From 8016334089bd6c61695293aff5c1e0bf92dc0abe Mon Sep 17 00:00:00 2001 From: lopierra Date: Mon, 30 Dec 2024 10:41:50 -0800 Subject: [PATCH 1/6] add CCDS to enum_studyCode --- src/linkml/include_study.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/linkml/include_study.yaml b/src/linkml/include_study.yaml index b2a51116..2ebce1ea 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -389,6 +389,9 @@ enums: bri_dsr: text: bri_dsr title: BRI-DSR + ccds: + text: ccds + title: CCDS child_ds: text: child_ds title: CHILD-DS From 24badbc7735000a7f817812f0a426282d643d341 Mon Sep 17 00:00:00 2001 From: lopierra Date: Mon, 30 Dec 2024 11:47:49 -0800 Subject: [PATCH 2/6] update guidMapped colname in validate_study; make studyDesign=multivalue and update validate_study accordingly --- src/data_validation/validate_study.py | 4 ++-- src/linkml/include_study.yaml | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) 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_study.yaml b/src/linkml/include_study.yaml index 2ebce1ea..13d6717b 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 From a18a45842febfeb92074a3f49d2ca9ee181feb3a Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 9 Jan 2025 16:00:20 -0800 Subject: [PATCH 3/6] change Immune Map to Immune Profiling in enum_dataCategory --- src/linkml/include_study.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/linkml/include_study.yaml b/src/linkml/include_study.yaml index 13d6717b..b4731e2c 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -599,8 +599,8 @@ enums: text: cognitive_behavioral title: Cognitive/Behavioral immune_maps: - text: immune_maps - title: Immune Maps + text: immune_profiling + title: Immune Profiling imaging: text: imaging title: Imaging From ca799b76d113bb5dd7a0de928e76637b34c21e65 Mon Sep 17 00:00:00 2001 From: lopierra Date: Tue, 28 Jan 2025 17:45:26 -0800 Subject: [PATCH 4/6] add DS-ARC and DSRRS to enumStudyCode --- src/linkml/include_study.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/linkml/include_study.yaml b/src/linkml/include_study.yaml index b4731e2c..22fa056b 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -402,6 +402,9 @@ enums: decidas: text: decidas title: DECIDAS + ds_arc: + text: ds_arc + title: DS-ARC ds_brain: text: ds_brain title: DS-Brain @@ -441,6 +444,9 @@ enums: dsc: text: dsc title: DSC + dsrrs: + text: dsrrs + title: DSRRS ecods: text: ecods title: ECODS From 3bc0dce16df5666814dfe6760dd9cc2eee7fccc1 Mon Sep 17 00:00:00 2001 From: lopierra Date: Tue, 28 Jan 2025 17:52:08 -0800 Subject: [PATCH 5/6] make studyCode and participantExternalId multivalued in Participant; correct immune_profiling in Study --- src/linkml/include_participant.yaml | 21 ++++++--------------- src/linkml/include_study.yaml | 2 +- 2 files changed, 7 insertions(+), 16 deletions(-) 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 22fa056b..237ced9b 100644 --- a/src/linkml/include_study.yaml +++ b/src/linkml/include_study.yaml @@ -604,7 +604,7 @@ enums: cognitive_behavioral: text: cognitive_behavioral title: Cognitive/Behavioral - immune_maps: + immune_profiling: text: immune_profiling title: Immune Profiling imaging: From 21222f8c87cbc2c99eed643a83950d26fee448d4 Mon Sep 17 00:00:00 2001 From: lopierra Date: Mon, 3 Feb 2025 18:07:32 -0800 Subject: [PATCH 6/6] moved fileUploadLocation to before fileS3Location --- src/linkml/include_assay.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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