_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "geneName", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Gene name for the gene being assayed.", "templateColumn" : "Gene Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Additional identifier(s) for the gene being assayed.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "other_gene_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "otherGeneAccession", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Additional identifier(s) for the gene being assayed.", "templateColumn" : "Other Gene Accession", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "pcr_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "pcr_results", "description" : "The qRT-PCR experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying at least the group of columns 'Entrez Gene ID' and 'Threshold Cycles(ct)' needed to describe each assay result." }, { "templateType" : "single", "fileName" : "protocols.txt", "schemaVersion" : "3.37", "jsonFileName" : "protocols.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol user defined ID is an identifier chosen by the data provider to refer to a protocol document. This ID may be referenced by other data records (e.g. study). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol file name in this column must be an exact spelling match to a file in the ZIP archive that is uploaded. This includes the file extensions which may be hidden depending upon your computer's settings. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "file_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "fileName", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The protocol file name is the document uploaded and linked to the protocol ID. The file name must be an exact spelling match including the file extension. The file size name limit is 240 characters.", "templateColumn" : "File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The protocol name is an alternate identifier that is visible when the protocol is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol type uses a preferred list of terms to characterize the protocol's content.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(100)", "cv" : true, "cvTableName" : "lk_protocol_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The protocol type is chosen from a list of preferred terms.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The summary is a brief description of the protocol's content.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The protocol summary describes the purpose of the protocol.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "protocols", "description" : "The protocol template defines and annotates protocol documents that are to be linked to study, subjects, biological samples or experiments." }, { "templateType" : "single", "fileName" : "publicRepositories.txt", "schemaVersion" : "3.37", "jsonFileName" : "publicRepositories.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "ImmPort expects array gene expression results to be deposited in NCBI GEO since this is a prerequisite for publication. Please choose this repository name from the list.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Array gene expression results are expected to be deposited in NCBI GEO Please choose this repository name from the list.", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The public repository accession should be the most granular or highest resolution provided (e.g. sample level accession, not sample group accession).", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "expsample_public_repository", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryAccession", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter the accession that links to the assay result file(s).", "templateColumn" : "Repository Accession", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "public_repositories", "description" : "The public repository template allows one or more public repository accession(s) and name(s) to be assigned to an experiment sample." }, { "templateType" : "single", "fileName" : "Reagent_Sets.txt", "schemaVersion" : "3.37", "jsonFileName" : "Reagent_Sets.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The individual reagents are defined in assay specific reagent templates (e.g. flow cytometry, ELISA). The data provider may define a set or panel of reagents used in a single assay (e.g a panel of fluorochrome conjugated monoclonal antibodies).", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "reagent", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent_set_2_reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reagent_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reagentIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Provide a list of individual reagents that comprise the reagent set. Separate the individual reagent IDs with a semi-colon.", "templateColumn" : "Reagent ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent set type indicates the assay type with which the reagent set is used.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "type", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_reagent_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Choose from a list of preferred assay types.", "templateColumn" : "Type", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "reagent_sets", "description" : "The reagent set template defines and annotates the groups of reagents that are used together in assays such as flow cytometry panels, or multiplex ELISA assays. This template is optional." }, { "templateType" : "multiple", "fileName" : "reagents.Array.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Array.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "array_reagents", "description" : "The array reagent template defines and annotates microarrays assay platforms." }, { "templateType" : "multiple", "fileName" : "reagents.CyTOF.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.CyTOF.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "antibody_registry_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "antibodyRegistryId", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier assigned by the Antibody Registry to the antibody reagent. http://antibodyregistry.org/", "templateColumn" : "Antibody Registry ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Mass cytometry reagents often consist of a monoclonal antibody linked to a isotope and the antibody binds to the target analyte.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "clone_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "cloneName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The detector in mass cytometry reagents is often a monoclonal antibody conjugated to an isotope. When there is no antibody in the reagent, enter 'NA'.", "templateColumn" : "Clone Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Mass cytometry reagents often consist of a monoclonal antibody linked to an isotope and the isotope provides the signal for the mass spectrometer's detectors.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reporter_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reporterName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reporter in a mass cytometry reagent is the isotope linked to an antibody.", "templateColumn" : "Reporter Name", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "cytof_reagents", "description" : "The mass cytometry reagent template defines and annotates the mass tagged antibody reagents used for CyTOF." }, { "templateType" : "multiple", "fileName" : "reagents.ELISA.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.ELISA.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "antibody_registry_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "antibodyRegistryId", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier assigned by the Antibody Registry to the antibody reagent. http://antibodyregistry.org/", "templateColumn" : "Antibody Registry ID", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elisa_reagents", "description" : "The ELISA reagent template defines and annotates the antibody reagents assay platforms for ELISA." }, { "templateType" : "multiple", "fileName" : "reagents.ELISPOT.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.ELISPOT.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "antibody_registry_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "antibodyRegistryId", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier assigned by the Antibody Registry to the antibody reagent. http://antibodyregistry.org/", "templateColumn" : "Antibody Registry ID", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "elispot_reagents", "description" : "The ELISPOT reagent template defines and annotates the antibody reagents assay platforms for ELISPOT." }, { "templateType" : "multiple", "fileName" : "reagents.Flow_Cytometry.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Flow_Cytometry.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "antibody_registry_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "antibodyRegistryId", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier assigned by the Antibody Registry to the antibody reagent. http://antibodyregistry.org/", "templateColumn" : "Antibody Registry ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Flow cytometry reagents often consist of a monoclonal antibody linked to a fluorescing compound and the antibody binds to the target analyte.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "clone_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "cloneName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The detector in flow cytometry reagents is often a monoclonal antibody conjugated to a fluorochrome. When there is no antibody in the reagent, enter 'NA'.", "templateColumn" : "Clone Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Flow Cytometry reagents often consist of a monoclonal antibody linked to a fluorescing compound and the fluorochrome provides the signal for the cytometer's detectors.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "reporter_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "reporterName", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reporter in a flow cytometry reagent is the fluorochrome linked to an antibody. When there is no antibody in the reagent, it is the fluorescing agent (e.g. CFSE).", "templateColumn" : "Reporter Name", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "flow_cytometry_reagents", "description" : "The flow cytometry reagent template defines and annotates the antibody reagents used for flow cytometry." }, { "templateType" : "multiple", "fileName" : "reagents.HAI.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.HAI.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hai_reagents", "description" : "The HAI reagent template defines and annotates reagents for hemagglutination inhibition assays. These include the cell type used. The viral stain and concentration would be defined in the treatments.txt template." }, { "templateType" : "multiple", "fileName" : "reagents.HLA_Typing.