From 2c3a9b83d2097f0f254b3fabb4f8fbe64314deac Mon Sep 17 00:00:00 2001 From: lopierra Date: Wed, 2 Jul 2025 11:30:30 -0700 Subject: [PATCH 1/6] delete periods from enumFamilyType Other description so it's not cut off in docs --- src/linkml/include_schema.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 65b995a8..32d91d43 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -991,8 +991,7 @@ enums: title: ECODS exceeds: title: EXcEEDS - htp: - title: HTP + HTP: ibis-ds: title: IBIS-DS jaki_ds: @@ -1134,8 +1133,7 @@ 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 +1224,7 @@ 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 From 4fb28ed8c28092706b3a782d3285308288eb3b75 Mon Sep 17 00:00:00 2001 From: lopierra Date: Fri, 11 Jul 2025 08:30:34 -0700 Subject: [PATCH 2/6] add Participant-DataFile Manifest Class --- src/linkml/include_schema.yaml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 32d91d43..9d6a5fc9 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -135,7 +135,23 @@ 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 From 1bf5243e3157606c1bdb1bcc33892f6c5b8d744e Mon Sep 17 00:00:00 2001 From: lopierra Date: Fri, 11 Jul 2025 08:38:43 -0700 Subject: [PATCH 3/6] add slot participantDataFileManifestLocation to DataFile --- src/linkml/include_schema.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 9d6a5fc9..a62d7174 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -252,8 +252,9 @@ 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 @@ -853,6 +854,11 @@ 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 From 01f33c1426335b4406d5bbf60870603e463ba348 Mon Sep 17 00:00:00 2001 From: lopierra Date: Fri, 11 Jul 2025 08:42:39 -0700 Subject: [PATCH 4/6] add Trial Readiness Study to enumStudyDesign --- src/linkml/include_schema.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index a62d7174..9a574b79 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1093,6 +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: From fafb36919157f57868ec1a1b9042e28ec8bf2fde Mon Sep 17 00:00:00 2001 From: lopierra Date: Tue, 22 Jul 2025 09:52:00 -0700 Subject: [PATCH 5/6] add MeSH term for Neurodevelopmental Disorders D065886 to enum_researchDomain --- src/linkml/include_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 9a574b79..35dddd4e 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1048,7 +1048,7 @@ enums: meaning: mesh:D006402 neurodevelopment: title: Neurodevelopment - meaning: + meaning: mesh:D065886 sleep_wake_disorders: title: Sleep Wake Disorders meaning: mesh:D012893 From 039cbd682de5837cc66e80f3159d61a09928eada Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 31 Jul 2025 09:54:28 -0700 Subject: [PATCH 6/6] make dataType multivalued=true --- src/linkml/include_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 35dddd4e..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 @@ -910,6 +909,7 @@ slots: definition_uri: include:dataType title: Data Type range: string + multivalued: true #slot_usage experimentalStrategy: definition_uri: include:experimentalStrategy