diff --git a/src/data_validation/validate_study.py b/src/data_validation/validate_study.py index a269d5bb..25bfba98 100644 --- a/src/data_validation/validate_study.py +++ b/src/data_validation/validate_study.py @@ -20,7 +20,7 @@ def validate_study_entry(row): researchDomain = row['research domain'].split('|') if handle_nan(row['research domain']) else [], participantLifespanStage = row['participant lifespan stage'].split('|') if handle_nan(row['participant lifespan stage']) else [], selectionCriteria = handle_nan(row['selection criteria']), - studyDesign = handle_nan(row['study design']), + studyDesign = row['study design'].split('|') if handle_nan(row['study design']) else [], clinicalDataSourceType = row['clinical data source type'].split('|') if handle_nan(row['clinical data source type']) else [], dataCategory = row['data category'].split('|') if handle_nan(row['data category']) else [], studyWebsite = handle_nan(row['study website']), @@ -28,7 +28,7 @@ def validate_study_entry(row): publication = str(row['publication']).split('|') if handle_nan(row['publication']) else [], expectedNumberOfParticipants = handle_nan(row['expected number of participants']), guidType = row['guid type'], - guidMapped = bool(row['guids mapped?']), + guidMapped = bool(row['guid mapped']), acknowledgments = row['acknowledgments'].split('|') if handle_nan(row['acknowledgments']) else [], citationStatement = row['citation statement'].split('|') if handle_nan(row['citation statement']) else [] ) diff --git a/src/linkml/include_assay.yaml b/src/linkml/include_assay.yaml index 5b0a3857..1f125ed5 100644 --- a/src/linkml/include_assay.yaml +++ b/src/linkml/include_assay.yaml @@ -88,8 +88,8 @@ classes: - sampleExternalId #usage of this field in multi-sample files is TBD - fileName - fileGlobalId - - fileS3Location - fileUploadLocation + - fileS3Location - drsUri - fileHash - dataAccess diff --git a/src/linkml/include_participant.yaml b/src/linkml/include_participant.yaml index 4f85916b..d2e38d15 100644 --- a/src/linkml/include_participant.yaml +++ b/src/linkml/include_participant.yaml @@ -52,21 +52,12 @@ classes: - firstPatientEngagementEvent - outcomesVitalStatus - ageAtLastVitalStatus - # FamilyGroup: - # name: FamilyGroup - # definition_uri: include:FamilyGroup - # annotations: - # required: - # tag: required - # value: 'False' - # requires_component: - # tag: requires_component - # value: Study,Participant - # description: A group of Participants in the same Study - # title: FamilyGroup - # is_a: Thing - # slots: - # - has_member # add this slot later + slot_usage: + studyCode: + multivalued: true + participantExternalId: + multivalued: true + Condition: title: Condition annotations: diff --git a/src/linkml/include_study.yaml b/src/linkml/include_study.yaml index b2a51116..237ced9b 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -224,6 +224,7 @@ slots: title: Study Design range: enum_studyDesign required: true + multivalued: true clinicalDataSourceType: definition_uri: include:clinicalDataSourceType description: Source(s) of data collected from study participants; pipe-separated if multiple @@ -389,6 +390,9 @@ enums: bri_dsr: text: bri_dsr title: BRI-DSR + ccds: + text: ccds + title: CCDS child_ds: text: child_ds title: CHILD-DS @@ -398,6 +402,9 @@ enums: decidas: text: decidas title: DECIDAS + ds_arc: + text: ds_arc + title: DS-ARC ds_brain: text: ds_brain title: DS-Brain @@ -437,6 +444,9 @@ enums: dsc: text: dsc title: DSC + dsrrs: + text: dsrrs + title: DSRRS ecods: text: ecods title: ECODS @@ -594,9 +604,9 @@ enums: cognitive_behavioral: text: cognitive_behavioral title: Cognitive/Behavioral - immune_maps: - text: immune_maps - title: Immune Maps + immune_profiling: + text: immune_profiling + title: Immune Profiling imaging: text: imaging title: Imaging