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.HLA_Typing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "hla_typing_reagents", "description" : "The HLA typing system reagents template defines and annotates the assay platforms for HLA typing. These reagents will be linked to HLA experiment sample records." }, { "templateType" : "multiple", "fileName" : "reagents.KIR_Typing.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.KIR_Typing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "kir_typing_reagents", "description" : "The KIR typing system reagents template defines and annotates the assay platforms for KIR typing. These reagents will be linked to KIR experiment sample records." }, { "templateType" : "multiple", "fileName" : "reagents.MBAA.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.MBAA.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : false, "description" : "The analyte describes what is being measured in an assay. The list of values displays common immunology gene symbol and gene symbol terms on the left and their preferred term on the right, each component separated by a semi-colon. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The analyte is the target (e.g protein, DNA, RNA) that is being assayed by the reagent. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" } ], "name" : "mbaa_reagents", "description" : "The MBAA reagent template defines and annotates the assay platforms for MBAA. This should include a row for each of the analytes assayed by the MBAA array." }, { "templateType" : "multiple", "fileName" : "reagents.Neutralizing_Antibody_Titer.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Neutralizing_Antibody_Titer.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "neutralizing_antibody_titer_reagents", "description" : "The neutralizing antibody titer reagent template defines and annotates reagents used for neutralizing antibody titer including the cell types, and antibodies if an ELISA approach is employed." }, { "templateType" : "multiple", "fileName" : "reagents.Other.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Other.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "other_reagents", "description" : "This reagent template is used to define and annotate reagents that are not described by other reagent templates." }, { "templateType" : "multiple", "fileName" : "reagents.PCR.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.PCR.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "pcr_reagents", "description" : "The PCR reagent template defines and annotates the reagents used for PCR assays." }, { "templateType" : "multiple", "fileName" : "reagents.Sequencing.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Sequencing.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "sequencing_reagents", "description" : "The sequencing reagent template defines and annotates the assay platforms used for sequencing." }, { "templateType" : "multiple", "fileName" : "reagents.Virus_Neutralization.txt", "schemaVersion" : "3.37", "jsonFileName" : "reagents.Virus_Neutralization.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent user defined ID is an identifier chosen by the data provider to refer to an assay reagent. The nature of the assay reagent is assay specific and may be an array, an antibody or a typing kit. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The reagent name is an alternate ID that is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay reagent description provides further details on the nature and purpose of the reagent.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A supplemental description of the assay reagent that expands on its Name and User Defined ID.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The source of a reagent may be important for evaluating assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "manufacturer", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "manufacturer", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g. collaborating labs).", "templateColumn" : "Manufacturer", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The reagent's catalog ID provides a reference to the reagent source and description.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "catalog_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "catalogNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.", "templateColumn" : "Catalog Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The lot number is helpful to understand possible batch specific differences in assay results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "lot_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lotNumber", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The lot number is often provided by a reagent source when the reagent is replenished over time.", "templateColumn" : "Lot Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The web link is often the vendor's web site.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "weblink", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "weblink", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "An internet address that may provide details of an assay reagent.", "templateColumn" : "Weblink", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If the reagent is from a non-commercial source, the contact information should indicate with whom to communicate to get further details.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "reagent", "ppvPreferredTableColumn" : null, "tableColumn" : "contact", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "contact", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The contact information is particularly helpful when the reagent is not from a commercial vendor.", "templateColumn" : "Contact", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "virus_neutralization_reagents", "description" : "The virus neutralization reagent template defines and annotates reagents used for virus neutralization including the cell types, and antibodies if an ELISA approach is employed." }, { "templateType" : "multiple", "fileName" : "RNA_SEQ_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "RNA_SEQ_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The NCBI ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "reference_transcript_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "referenceTranscriptId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided.", "templateColumn" : "Reference Transcript ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The public repository name for the transcript (for example, Ensembl or NCBI Gene).", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "repository_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "repositoryName", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_public_repository", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The public repository name for the transcript (for example, Ensembl or NCBI Gene).", "templateColumn" : "Repository Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_transcript_type", "pv" : true, "conditionalRequired" : false, "description" : "The type of transcript reported.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "transcript_type_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "transcriptTypeReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The type of transcript reported.", "templateColumn" : "Transcript Type Reported", "foreignKey" : false, "pvPreferredTableColumn" : "transcript_preferred" }, { "pvTableName" : "lk_rna_sequence_result_unit_type", "pv" : true, "conditionalRequired" : false, "description" : "The unit for the result_value.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "result_unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultUnitReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit for the result value.", "templateColumn" : "Result Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "result_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The transcripts or gene count for the transcript.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The count or gene count for the transcript.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information that is added to the result.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "rna_seq_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information that is added to the result.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "rna_seq_results", "description" : "The RNA sequencing Transcripts results experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together." }, { "templateType" : "combined", "fileName" : "standardCurves.txt", "schemaVersion" : "3.37", "jsonFileName" : "standardCurves.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Standard Curve user defined ID is an identifier chosen by the data provider to refer to a Standard Curve. This ID may be referenced by other data records (e.g. MBAA results). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "standardCurveId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Standard Curve ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The formula used to calculate the standard curve from the input data.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "formula", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "formula", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The formula used to calculate the standard curve from the input data.", "templateColumn" : "Formula", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_analyte", "pv" : true, "conditionalRequired" : true, "description" : "The molecule or entity being measured. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "analyte_reported", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "analyteReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The molecule or entity being measured. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Analyte Reported", "foreignKey" : false, "pvPreferredTableColumn" : "immunology_symbol and short_label and analyte_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_id", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The assay ID represents the plate or array ID where standard curves, control samples, and experiment samples were collected and assayed. This ID will be used to link standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "assay_group_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "assayGroupId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The assay group ID represents a collection of plates or arrays. This ID may be used to link collections of standard curves, control samples, and experiment samples results.", "templateColumn" : "Assay Group ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A number is expected.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "lower_limit", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lowerLimit", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "Lower limit value established by the standard curve.", "templateColumn" : "Lower Limit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Lower limit unit established by the standard curve.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "lower_limit_unit", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lowerLimitUnit", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "Lower limit unit established by the standard curve.", "templateColumn" : "Lower Limit Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A number is expected.