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Merged
lopierra merged 10 commits into from
Apr 30, 2026
Merged

2026 02 19 pl #292

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ae70e08
change back to ParticipantDataFileManifest (no sample) and update slo…
lopierra Feb 19, 2026
681adaa
make vbrEmail multivalued
lopierra Feb 26, 2026
95fdfca
add studyGlobalId to Study class; update studyCode description to des…
lopierra Mar 6, 2026
b80960c
comment out accessLimitations and accessRequirements from Dataset sin…
lopierra Mar 6, 2026
fc63089
make datasetDescription required
lopierra Mar 25, 2026
fbe288d
add Hearing Disorders to enum_researchDomain
lopierra Apr 30, 2026
95d23ec
add Speech/Language/Hearing to enum_dataCategory
lopierra Apr 30, 2026
3ac0cc6
update schemasheet
lopierra Apr 30, 2026
6c6d34c
remove Study Global ID for now
lopierra Apr 30, 2026
8cac0ee
add DS-SAH to enum_studyCode
lopierra Apr 30, 2026
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19 changes: 9 additions & 10 deletions src/data/sheets/schemasheet.tsv
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
class slot title description required range any_of minimum_value maximum_value multivalued enum permissible_value meaning
>class slot title description required range any_of minimum_value maximum_value multivalued enum permissible_value meaning
studyCode Study Code Unique identifier for the study (generally a short acronym) true enum_studyCode
studyCode Study Code Unique short acronym for the study true enum_studyCode
studyTitle Study Title Full title of the study true string
program Program Funding source(s) for the study (pipe-separated if multiple) true enum_program true
studyDescription Study Description Brief description of the study (2-4 sentences) true string
principalInvestigatorName Principal Investigator Name Name(s) of Principal Investigator(s) of this study; pipe-separated if multiple true string true
studyContactName Study Contact Name Name of contact person for this study; pipe-separated if multiple true string true
studyContactInstitution Study Contact Institution Institution of contact person for this study; pipe-separated if multiple true string true
studyContactEmail Study Contact Email Email address of contact person for this study; pipe-separated if multiple true string true
vbrEmail VBR Email Email address for Virtual Biorepository requests/inquiries, if participating string
vbrEmail VBR Email Email address for Virtual Biorepository requests/inquiries, if participating string true
vbrUrl VBR URL Link to Virtual Biorepository request form, if participating uri
vbrReadme VBR Readme Instructions for contacting or requesting samples from Virtual Biorepository, if participating string
researchDomain Research Domain Main research domain(s) of the study, other than Down syndrome; pipe-separated if multiple true enum_researchDomain true
Expand Down Expand Up @@ -38,13 +38,11 @@ class slot title description required range any_of minimum_value maximum_value m
secondaryOutcomeMeasure Secondary Outcome Measure A description of each secondary outcome measure (title, description, and time point/duration of assessment). Multiple values should be pipe-separated. string true
otherOutcomeMeasure Other Outcome Measure A description of other outcome measures (title, description, and time point/duration of assessment). Multiple values should be pipe-separated. string true
datasetName Dataset Name Full name of the dataset, provided by contributor true string
datasetDescription Dataset Description Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields string
datasetDescription Dataset Description Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields true string
datasetGlobalId Dataset Global ID Unique Global ID for dataset, generated by DCC false string
datasetExternalId Dataset External ID Unique identifier or code for dataset, if provided by contributor string
dataCollectionStartYear Data Collection Start Year Year that data collection started false string
dataCollectionEndYear Data Collection End Year Year that data collection ended false string
accessLimitations Access Limitations Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) false string
accessRequirements Access Requirements Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated) false string
otherRepository Other Repository URL if dataset is already deposited in a public repository other than dbGaP (e.g. LONI, Metabolomics Workbench, etc.) uri true
otherAccessAuthority Other Access Authority Email or URL for dataset's Access Authority, if not dbGaP string
isHarmonized Is Harmonized All of the elements in this Dataset are harmonized and available in the INCLUDE Data Hub boolean
Expand Down Expand Up @@ -136,11 +134,9 @@ DatasetManifest Dataset Manifest Mapping information for files in Dataset
DatasetManifest studyCode Study
DatasetManifest fileGlobalId DataFile
DatasetManifest datasetGlobalId Dataset
ParticipantSampleDataFileManifest Participant-Sample-DataFile Manifest List of Participants and/or Samples in DataFiles with multiple Participants and/or Samples
ParticipantSampleDataFileManifest studyCode Study
ParticipantSampleDataFileManifest fileName DataFile
ParticipantSampleDataFileManifest participantExternalId Participant
ParticipantSampleDataFileManifest sampleExternalId Biospecimen
ParticipantDataFileManifest Participant-DataFile Manifest List of Participants in DataFiles with multiple Participants
ParticipantDataFileManifest fileName DataFile
ParticipantDataFileManifest participantExternalId Participant
Participant Participant Demographic and clinical information about the participant
Condition Condition Co-occurring conditions and other observations for the participant
Condition studyCode Study
Expand Down Expand Up @@ -181,6 +177,7 @@ DataFile sampleGlobalId Biospecimen
DS-Nexus enum_studyCode ds_nexus
DS-PALS enum_studyCode ds_pals
DS-PCGC enum_studyCode ds_pcgc
DS-SAH enum_studyCode ds_sah
DS-Sleep enum_studyCode ds_sleep
DS-VitE enum_studyCode ds_vite
DS360-CHD enum_studyCode ds360_chd
Expand Down Expand Up @@ -210,6 +207,7 @@ DataFile sampleGlobalId Biospecimen
Behavior and Behavior Mechanisms enum_researchDomain behavior_and_behavior_mechanisms mesh:D001520
Congenital Heart Defects enum_researchDomain congenital_heart_defects mesh:D006330
Embryonic and Fetal Development enum_researchDomain embryonic_and_fetal_development mesh:D005314
Hearing Disorders enum_researchDomain hearing_disorders D006311
Immune System Diseases enum_researchDomain immune_system_diseases mesh:D007154
Hematologic Diseases enum_researchDomain hematologic_diseases mesh:D006402
Neurodevelopment enum_researchDomain neurodevelopment mesh:D065886
Expand Down Expand Up @@ -265,6 +263,7 @@ DataFile sampleGlobalId Biospecimen
Physical Activity enum_dataCategory physical_activity
Other enum_dataCategory other
Sleep enum_dataCategory sleep_study
Speech/Language/Hearing enum_dataCategory speech_language_hearing
enum_guidType
NDAR GUID generated by NIMH Data Archive (NDA) GUID tool enum_guidType ndar
Other GUID generated by other system enum_guidType other
Expand Down
63 changes: 38 additions & 25 deletions src/linkml/include_schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ classes:
description: General information about the study
title: Study
slots:
# - studyGlobalId
- studyCode
- studyTitle
- program
Expand Down Expand Up @@ -109,8 +110,8 @@ classes:
- experimentalStrategy
- experimentalPlatform
- publication
- accessLimitations
- accessRequirements
# - accessLimitations
# - accessRequirements
- dbgap
- otherRepository
- otherAccessAuthority
Expand Down Expand Up @@ -156,26 +157,22 @@ classes:
range: DataFile
datasetGlobalId:
range: Dataset
ParticipantSampleDataFileManifest:
definition_uri: include:ParticipantSampleDataFileManifest
description: List of Participants and/or Samples in DataFiles with multiple Participants and/or Samples
title: Participant-Sample-DataFile Manifest
ParticipantDataFileManifest:
definition_uri: include:ParticipantDataFileManifest
description: List of Participants in DataFiles with multiple Participants
title: Participant-DataFile Manifest
slots:
- studyCode
- participantExternalId
- sampleExternalId
- participantGlobalId
- fileName
- fileGlobalId
#TODO: add Dictonary File Name & Global ID
slot_usage:
# Reference Slots
studyCode:
range: Study
fileName:
range: DataFile
participantExternalId:
range: Participant
sampleExternalId:
range: Biospecimen
Participant:
definition_uri: include:Participant
description: Demographic and clinical information about the participant
Expand Down Expand Up @@ -338,9 +335,14 @@ classes:
####################################################################################################

