From ec55485d8f73f5cde42027bb3562a408434fc6e6 Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 15 May 2025 10:05:27 -0700 Subject: [PATCH 1/5] added Study enums for new cohorts --- src/linkml/include_schema.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index cd6dcbd5..aca96ea7 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -946,6 +946,8 @@ enums: title: DS-COG-AML ds_determined: title: DS-DETERMINED + ds_home: + title: DS-HOME ds_hsat: title: DS-HSAT ds_isp: @@ -972,10 +974,16 @@ enums: title: EXcEEDS htp: title: HTP + ibis-ds: + title: IBIS-DS + jaki_ds: + title: JAKi-DS optimal: title: OPTimal team_ds: title: TEAM-DS + tomi: + title: TOMI trc_ds: title: TRC-DS x01_desmith: From bd738f2b6beea2b1e53dcb7bec77fd1429d2676f Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 15 May 2025 10:57:06 -0700 Subject: [PATCH 2/5] added DOI and DOI Citation slots to Study and Dataset --- src/linkml/include_schema.yaml | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index aca96ea7..7d6fdcca 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -56,6 +56,8 @@ classes: - guidMapped - acknowledgments - citationStatement + - doi + - doiCitation slot_usage: dataCategory: description: Categories of data expected to be collected in this study @@ -92,6 +94,8 @@ classes: - otherAccessAuthority - isHarmonized - datasetManifestLocation + - doi + - doiCitation slot_usage: dataCategory: description: General category of data in Dataset; pipe-separated if multiple @@ -264,13 +268,14 @@ classes: range: Participant sampleGlobalId: range: Biospecimen + #################################################################################################### # Slot Usage Overview # ==================== # This section outlines the use of various slots (fields) across different entity classes, # including how slots can be customized or referenced within specific classes. # Slot usage enables fine-grained control over how each slot behaves within the context of each class. - +# # Slot Usage: Directly Assigned to Entity Classes # ------------------------------------------------------- # These slots are associated with specific classes, defining essential attributes for each entity. @@ -283,7 +288,7 @@ classes: # - experimentalStrategy: Used in DataFile, Dataset # - studyCode: Used in Participant # - participantExternalId: Used in Participant - +# # Referential Slot Usage: Cross-Class References # ------------------------------------------------ # These slots are used in multiple classes to establish relationships and link data across entities. @@ -295,8 +300,8 @@ classes: # - sampleGlobalId: Referenced in DataFile, DatasetManifest # - fileGlobalId: Referenced in DatasetManifest # - datasetGlobalId: (Usage not fully defined, consider adding specific references) - #################################################################################################### + slots: studyCode: definition_uri: include:studyCode @@ -447,6 +452,18 @@ slots: title: Citation Statement range: string multivalued: true + doi: + definition_uri: include:doi + description: Unique Digital Object Identifier for each Study and Dataset, minted by the DCC using DataCite + title: DOI + range: uri + required: false #change to true after pilot + doiCitation: + definition_uri: include:doiCitation + description: Bibliographic citation for DOI, generated by DataCite + title: DOI Citation + range: string + required: false #change to true after pilot datasetName: definition_uri: include:datasetName description: Full name of the dataset, provided by contributor From 8d6b66f1034c69967c263b27c6e8529d44aba613 Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 15 May 2025 11:44:11 -0700 Subject: [PATCH 3/5] added description to enum_ClinicalDataSourceType Other to include data obtained from tissue bank --- src/linkml/include_schema.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 7d6fdcca..d4b4185c 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1083,6 +1083,7 @@ enums: description: Data obtained from survey, questionnaire, etc. filled out by participant or caregiver other: title: Other + description: Data obtained from other source, such as tissue bank unknown: title: Unknown enum_dataCategory: From a9850b87bd2ab8e417f0558cda3959cc46976239 Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 15 May 2025 11:50:58 -0700 Subject: [PATCH 4/5] change Patient to Participant in ageAtFirstParticipantEngagement and firstParticipantEngagementEvent --- src/linkml/include_schema.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index d4b4185c..b622501f 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -155,8 +155,8 @@ classes: - race - ethnicity - downSyndromeStatus - - ageAtFirstPatientEngagement - - firstPatientEngagementEvent + - ageAtFirstParticipantEngagement + - firstParticipantEngagementEvent - outcomesVitalStatus - ageAtLastVitalStatus slot_usage: @@ -613,18 +613,18 @@ slots: title: Down Syndrome Status range: enum_downSyndromeStatus required: true - ageAtFirstPatientEngagement: - definition_uri: include:ageAtFirstPatientEngagement + ageAtFirstParticipantEngagement: + definition_uri: include:ageAtFirstParticipantEngagement description: Age in days of Participant at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available. - title: Age at First Patient Engagement + title: Age at First Participant Engagement range: integer minimum_value: 0 maximum_value: 33000 required: true - firstPatientEngagementEvent: - definition_uri: include:firstPatientEngagementEvent - description: Event for which Age at First Patient Engagement is given (e.g. enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available. - title: First Patient Engagement Event + firstParticipantEngagementEvent: + definition_uri: include:firstParticipantEngagementEvent + description: Event for which Age at First Participant Engagement is given (e.g. enrollment, visit, observation, sample collection, survey completion, etc.). Age at enrollment is preferred, if available. + title: First Participant Engagement Event required: true range: string outcomesVitalStatus: From aa1fbfdb156867891dfae50c7fe9852f74b91889 Mon Sep 17 00:00:00 2001 From: lopierra Date: Mon, 19 May 2025 08:01:33 -0700 Subject: [PATCH 5/5] add Neurodevelopment to enum_researchDomain --- src/linkml/include_schema.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index b622501f..7c05a221 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1008,6 +1008,7 @@ enums: x01_hakonarson: title: X01-Hakonarson enum_researchDomain: + #TODO: replace/add NIH internal categories from Huiqing definition_uri: include:enum_researchDomain permissible_values: behavior_and_behavior_mechanisms: @@ -1022,6 +1023,9 @@ enums: hematologic_diseases: title: Hematologic Diseases meaning: mesh:D006402 + neurodevelopment: + title: Neurodevelopment + meaning: sleep_wake_disorders: title: Sleep Wake Disorders meaning: mesh:D012893