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "upper_limit", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "upperLimit", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "Upper limit value established by the standard curve.", "templateColumn" : "Upper Limit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Upper limit value established by the standard curve.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "standard_curve", "ppvPreferredTableColumn" : null, "tableColumn" : "upper_limit_unit", "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "upperLimitUnit", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "Upper limit value established by the standard curve.", "templateColumn" : "Upper Limit Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The format of the result file depends on the assay type. ImmPort supports results templates (MBAA_Results.txt) for some of the commonly used immunological assay methods. These template facilitate the sharing and re-use of results data in a standard format. If the result file is the ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "standard_curve_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : "you are defining a new Standard Curve in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "immportTemplate", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "The format of the result file depends on the assay type. ImmPort supports results templates (MBAA_Results.txt) for some of the commonly used immunological assay methods. These template facilitate the sharing and re-use of results data in a standard format. If the result file is the ImmPort results template (strongly recommended by NIAID DAIT), choose 'Yes' from the drop down list and do not include a file name in the \"Result File Name\" column. If the result file is not an ImmPort results template, choose 'No' from the drop down list and include a file name in the \"Result File Name\" column.", "templateColumn" : "ImmPort Template?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter the full result file name including file extension. The file size name limit is 240 characters.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultFileName", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "Enter the full result file name including file extension. The file size name limit is 240 characters.", "templateColumn" : "Result File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "See the ImmPort Data Upload Guide for details on where MBAA bead level files are stored depending on the assay platform used. Separate file names by a semi-colon (;). The file size name limit is 240 characters.", "jsonDataType" : "array", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "additionalResultFileNames", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "standard_curve", "ppv" : false, "comment" : "HIPC recommends including bead level result files if they are available. The file size name limit is 240 characters.", "templateColumn" : "Additional Result File Names", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment identifier must be stored in ImmPort or in the experiments.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "experimentId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a experiment user defined ID or ImmPort accession.", "templateColumn" : "Experiment ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "An experiment may be linked to a single study.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a study user defined ID or ImmPort accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;).", "jsonDataType" : "array", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : "protocol", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolIds", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Please enter either a protocol user defined ID or ImmPort accession.", "templateColumn" : "Protocol ID(s)", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The experiment name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment name is an alternate identifier that is visible when the sample is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment description is used to describe details of the experiment not captured in other columns.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "The experiment description is used to describe details of the experiment not captured in other columns.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The measurement technique describes the assay method.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "experiment_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "experiment", "ppvPreferredTableColumn" : null, "tableColumn" : "measurement_technique", "conditionalRequiredWhenText" : "you are defining a new Experiment in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "measurementTechnique", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_exp_measurement_tech", "conditionalRequiredTableName" : "experiment", "ppv" : false, "comment" : "Choose from a drop down list.", "templateColumn" : "Measurement Technique", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "standardcurves", "description" : "The standard curve template defines and annotates the standard curves derived from the control sample's concentration and MFI to interpret the experiment sample's MFI in terms of its analyte concentration. This template requires that the standard curve be always new, while the experiment can be new or pre-defined. The standard curve is the key the template and must be unique." }, { "templateType" : "compound", "fileName" : "study_design_edit.txt", "schemaVersion" : "3.37", "jsonFileName" : "study_design_edit.json", "validationLevel" : "", "templates" : [ { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_categorization", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A research focus for the study from the drop down list", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_categorization", "ppvPreferredTableColumn" : null, "tableColumn" : "research_focus", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "researchFocus", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_research_focus", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please use the drop down list", "templateColumn" : "Research Focus", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_categorization", "jsonCompoundAttribute" : "studyCategorization", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_condition_or_disease", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease_condition", "pv" : true, "conditionalRequired" : false, "description" : "The condition(s)/disease(s) that is (are) being researched or evaluated in the study. Please select condition or disease from the list provided if the condition or disease matches yours or enter a condition or disease if there is not an appropriate one provided. Values provided by the user are further checked against the pref mapping table lk_study_condition_pref_mappng.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_condition_or_disease", "ppvPreferredTableColumn" : "condition_preferred", "tableColumn" : "condition_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_study_condition_pref_mappng", "jsonAttribute" : "conditionReported", "columnType" : "varchar(550)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "The condition(s)/disease(s) that is (are) being researched or evaluated in the study. Please select condition or disease from the list provided if the condition or disease matches yours or enter a condition or disease if there is not an appropriate one provided. Values provided by the user are further checked against the pref mapping table lk_study_condition_pref_mappng.", "templateColumn" : "Condition Reported", "foreignKey" : false, "pvPreferredTableColumn" : "condition_preferred" } ], "name" : "study_2_condition_or_disease", "jsonCompoundAttribute" : "study2ConditionOrDisease", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_data_release", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The version of the study data release. It is a positive integer.", "jsonDataType" : "positive", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_data_release", "ppvPreferredTableColumn" : null, "tableColumn" : "data_release_version", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dataReleaseVersion", "columnType" : "integer", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The version of the study data release. It is a positive integer.", "templateColumn" : "Data Release Version", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The date format is either dd-MMM-yy or dd-MMM-yyyy where day (dd) is one or two digits 1..31 appropriate to the month, month (MMM) is case-insensitive value (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec), and year is either (yy) two digits, for example 05 means 2005, and 96 means 1996, or (yyyy) is four digit year, for example 2005.", "jsonDataType" : "date", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_data_release", "ppvPreferredTableColumn" : null, "tableColumn" : "data_release_date", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dataReleaseDate", "columnType" : "date", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The release date for the given version (Data Release Version) study. The date format is either dd-MMM-yy or dd-MMM-yyyy.", "templateColumn" : "Data Release Date", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The status of the data release for the study. Either it is the 'Initial' release or an 'Updated' release.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_data_release", "ppvPreferredTableColumn" : null, "tableColumn" : "status", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "dataReleaseStatus", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_release_status", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The status of the data release for the study. Either it is the 'Initial' release or an 'Updated' release.", "templateColumn" : "Data Release Status", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_data_release", "jsonCompoundAttribute" : "studyDataRelease", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If there are additional files (e.g. as data dictionaries, CRFs, custom formatted lab tests or assements) that should be linked to the study please indicate them in this block. Insert rows in the template to link additional files to the study. The file size name limit is 250 characters. For a given study, all file names for study_file must be unique.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "file_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "fileName", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the file, including file extension, that is to be linked to the study. The file size name limit is 250 characters. For a given study, all file names for study_file must be unique.", "templateColumn" : "File Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A brief description of the file.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A brief description of the file.