slots:
# studyGlobalId:
# definition_uri: include:studyGlobalId
# description: Unique identifier for the study, assigned by DCC
# title: Study Global ID
# required: true
studyCode:
definition_uri: include:studyCode
description: Unique identifier for the study (generally a short acronym)
description: Unique short acronym for the study
title: Study Code
range: enum_studyCode
required: true
Expand Down Expand Up @@ -397,6 +399,7 @@ slots:
description: Email address for Virtual Biorepository requests/inquiries, if participating
title: VBR Email
range: string
multivalued: true
vbrUrl:
definition_uri: include:vbrUrl
description: Link to Virtual Biorepository request form, if participating
Expand Down Expand Up @@ -606,6 +609,7 @@ slots:
description: Brief additional notes about the dataset (1-3 sentences) that are not already captured in the other fields
title: Dataset Description
range: string
required: true
datasetGlobalId:
definition_uri: include:datasetGlobalId
description: Unique Global ID for dataset, generated by DCC
Expand Down Expand Up @@ -637,18 +641,18 @@ slots:
range: string
#pattern: "^1|2\\d(3)$|nan"
required: false
accessLimitations:
definition_uri: include:accessLimitations
description: Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated)
title: Access Limitations
range: string
required: false #make true when we have enums
accessRequirements:
definition_uri: include:accessRequirements
description: Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated)
title: Access Requirements
range: string
required: false #make true when we have enums
# accessLimitations:
# definition_uri: include:accessLimitations
# description: Data access limitations, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated)
# title: Access Limitations
# range: string
# required: false
# accessRequirements:
# definition_uri: include:accessRequirements
# description: Data access requirements, as defined in the GA4GH Data Use Ontology (DUO; can list more than one, pipe separated)
# title: Access Requirements
# range: string
# required: false
otherRepository:
definition_uri: include:otherRepository
description: URL if dataset is already deposited in a public repository other than dbGaP (e.g. LONI, Metabolomics Workbench, etc.)
Expand Down Expand Up @@ -1121,6 +1125,8 @@ enums:
title: DS-PALS
ds_pcgc:
title: DS-PCGC
ds_sah:
title: DS-SAH
ds_sleep:
title: DS-Sleep
ds_vite:
Expand Down Expand Up @@ -1186,6 +1192,9 @@ enums:
embryonic_and_fetal_development:
title: Embryonic and Fetal Development
meaning: mesh:D005314
hearing_disorders:
title: Hearing Disorders
meaning: D006311
immune_system_diseases:
title: Immune System Diseases
meaning: mesh:D007154
Expand Down Expand Up @@ -1289,8 +1298,10 @@ enums:
permissible_values:
demographic_clinical_data:
title: Demographic/Clinical Data
#use for Study Expected Data Category
unharmonized_demographic_clinical_data:
title: Unharmonized Demographic/Clinical Data
#use for Dataset Data Category
genomics:
title: Genomics
transcriptomics:
Expand Down Expand Up @@ -1319,6 +1330,8 @@ enums:
title: Other
sleep_study:
title: Sleep
speech_language_hearing:
title: Speech/Language/Hearing
enum_guidType:
definition_uri: include:enum_guidType
permissible_values:
Expand Down
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