diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 65b995a8..b49ab537 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -108,7 +108,6 @@ classes: description: Expected number of participants in this Dataset (or actual number, if data has been submitted to INCLUDE DCC). If additional explanation is needed, please add to Dataset Description field. dataType: description: Specific type of data contained in Dataset; pipe-separated if multiple (e.g. Preprocessed metabolite relative abundance, Absolute protein concentration, Aligned reads, Simple nucleotide variations, GVCF, Gene expression quantifications, Gene fusions, Somatic copy number variations, Somatic structural variations) - multivalued: true experimentalStrategy: description: Experimental method used to obtain data in Dataset; pipe-separated if multiple (e.g. Whole genome sequencing, RNAseq, Multiplex immunoassay, Mass spec metabolomics) multivalued: true @@ -135,7 +134,23 @@ classes: range: DataFile datasetGlobalId: range: Dataset - + ParticipantDataFileManifest: + definition_uri: include:ParticipantDataFileManifest + description: List of Participants in DataFiles with multiple Participants + title: Participant-DataFile Manifest + slots: + - studyCode + - participantExternalId + - fileName + #TODO: add Dictonary File Name & Global ID + slot_usage: + # Reference Slots + studyCode: + range: Study + fileGlobalId: + range: DataFile + datasetGlobalId: + range: Dataset Participant: definition_uri: include:Participant description: Demographic and clinical information about the participant @@ -236,8 +251,9 @@ classes: title: Data File slots: - studyCode - - participantGlobalId #usage of this field in multi-participant files is TBD - - participantExternalId #usage of this field in multi-participant files is TBD + - participantGlobalId + - participantExternalId + - participantDataFileManifestLocation - sampleGlobalId #usage of this field in multi-sample files is TBD - sampleExternalId #usage of this field in multi-sample files is TBD - fileName @@ -837,6 +853,11 @@ slots: description: Whether or not the specific Container is potentially available for sharing through the Virtual Biorepository title: Container Availability range: enum_Availability + participantDataFileManifestLocation: + definition_uri: include:participantDataFileManifestLocation + description: Location of Participant-DataFile Manifest, if file contains multiple Participants + title: Participant-DataFile Manifest Location + range: string fileName: definition_uri: include:fileName description: Name of file, assigned by data contributor @@ -888,6 +909,7 @@ slots: definition_uri: include:dataType title: Data Type range: string + multivalued: true #slot_usage experimentalStrategy: definition_uri: include:experimentalStrategy @@ -991,8 +1013,7 @@ enums: title: ECODS exceeds: title: EXcEEDS - htp: - title: HTP + HTP: ibis-ds: title: IBIS-DS jaki_ds: @@ -1027,7 +1048,7 @@ enums: meaning: mesh:D006402 neurodevelopment: title: Neurodevelopment - meaning: + meaning: mesh:D065886 sleep_wake_disorders: title: Sleep Wake Disorders meaning: mesh:D012893 @@ -1072,6 +1093,8 @@ enums: title: Interventional longitudinal: title: Longitudinal + trial_readiness_study: + title: Trial Readiness Study tumor_vs_matched_normal: title: Tumor vs Matched Normal enum_clinicalDataSourceType: @@ -1134,8 +1157,7 @@ enums: other: title: Other description: GUID generated by other system - no_guid: - title: No GUID + No GUID: description: No GUIDs used in this study enum_conditionInterpretation: permissible_values: @@ -1226,7 +1248,7 @@ enums: description: Proband + one parent other: title: Other - description: Other family structure, e.g. one parent + twins + description: Other family structure, eg one parent + twins proband_only: title: Proband-only description: Proband only, no family members participating in study