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Additional study data or study description are current preferred terms.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_file", "ppvPreferredTableColumn" : null, "tableColumn" : "study_file_type", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyFileType", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_study_file_type", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Study File Type", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_file", "jsonCompoundAttribute" : "studyFile", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_image", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The name of the file containing the study image for the study. The file size name limit is 250 characters. For a given study, all file names for study_file must be unique.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_image", "ppvPreferredTableColumn" : null, "tableColumn" : "image_filename", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "imageFilename", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the file containing the study image for the study. ", "templateColumn" : "Image Filename", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The name or title for the study schematic.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_image", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name or title for the study schematic.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A brief description of the study image file.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_image", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A brief description of the study image file.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_image", "jsonCompoundAttribute" : "studyImage", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_link", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The name of the website to which the link refers.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_link", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the website to which the link refers.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If this is a clinical trial, please include the clinicalTrial.gov URL.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_link", "ppvPreferredTableColumn" : null, "tableColumn" : "value", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "value", "columnType" : "varchar(2000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Define websites that are linked to the study. Insert rows in the template to define additional websites linked to the study.", "templateColumn" : "Value", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_link", "jsonCompoundAttribute" : "studyLink", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Pubmed or PubMedCentral identifier of an article that includes data from this study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "pubmed_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "pubmedId", "columnType" : "varchar(16)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Pubmed or PubMedCentral identifier of an article that includes data from this study.", "templateColumn" : "Pubmed ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Digital Object Identifier is a persistent identifier or handle used to uniquely identify an object. ImmPort DOIs are generated by DataCite (https://www.datacite.org/)", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "doi", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "doi", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Digital Object Identifier is a persistent identifier or handle used to uniquely identify an object.", "templateColumn" : "DOI", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The title of an article that includes data from this study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "title", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "title", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The title of an article that includes data from this study.", "templateColumn" : "Title", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The journal name that publishes an article that includes data from this study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "journal", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "journal", "columnType" : "varchar(250)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The journal name that publishes an article that includes data from this study.", "templateColumn" : "Journal", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "year", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "year", "columnType" : "varchar(4)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : null, "templateColumn" : "Year", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "month", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "month", "columnType" : "varchar(12)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : null, "templateColumn" : "Month", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "issue", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "issue", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : null, "templateColumn" : "Issue", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "pages", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "pages", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : null, "templateColumn" : "Pages", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_pubmed", "ppvPreferredTableColumn" : null, "tableColumn" : "authors", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "authors", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : null, "templateColumn" : "Authors", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_pubmed", "jsonCompoundAttribute" : "studyPubmed", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study's arm(s) or cohort(s) group subjects by criteria relevant to the study (e.g. age, condition) and/or treatments or interventions. Insert rows in the template to define additional arms or cohorts linked to the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The arm or cohort user defined ID is an identifier chosen by the data provider to refer to a subject grouping in the study document. This ID may be referenced by other data records (e.g. subjects). The user defined ID is not shared.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The arm or cohort name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(126)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The arm or cohort name is an alternate identifier that is visible when the study is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The description should expand any abbreviations used in the arm or cohort name. For example for an observational study with a cohort whose name was \"ADEH+\", the description would be \"Atopic dermatitis with eczema herpeticum\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The description should expand any abbreviations used in the arm or cohort name.", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_arm_type", "pv" : true, "conditionalRequired" : false, "description" : "The drop down list provides the list of preferred study arm types derived from the National Cancer Institute Thesaurus (NCIT). For an interventional study, the type defines the treatment/control attributes of the arms. The attributes are selected from the values listed below (a study may have more than one arm of a given value). Clinical studies often use the following terms. Experimental - Arm for procedure or drug being evaluated. Active Comparator - arm receiving \"standard of care\" treatment. Placebo Comparator - arm receiving placebo treatment. Sham Comparator - arm receiving a sham procedure such as a urgery or a sham device. No Intervention - arm receiving neither \"standard of care\" treatment a placebo, or sham procedure or device. For an observational study, the type should be Observational - All arms are observing differences in cohorts", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : "type_preferred", "tableColumn" : "type_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_arm_type_pref_mapping", "jsonAttribute" : "typeReported", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "Please select a preferred arm study type from the the drop down list. Terms are derived from the National Cancer Institute Thesaurus (NCIT). The study arm type is a preferred value and the table lk_arm_type_pref_mapping is also used to map the reported type to the drop down list (lk_arm_type).", "templateColumn" : "Type Reported", "foreignKey" : false, "pvPreferredTableColumn" : "type_preferred" } ], "name" : "arm_or_cohort", "jsonCompoundAttribute" : "armOrCohort", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject ID can be either subject user defined ID or a subject accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "subject", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The subject ID can be either subject user defined ID or a subject accession.", "templateColumn" : "Subject ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A subject may be assigned to a single arm within a study. To link a subject to more than one study's arm, create a new record for each subject to arm link.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "arm_or_cohort", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "arm_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "armOrCohortId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The arm or cohort ID can be either arm or cohort user defined ID or an arm or cohort accession.", "templateColumn" : "Arm Or Cohort ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject age at the outset of the study may be determined form one of several study milestones as indicated in the Age Event column.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "min_subject_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Min Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject age at the end of the study may be determined form one of several study milestones.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "max_subject_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maxSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Max Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A list of preferred terms is available.. The age unit must conform to the age unit assigned to the study.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list. The age unit must conform to the age unit assigned to the study.", "templateColumn" : "Age Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEvent", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_age_event", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Age Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "This column supports providing study milestones for subject's age determination that ImmPort does not support.