From ee04d1c11692a196eb9afeecb040db2efa0dc585 Mon Sep 17 00:00:00 2001 From: lopierra Date: Fri, 30 Jan 2026 17:16:27 -0800 Subject: [PATCH 1/7] added enums to enum_researchDomain --- src/linkml/include_schema.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index b4055fe..fc88446 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1168,18 +1168,27 @@ 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 hematologic_diseases: title: Hematologic Diseases meaning: mesh:D006402 + mental_disorders: + title: Mental Disorders + meaning: mesh:D001523 neurodevelopment: title: Neurodevelopment meaning: mesh:D065886 @@ -1198,6 +1207,9 @@ enums: 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: From 7b4d8448d7802591bc2f60d5dbafae17b14ff836 Mon Sep 17 00:00:00 2001 From: lopierra Date: Wed, 4 Feb 2026 11:13:06 -0800 Subject: [PATCH 2/7] add enums to studyCode --- src/linkml/include_schema.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index fc88446..0395c9d 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1083,6 +1083,8 @@ enums: title: APAP21 arc_ds: title: ARC-DS + aspire: + title: ASPIRE best21: title: BEST21 brainpower: @@ -1135,6 +1137,8 @@ enums: title: ECODS exceeds: title: EXcEEDS + homegrown: + title: HomeGrown htp: title: HTP ibis-ds: @@ -1149,6 +1153,8 @@ enums: title: TEAM-DS tomi: title: TOMI + tops_ds: + title: TOPS-DS trc_ds: title: TRC-DS x01_desmith: From 2763a13b6e934f5ddfa56599a5753153617d9830 Mon Sep 17 00:00:00 2001 From: lopierra Date: Wed, 4 Feb 2026 11:15:23 -0800 Subject: [PATCH 3/7] add/update enum_researchDomain --- src/linkml/include_schema.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 0395c9d..2602af7 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1192,9 +1192,6 @@ enums: hematologic_diseases: title: Hematologic Diseases meaning: mesh:D006402 - mental_disorders: - title: Mental Disorders - meaning: mesh:D001523 neurodevelopment: title: Neurodevelopment meaning: mesh:D065886 @@ -1210,6 +1207,9 @@ 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 From 63f1416b4151ed4a0629634ef7b7f58b02ec31ae Mon Sep 17 00:00:00 2001 From: lopierra Date: Wed, 4 Feb 2026 12:16:27 -0800 Subject: [PATCH 4/7] combine Unharmonized/Harmonized Demographic/Clinical Data into one enum --- src/linkml/include_schema.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/linkml/include_schema.yaml b/src/linkml/include_schema.yaml index 2602af7..14f90ac 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -1287,10 +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: From 400f3555c588092dc2b9554e4d421f90fe9926fe Mon Sep 17 00:00:00 2001 From: lopierra Date: Wed, 4 Feb 2026 16:09:12 -0800 Subject: [PATCH 5/7] update schemasheet --- src/data/sheets/schemasheet.tsv | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/data/sheets/schemasheet.tsv b/src/data/sheets/schemasheet.tsv index 90f832f..08fbeaa 100644 --- a/src/data/sheets/schemasheet.tsv +++ b/src/data/sheets/schemasheet.tsv @@ -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 @@ -188,6 +189,7 @@ 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 @@ -195,6 +197,7 @@ DataFile sampleGlobalId Biospecimen 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 @@ -203,8 +206,10 @@ 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 @@ -212,7 +217,9 @@ DataFile sampleGlobalId Biospecimen 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 @@ -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 From 49b506d1b7047359c486a64fe9d08b05243992ae Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 5 Feb 2026 11:32:33 -0800 Subject: [PATCH 6/7] correct title of guidMapped --- 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 14f90ac..87a77c3 100644 --- a/src/linkml/include_schema.yaml +++ b/src/linkml/include_schema.yaml @@ -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 From 0b94b5810c5a56e27b9586deaec30b8383eae05d Mon Sep 17 00:00:00 2001 From: lopierra Date: Thu, 5 Feb 2026 12:18:59 -0800 Subject: [PATCH 7/7] update schemasheet --- src/data/sheets/schemasheet.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/data/sheets/schemasheet.tsv b/src/data/sheets/schemasheet.tsv index 08fbeaa..b78d9c5 100644 --- a/src/data/sheets/schemasheet.tsv +++ b/src/data/sheets/schemasheet.tsv @@ -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 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 , and were accessed from the INCLUDE Data Hub and .""" string true