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Merged
lopierra merged 7 commits into from
Feb 5, 2026
Merged

2026 02 02 pl #290

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ee04d1c
added enums to enum_researchDomain
lopierra Jan 31, 2026
7b4d844
add enums to studyCode
lopierra Feb 4, 2026
2763a13
add/update enum_researchDomain
lopierra Feb 4, 2026
63f1416
combine Unharmonized/Harmonized Demographic/Clinical Data into one enum
lopierra Feb 4, 2026
400f355
update schemasheet
lopierra Feb 5, 2026
49b506d
correct title of guidMapped
lopierra Feb 5, 2026
0b94b58
update schemasheet
lopierra Feb 5, 2026
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12 changes: 9 additions & 3 deletions src/data/sheets/schemasheet.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ class slot title description required range any_of minimum_value maximum_value m
publication Publication uri true
expectedNumberOfParticipants Expected Number of Participants true integer
guidType GUID Type System used to generate globally unique identifiers (GUIDs) true enum_guidType
guidMapped GUIDs Mapped? For studies using NDAR GUIDs, have the GUIDs been added to the INCLUDE GUID Mapping File? boolean
guidMapped GUID Mapped For studies using NDAR GUIDs, have the GUIDs been added to the INCLUDE GUID Mapping File? boolean
dbgap dbGaP string true
acknowledgments Acknowledgments Funding statement and acknowledgments for this study string true
citationStatement Citation Statement "Statement that secondary data users should use to acknowledge use of this dataset. E.g., ""The results analyzed and <published or shown> here are based in whole or in part upon data generated by the INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project <insert accession number(s) and/or study DOI(s)>, and were accessed from the INCLUDE Data Hub and <insert other database(s)>.""" string true
Expand Down Expand Up @@ -162,6 +162,7 @@ DataFile sampleGlobalId Biospecimen
AECOM-DS enum_studyCode aecom_ds
APAP21 enum_studyCode apap21
ARC-DS enum_studyCode arc_ds
ASPIRE enum_studyCode aspire
BEST21 enum_studyCode best21
BrainPower enum_studyCode brainpower
BRI-DSR enum_studyCode bri_dsr
Expand All @@ -188,13 +189,15 @@ DataFile sampleGlobalId Biospecimen
EACH-DS enum_studyCode each_ds
ECODS enum_studyCode ecods
EXcEEDS enum_studyCode exceeds
HomeGrown enum_studyCode homegrown
HTP enum_studyCode htp
IBIS-DS enum_studyCode ibis-ds
JAKi-DS enum_studyCode jaki_ds
MOSAIC-DS enum_studyCode mosaic_ds
OPTimal enum_studyCode optimal
TEAM-DS enum_studyCode team_ds
TOMI enum_studyCode tomi
TOPS-DS enum_studyCode tops_ds
TRC-DS enum_studyCode trc_ds
X01-deSmith enum_studyCode x01_desmith
X01-Hakonarson enum_studyCode x01_hakonarson
Expand All @@ -203,16 +206,20 @@ DataFile sampleGlobalId Biospecimen
KF enum_program kf
Other enum_program other
enum_researchDomain
Auditory Perception enum_researchDomain auditory_perception mesh:D001307
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
Immune System Diseases enum_researchDomain immune_system_diseases mesh:D007154
Hematologic Diseases enum_researchDomain hematologic_diseases mesh:D006402
Neurodevelopment enum_researchDomain neurodevelopment mesh:D065886
Nutritional and Metabolic Diseases enum_researchDomain nutritional_and_metabolic_diseases mesh:D009750
Sleep Wake Disorders enum_researchDomain sleep_wake_disorders mesh:D012893
All Co-occurring Conditions enum_researchDomain all_co_occurring_conditions mesh:D013568
Physical Fitness enum_researchDomain physical_fitness mesh:D010809
Psychiatric Disorders enum_researchDomain psychiatric_disorders mesh:D001523
Respiratory Tract Diseases enum_researchDomain respiratory_tract_diseases mesh:D012140
Social Determinants of Health enum_researchDomain social_determinants_of_health mesh:D064890
Other enum_researchDomain other
enum_participantLifespanStage
Fetal enum_participantLifespanStage fetal
Expand Down Expand Up @@ -242,8 +249,7 @@ DataFile sampleGlobalId Biospecimen
Other Data obtained from other source, such as tissue bank enum_clinicalDataSourceType other
Unknown enum_clinicalDataSourceType unknown
enum_dataCategory
Unharmonized Demographic/Clinical Data enum_dataCategory unharmonized_demographic_clinical_data
Harmonized Demographic/Clinical Data enum_dataCategory harmonized_demographic_clinical_data
Demographic/Clinical Data enum_dataCategory demographic_clinical_data
Genomics enum_dataCategory genomics
Transcriptomics enum_dataCategory transcriptomics
Epigenomics enum_dataCategory epigenomics
Expand Down
26 changes: 21 additions & 5 deletions src/linkml/include_schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -469,7 +469,7 @@ slots:
guidMapped:
definition_uri: include:guidMapped
description: For studies using NDAR GUIDs, have the GUIDs been added to the INCLUDE GUID Mapping File?
title: GUIDs Mapped?
title: GUID Mapped
range: boolean
dbgap:
definition_uri: include:dbgap
Expand Down Expand Up @@ -1083,6 +1083,8 @@ enums:
title: APAP21
arc_ds:
title: ARC-DS
aspire:
title: ASPIRE
best21:
title: BEST21
brainpower:
Expand Down Expand Up @@ -1135,6 +1137,8 @@ enums:
title: ECODS
exceeds:
title: EXcEEDS
homegrown:
title: HomeGrown
htp:
title: HTP
ibis-ds:
Expand All @@ -1149,6 +1153,8 @@ enums:
title: TEAM-DS
tomi:
title: TOMI
tops_ds:
title: TOPS-DS
trc_ds:
title: TRC-DS
x01_desmith:
Expand All @@ -1168,12 +1174,18 @@ enums:
#TODO: replace/add NIH internal categories from Huiqing
definition_uri: include:enum_researchDomain
permissible_values:
auditory_perception:
title: Auditory Perception
meaning: mesh:D001307
behavior_and_behavior_mechanisms:
title: Behavior and Behavior Mechanisms
meaning: mesh:D001520
congenital_heart_defects:
title: Congenital Heart Defects
meaning: mesh:D006330
embryonic_and_fetal_development:
title: Embryonic and Fetal Development
meaning: mesh:D005314
immune_system_diseases:
title: Immune System Diseases
meaning: mesh:D007154
Expand All @@ -1195,9 +1207,15 @@ enums:
physical_fitness:
title: Physical Fitness
meaning: mesh:D010809
psychiatric_disorders:
title: Psychiatric Disorders
meaning: mesh:D001523
respiratory_tract_diseases:
title: Respiratory Tract Diseases
meaning: mesh:D012140
social_determinants_of_health:
title: Social Determinants of Health
meaning: mesh:D064890
other:
title: Other
enum_participantLifespanStage:
Expand Down Expand Up @@ -1269,10 +1287,8 @@ enums:
enum_dataCategory:
definition_uri: include:enum_dataCategory
permissible_values:
unharmonized_demographic_clinical_data:
title: Unharmonized Demographic/Clinical Data
harmonized_demographic_clinical_data:
title: Harmonized Demographic/Clinical Data
demographic_clinical_data:
title: Demographic/Clinical Data
genomics:
title: Genomics
transcriptomics:
Expand Down
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