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Age Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event_specify", "conditionalRequiredWhenText" : "Age Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "If \"Age Event\" = Other, this field specifies the age event (free text). Otherwise, leave this column blank.", "templateColumn" : "Age Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject phenotype captures key aspects of the subject's disposition for the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_phenotype", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectPhenotype", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter a description of the subject.", "templateColumn" : "Subject Phenotype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A list of subject locations is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_location", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectLocation", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_subject_location", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Subject Location", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "arm_2_subject", "jsonCompoundAttribute" : "arm2Subject", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The planned visit user defined ID is an identifier chosen by the data provider to refer to a protocol document. This ID may be referenced by other data records (e.g. biological samples). The user defined ID is not shared. Insert rows in the template to define additional planned visits linked to the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "the visit name should indicate the purpose of the visit (e.g. screening, assessment, inoculation, sample drawn). The visit name is not referenced by other data records.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The visit name is an alternate identifier that is visible when the protocol is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive whole number value.", "jsonDataType" : "positive", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "order_number", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "orderNumber", "columnType" : "integer", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The order of the visit within the study design schedule.", "templateColumn" : "Order Number", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive or negative numeric value.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "min_start_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minStartDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The minimum start day for a visit as defined in the study schedule.", "templateColumn" : "Min Start Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This is a positive or negative numeric value. If no value is entered, the maximum start day will be set equal to the minimum start day.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "max_start_day", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maxStartDay", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The maximum start day for a visit as defined in the study schedule.", "templateColumn" : "Max Start Day", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter a start rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "start_rule", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "startRule", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter a start rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "templateColumn" : "Start Rule", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter an end rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "planned_visit", "ppvPreferredTableColumn" : null, "tableColumn" : "end_rule", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "endRule", "columnType" : "varchar(256)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter an end rule only if it is more interesting than \"subject has arrived for a scheduled visit\".", "templateColumn" : "End Rule", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "planned_visit", "jsonCompoundAttribute" : "plannedVisit", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The personnel user defined ID is an identifier chosen by the data provider to refer to personnel who may be contacted for more details about the study document. If more than one study personnel record is to be defined, copy the block of rows from Study_Personnel_ID to Site_Name for each additional study personnel record.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Usually, the education achievement level of the person.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "honorific", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "honorific", "columnType" : "varchar(20)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Usually, the education achievement level of the person.", "templateColumn" : "Honorific", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The last name of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "last_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "lastName", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The last name of the study personnel being described.", "templateColumn" : "Last Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The first name of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "first_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "firstName", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The first name of the study personnel being described.", "templateColumn" : "First Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Suffixes that are part of the study personnel's name being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "suffixes", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "suffixes", "columnType" : "varchar(40)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Suffixes that are part of the study personnel's name being described.", "templateColumn" : "Suffixes", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The organization with whom the study personnel being described is affiliated.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "organization", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "organization", "columnType" : "varchar(125)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The organization with whom the study personnel being described is affiliated.", "templateColumn" : "Organization", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "ORCID (Open Researcher and Contributor Identification), a non-profit organization that promotes the use of its unique digital identifier to connect researchers with their science contributions over time and across changes of name, location and institutional affiliation. The NIH encourages use of this ID. See the link https://nexus.od.nih.gov/all/2019/08/05/linking-orcid-identifiers-to-era-profiles-to-streamline-application-processes-and-to-enhance-tracking-of-career-outcomes/.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "orcid", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "orcidId", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "ORCID (Open Researcher and Contributor Identification), a non-profit organization that promotes the use of its unique digital identifier to connect researchers with their science contributions over time and across changes of name, location and institutional affiliation. The NIH encourages use of this ID.", "templateColumn" : "ORCID ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Contact information of the study personnel being described.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "email", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "email", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Contact information of the study personnel being described.", "templateColumn" : "Email", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The role the personnel play in the study as defined by the research team.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "title_in_study", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "titleInStudy", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The role the personnel play in the study as defined by the research team.", "templateColumn" : "Title In Study", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The ImmPort display will show the personnel listed as 'PI' in the study.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "role_in_study", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "roleInStudy", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_personnel_role", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please use the drop down list.", "templateColumn" : "Role In Study", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Enter the site name if there is a need to further differentiate the affiliation of the study personnel form the Organization.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_personnel", "ppvPreferredTableColumn" : null, "tableColumn" : "site_name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "siteName", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Enter the site name if there is a need to further differentiate the affiliation of the study personnel form the Organization.", "templateColumn" : "Site Name", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "study_personnel", "jsonCompoundAttribute" : "studyPersonnel", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The inclusion or exclusion user defined ID is an identifier chosen by the data provider to refer to a criterion used to determine whether a subject may be enrolled in a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "One or more criterion must be described to decide whether a subject may be enrolled in a study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "criterion", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "criterion", "columnType" : "varchar(750)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The criterion describes the parameter used to decide if a subject may be enrolled in a study.", "templateColumn" : "Criterion", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The criterion category is selected from a preferred list of terms.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "inclusion_exclusion", "ppvPreferredTableColumn" : null, "tableColumn" : "criterion_category", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "criterionCategory", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_criterion_category", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "There are two values to choose from: inclusion or exclusion.", "templateColumn" : "Criterion Category", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "inclusion_exclusion", "jsonCompoundAttribute" : "inclusionExclusion", "templateRequired" : "no" }, { "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The study ID can be either the study user defined ID or a study accession.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "study", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "study_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "studyId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The study ID can be either the study user defined ID or a study accession.", "templateColumn" : "Study ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The protocol ID for the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "protocol", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "study_2_protocol", "ppvPreferredTableColumn" : null, "tableColumn" : "protocol_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "protocolId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded. It can be either a protocol user defined ID or an Accession.", "templateColumn" : "Protocol ID", "foreignKey" : true, "pvPreferredTableColumn" : null } ], "name" : "study_2_protocol", "jsonCompoundAttribute" : "study2Protocol", "templateRequired" : "no" } ], "name" : "study_design_edit", "description" : "The optional study design edit template defines and annotates elements of a study that are optional when it is initially defined (e.g. weblinks, publications) and for which updates are available after the initial design is uploaded. Use the study_design_edit template to add additional information for a study after a study is defined in ImmPort. IF ANY OF THE FOLLOWING SECTIONS ARE NOT USED, THEY NEED TO BE DELETED FROM THE TEMPLATE PRIOR TO UPLOADING THE TEMPLATE: arm_2_subject, arm_or_cohort, inclusion_exclusion, planned_visit, study_2_condition_or_disease, study_2_protocol, study_categorization, study_data_release, study_file, study_image, study_link, study_personnel, or study_pubmed." }, { "templateType" : "combined-result", "fileName" : "subjectAnimals.txt", "schemaVersion" : "3.37", "jsonFileName" : "subjectAnimals.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject defined ID is an identifier chosen by the data provider to refer to a subject. This ID may be referenced by other data records (e.g. biological sample). The user defined ID is not shared. For human subjects, the ID should not be identifying.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Subject ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "gender", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "sex", "columnType" : "varchar(20)", "cv" : true, "cvTableName" : "lk_animal_sex", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Sex", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The subject age at the outset of the study may be determined form one of several study milestones as indicated in the Age Event column.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "min_subject_age", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Min Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject age at the end of the study may be determined form one of several study milestones.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "max_subject_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maxSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Max Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available. The age unit must conform to the age unit assigned to the study.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_unit", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list. The age unit must conform to the age unit assigned to the study.", "templateColumn" : "Age Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEvent", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_age_event", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Age Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "This column supports providing study milestones for subject's age determination that ImmPort does not support.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Age Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event_specify", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one) and Age Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "If \"Age Event\" = Other, this field specifies the age event (free text). Otherwise, leave this column blank.", "templateColumn" : "Age Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject phenotype captures key aspects of the subject's disposition for the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_phenotype", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectPhenotype", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Enter a description of the subject.", "templateColumn" : "Subject Phenotype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of subject locations is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_location", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectLocation", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_subject_location", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Subject Location", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available. Macaca fascicularis is also commonly called cynomologus monkey, crab eating macaque, long-tailed macaque. Macaca mulatta is also commonly called rhesus macaque", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "species", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "species", "columnType" : "varchar(30)", "cv" : true, "cvTableName" : "lk_species", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Species", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "Please provide strain and breed information as available.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "strain", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "strain", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please provide strain and breed information as available.", "templateColumn" : "Strain", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Strain or breed characteristics that are relevant for the study (e.g. susceptibility).", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "strain_characteristics", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "strainCharacteristics", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Strain or breed characteristics that are relevant for the study (e.g. susceptibility).", "templateColumn" : "Strain Characteristics", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A subject may be assigned to a single arm within a study. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "armOrCohortId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "arm_or_cohort", "ppv" : false, "comment" : "Please enter either a study arm or cohort user defined ID or ImmPort accession. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "templateColumn" : "Arm Or Cohort ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_exposure_process", "pv" : true, "conditionalRequired" : false, "description" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_process_preferred", "tableColumn" : "exposure_process_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_process_pref_map", "jsonAttribute" : "exposureProcessReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "templateColumn" : "Exposure Process Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_process_preferred" }, { "pvTableName" : "lk_exposure_material", "pv" : true, "conditionalRequired" : true, "description" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_material_preferred", "tableColumn" : "exposure_material_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_material_pref_map", "jsonAttribute" : "exposureMaterialReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "templateColumn" : "Exposure Material Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_material_preferred and exposure_material_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Exposure Material Reported", "operator" : "not-preferred-value", "value" : "lk_exposure_material" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "exposure_material_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\" and Exposure Material Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "exposureMaterialId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "templateColumn" : "Exposure Material ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease", "pv" : true, "conditionalRequired" : true, "description" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The Value provide by the user is further checked against the pref mapping table lk_study_condition_pref_mappng.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "disease_preferred", "tableColumn" : "disease_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_study_condition_pref_mappng", "jsonAttribute" : "diseaseReported", "columnType" : "varchar(550)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The Value provide by the user is further checked against the pref mapping table lk_study_condition_pref_mappng.", "templateColumn" : "Disease Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_preferred and disease_ontology_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "infectious challenge" }, { "field" : "Disease Reported", "operator" : "not-empty-value", "value" : "" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] }, { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_ontology_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"infectious challenge\" and Disease Reported is provided and Disease Reported does not match a recognized preferred term OR Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\" and Disease Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseOntologyId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "templateColumn" : "Disease Ontology ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease_stage", "pv" : true, "conditionalRequired" : true, "description" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_stage_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseStageReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "templateColumn" : "Disease Stage Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_stage_preferred" } ], "name" : "subjectanimals", "description" : "The subject animal template defines and annotates key elements of study subjects including demographics and links subjects to an arm within a study. In mouse studies, data providers may choose to define a single subject to represent a set of inbred mice treated the same way rather than describe each mouse (i.e. a cage of mice treated the same way). This approach is driven by how the assay results are recorded: if assay results are available for individual animals, then each animal should be defined to ImmPort." }, { "templateType" : "combined-result", "fileName" : "subjectHumans.txt", "schemaVersion" : "3.37", "jsonFileName" : "subjectHumans.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject defined ID is an identifier chosen by the data provider to refer to a subject. This ID may be referenced by other data records (e.g. biological sample). The user defined ID is not shared. For human subjects, the ID should not be identifying.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "Subject ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "gender", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "sex", "columnType" : "varchar(20)", "cv" : true, "cvTableName" : "lk_human_sex", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Sex", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The subject age at the outset of the study may be determined form one of several study milestones as indicated in the Age Event column.", "jsonDataType" : "number", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "min_subject_age", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "minSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Min Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject age at the end of the study may be determined form one of several study milestones.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "max_subject_age", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "maxSubjectAge", "columnType" : "float", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please enter a number.", "templateColumn" : "Max Subject Age", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available. The age unit must conform to the age unit assigned to the study.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_unit", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list. The age unit must conform to the age unit assigned to the study.", "templateColumn" : "Age Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEvent", "columnType" : "varchar(40)", "cv" : true, "cvTableName" : "lk_age_event", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Age Event", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "This column supports providing study milestones for subject's age determination that ImmPort does not support.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Age Event", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "age_event_specify", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one) and Age Event = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ageEventSpecify", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "If \"Age Event\" = Other, this field specifies the age event (free text). Otherwise, leave this column blank.", "templateColumn" : "Age Event Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject phenotype captures key aspects of the subject's disposition for the study.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_phenotype", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectPhenotype", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Enter a description of the subject.", "templateColumn" : "Subject Phenotype", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of subject locations is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "arm_2_subject", "ppvPreferredTableColumn" : null, "tableColumn" : "subject_location", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "subjectLocation", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_subject_location", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Subject Location", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "ethnicity", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "ethnicity", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_ethnicity", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Ethnicity", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "A list of preferred terms is available.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "race", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one)", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "race", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_race", "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "Please choose from the drop down list.", "templateColumn" : "Race", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "This column supports providing subject race descriptions that ImmPort does not support.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "subject_required", "operator" : "case-insensitive-equals", "value" : "Yes" }, { "field" : "Race", "operator" : "case-insensitive-equals", "value" : "other" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "race_specify", "conditionalRequiredWhenText" : "you are defining a new Subject in this row (rather than referencing an existing one) and Race = \"other\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "raceSpecify", "columnType" : "varchar(1000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "If Race='Other', the race should be specified, otherwise leave blank.", "templateColumn" : "Race Specify", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The subject description may be used to augment the arm or cohort based description of a subject.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : "subject", "ppvPreferredTableColumn" : null, "tableColumn" : "description", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "description", "columnType" : "varchar(4000)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "The subject description may be used to augment the arm or cohort based description of a subject. ", "templateColumn" : "Description", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "A subject may be assigned to a single arm within a study. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : true, "metaResultDataType" : "metaData", "tableName" : "arm_or_cohort", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "armOrCohortId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "arm_or_cohort", "ppv" : false, "comment" : "Please enter either a study arm or cohort user defined ID or ImmPort accession. When subjects are initially uploaded to ImmPort, they may be assigned to a single study's arm.", "templateColumn" : "Arm Or Cohort ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "This pseudo column separates meta data from results.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "metaData", "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "resultSeparatorColumn", "columnType" : null, "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : "subject", "ppv" : false, "comment" : "This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.", "templateColumn" : "Result Separator Column", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_exposure_process", "pv" : true, "conditionalRequired" : false, "description" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_process_preferred", "tableColumn" : "exposure_process_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_process_pref_map", "jsonAttribute" : "exposureProcessReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This identifies the type of process through which a host is exposed and the type of evidence for that exposure to have happened, which are tightly intertwined. This is the only element of the four that is always mandatory. Please select an exposure process from the list provided if the process matches yours or enter a exposure process if there is not an appropriate one provided. This exposure process is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_process_pref_map.", "templateColumn" : "Exposure Process Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_process_preferred" }, { "pvTableName" : "lk_exposure_material", "pv" : true, "conditionalRequired" : true, "description" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "exposure_material_preferred", "tableColumn" : "exposure_material_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_exposure_material_pref_map", "jsonAttribute" : "exposureMaterialReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This describes what substance(s) the host is exposed to and/or develops immune reactions to as part of the exposure process. Please select an exposure material from the list provided if the exposure material matches yours or enter a exposure material if there is not an appropriate one provided. This exposure material is visible when the result is shared. The value provided by the user is further checked against the pref mapping table lk_exposure_material_pref_map.", "templateColumn" : "Exposure Material Reported", "foreignKey" : false, "pvPreferredTableColumn" : "exposure_material_preferred and exposure_material_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Exposure Material Reported", "operator" : "not-preferred-value", "value" : "lk_exposure_material" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "exposure_material_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"administering substance in vivo ; occurrence of asymptomatic infection ; environmental exposure to endemic/ubiquitous agent without evidence for disease ; documented exposure without evidence for disease ; exposure with existing immune reactivity without evidence for disease ; exposure to substance without evidence for disease ; infectious challenge ; transplantation or transfusion ; vaccination ; occurrence of infectious disease ; occurrence of allergy\" and Exposure Material Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "exposureMaterialId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI or Vaccine Ontology ID associated with the exposure material. If the Exposure Material Reported is not a preferred value, then the Exposure Material ID must be provided. If the Exposure Material Reported is a preferred value, then the Exposure Material ID will be automatically be the ID associated with the preferred value and user will NOT need to supply this ID.", "templateColumn" : "Exposure Material ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease", "pv" : true, "conditionalRequired" : true, "description" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The Value provide by the user is further checked against the pref mapping table lk_study_condition_pref_mappng.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : "disease_preferred", "tableColumn" : "disease_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : "lk_study_condition_pref_mappng", "jsonAttribute" : "diseaseReported", "columnType" : "varchar(550)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : true, "comment" : "This indicates the specific disease of the host associated with the exposure. Please select a disease from the list provided if the disease matches yours or enter a disease if there is not an appropriate one provided. This disease is visible when the result is shared. The Value provide by the user is further checked against the pref mapping table lk_study_condition_pref_mappng.", "templateColumn" : "Disease Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_preferred and disease_ontology_id" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : true, "description" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "jsonDataType" : "string", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "infectious challenge" }, { "field" : "Disease Reported", "operator" : "not-empty-value", "value" : "" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] }, { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" }, { "field" : "Disease Reported", "operator" : "not-preferred-value", "value" : "lk_disease" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_ontology_id", "conditionalRequiredWhenText" : "Exposure Process Reported = \"infectious challenge\" and Disease Reported is provided and Disease Reported does not match a recognized preferred term OR Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\" and Disease Reported does not match a recognized preferred term", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseOntologyId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The NCBI Disease Ontology ID associated with the disease. If the Disease Reported is not a preferred value, then the Disease Ontology ID must be provided. If the disease is a preferred value, then the Disease Ontology ID will be the DOID associated with the preferred value.", "templateColumn" : "Disease Ontology ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_disease_stage", "pv" : true, "conditionalRequired" : true, "description" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : [ { "allOf" : [ { "field" : "Exposure Process Reported", "operator" : "case-insensitive-equals", "value" : "occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy" } ] } ], "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : "resultData", "tableName" : "immune_exposure", "ppvPreferredTableColumn" : null, "tableColumn" : "disease_stage_reported", "conditionalRequiredWhenText" : "Exposure Process Reported = \"occurrence of autoimmune disease ; occurrence of cancer ; occurrence of disease ; occurrence of infectious disease ; occurrence of allergy\"", "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "diseaseStageReported", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "This provides a broad classification of how the disease has progressed. Please select a disease stage from the list provided if the disease stage matches yours or enter a disease stage if there is not an appropriate one provided. This disease stage is visible when the result is shared.", "templateColumn" : "Disease Stage Reported", "foreignKey" : false, "pvPreferredTableColumn" : "disease_stage_preferred" } ], "name" : "subjecthumans", "description" : "The subject human template defines and annotates key elements of study subjects including demographics and links subjects to an arm within a study." }, { "templateType" : "single", "fileName" : "treatments.txt", "schemaVersion" : "3.37", "jsonFileName" : "treatments.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The treatment user defined ID is an identifier chosen by the data provider to refer to a treatment agent which can be a molecule, time or temperature. This ID may be referenced by other data records (e.g. study). The user defined ID is not shared.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "user_defined_id", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "userDefinedId", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The identifier should be unique to the ImmPort workspace to which the data will be uploaded.", "templateColumn" : "User Defined ID", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The treatment name is not referenced directly by other data records. The name should be an informative to a researcher reviewing the data. Treatments may be referenced by more than one biological or experiment sample. There are three categories to describe the molecular content, time and/or temperature applied in a sample treatment. You may enter data for amount, duration or temperature only any combination of these categories (e.g. amount and duration).", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "name", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "name", "columnType" : "varchar(100)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Treatments refer to in vitro modifications of samples. The treatment name is an alternate identifier that is visible when the treatment is shared.", "templateColumn" : "Name", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "If 'No' is selected, you must enter a value in the Treatment User Defined ID and Name columns and that is all. If 'Yes' is selected, you must enter a value in the Treatment User Defined ID and Name columns and the value/unit pair of columns for amount or duration or temperature.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : null, "ppvPreferredTableColumn" : null, "tableColumn" : null, "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "useTreatment", "columnType" : null, "cv" : true, "cvTableName" : "lk_yes_no", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Was a treatment applied to a sample?", "templateColumn" : "Use Treatment?", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The value should be a number.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "amount_value", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Amount Unit (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "amountValue", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The Amount Value indicates how much (concentration, mass, volume) of a treatment agent was applied to a sample.", "templateColumn" : "Amount Value", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The amount unit preferred terms list has commonly used units. If additional units are needed, please contact the ImmPort HelpDesk.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "amount_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Amount Value (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "amountUnit", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_amount_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit should be selected from the drop down list.", "templateColumn" : "Amount Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Duration Value indicates how long a treatment agent was applied to a sample.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "duration_value", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Duration Unit (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "durationValue", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The value should be a number.", "templateColumn" : "Duration Value", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The duration unit preferred terms list has commonly used units. If additional units are needed, please contact the ImmPort HelpDesk.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "duration_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Duration Value (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "durationUnit", "columnType" : "varchar(25)", "cv" : true, "cvTableName" : "lk_time_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit should be selected from the drop down list.", "templateColumn" : "Duration Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Temperature Value indicates how long a treatment agent was applied to a sample.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "temperature_value", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Temperature Unit (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "temperatureValue", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The value should be a number.", "templateColumn" : "Temperature Value", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The temperature unit preferred terms list has commonly used units. If additional units are needed, please contact the ImmPort HelpDesk.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "temperature_unit", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ "Must be provided together with Temperature Value (or leave both blank).", "At least one of Amount Value, Amount Unit, Duration Value, Duration Unit, Temperature Value, Temperature Unit is required when Use Treatment? = \"Yes\"." ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "temperatureUnit", "columnType" : "varchar(50)", "cv" : true, "cvTableName" : "lk_temperature_unit", "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The unit should be selected from the drop down list.", "templateColumn" : "Temperature Unit", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The Comments column allows the data provider to provide additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "treatment", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please provide additional comments as needed.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "treatments", "description" : "The treatment template defines and annotates the in vitro modifications (molecule added, temperature, duration) made to a sample. Treatments are required to be referenced by experiment samples and optionally by biologic samples." }, { "templateType" : "multiple", "fileName" : "Virus_Neutralization_Results.txt", "schemaVersion" : "3.37", "jsonFileName" : "Virus_Neutralization_Results.json", "validationLevel" : "", "columns" : [ { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The experiment sample identifier must be stored in ImmPort or in the experimentsamples.txt template.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : "expsample", "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "neut_ab_titer_result And expsample_2_file_info", "ppvPreferredTableColumn" : null, "tableColumn" : "expsample_accession", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "expsampleId", "columnType" : "varchar(15)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Please enter either an experiment sample user defined ID or ImmPort accession.", "templateColumn" : "Expsample ID", "foreignKey" : true, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_virus_strain", "pv" : true, "conditionalRequired" : false, "description" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "virus_strain_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "virusStrainReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The name of the virus strain used in the assay. Please select a name from the list provided if the name matches your name or enter a name if there is not an appropriate one provided. This name is visible when the result is shared.", "templateColumn" : "Virus Strain Reported", "foreignKey" : false, "pvPreferredTableColumn" : "virus_strain_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "The maximum sample dilution factor that continues to demonstrate virus neutralization.", "jsonDataType" : "number", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "value_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "valueReported", "columnType" : "varchar(50)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "A number is expected.", "templateColumn" : "Value Reported", "foreignKey" : false, "pvPreferredTableColumn" : null }, { "pvTableName" : "lk_titer_unit", "pv" : true, "conditionalRequired" : false, "description" : "The dilution factor unit.", "jsonDataType" : "enum", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : true, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "unit_reported", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "unitReported", "columnType" : "varchar(200)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "The dilution factor unit.", "templateColumn" : "Unit Reported", "foreignKey" : false, "pvPreferredTableColumn" : "titer_unit_preferred" }, { "pvTableName" : null, "pv" : false, "conditionalRequired" : false, "description" : "Comments captures additional descriptive information.", "jsonDataType" : "string", "conditionalRequiredWhen" : null, "foreignKeyTableName" : null, "required" : false, "combinedColumn" : false, "metaResultDataType" : null, "tableName" : "neut_ab_titer_result", "ppvPreferredTableColumn" : null, "tableColumn" : "comments", "conditionalRequiredWhenText" : null, "crossFieldRuleNotes" : [ ], "conditionalDuplicateRequired" : false, "ppvTableName" : null, "jsonAttribute" : "comments", "columnType" : "varchar(500)", "cv" : false, "cvTableName" : null, "conditionalRequiredTableName" : null, "ppv" : false, "comment" : "Comments captures additional descriptive information.", "templateColumn" : "Comments", "foreignKey" : false, "pvPreferredTableColumn" : null } ], "name" : "virus_neutralization_results", "description" : "The virus neutralization experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying the group of columns 'Virus Strain'and 'Titration Dilution Value' needed to describe each assay result." } ]