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Added values 'Tulsa LIBR-1000', 'MIND', 'BEAM', 'MARS-WI', 'POINTER',… #104

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Sep 5, 2024
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Added values 'Tulsa LIBR-1000', 'MIND', 'BEAM', 'MARS-WI', 'POINTER',… #104

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fef1bc3
Added values 'Tulsa LIBR-1000', 'MIND', 'BEAM', 'MARS-WI', 'POINTER',…
MasterPastures Sep 5, 2024
a727c02
Merge fef1bc3236a9dd8fb6c320cce21ac834565a8a25 into 8a4c3e2f23f63d26c…
MasterPastures Sep 5, 2024
f3693bb
GitHub Action: assemble *.model.csv from modules directory
MasterPastures Sep 5, 2024
015a991
GitHub Action: convert *.model.csv to *.model.jsonld
MasterPastures Sep 5, 2024
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8 changes: 7 additions & 1 deletion AD.model.csv
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -425,7 +425,9 @@ Y,Chromosome Y,,,,,chromosome,,Sage Bionetworks,,string,sequencing
ABC-DS,Alzheimer's Biomarkers Consortium - Down Syndrome,,,,False,cohort,,https://www.abcds.pitt.edu/,,string,clinical
ACT,Adult Changes in Thought - Kaiser Permanente Washington Health Research Institute,,,,False,cohort,,https://actagingresearch.org/about,,string,clinical
ADNI,Alzheimer's Disease Neuroimaging Initative,,,,False,cohort,,https://adni.loni.usc.edu/,,string,clinical
ADRC,Alzheimer Disease Research Centers,,,,False,cohort,,https://www.nia.nih.gov/health/clinical-trials-and-studies/alzheimers-disease-research-centers,,string,clinical
Banner,Banner Sun Health Research Institute's Brain and Body Donation Program.,,,,False,cohort,,https://www.bannerhealth.com/research/locations/sun-health-institute/programs/body-donation,,string,clinical
BEAM,Effect of a Modified Ketogenic-Mediterranean Diet on Alzheimer's Disease (BEAM Study),,,,False,cohort,,https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(19)30554-7/fulltext,,string,clinical
BEB-Miller,University of Miami Miller School of Medicine Brain Endowment Bank,,,,False,cohort,,https://med.miami.edu/programs/brain-endowment-bank,,string,clinical
Biggs Institute Brain Bank,University of Texas Health San Antonio Biggs Institute Brain Bank,,,,False,cohort,,https://biggsinstitute.org/research/brain-donation/,,string,clinical
BLSA,NIA's Baltimore Longitudinal Study of Aging,,,,False,cohort,,https://www.blsa.nih.gov/,,string,clinical
Expand All @@ -444,16 +446,20 @@ HPGP,Harvard Personal Genome Project,,,,False,cohort,,https://pgp.med.harvard.ed
HUP,Hospital of the University of Pennsylvania autopsy service,,,,False,cohort,,https://pathology.med.upenn.edu/clinical-services/anatomic-pathology/medical-pathology,,string,clinical
LBP,Living Brain Project,,,,False,cohort,,https://labs.icahn.mssm.edu/minervalab/resources/data-ark/lbp/,,string,clinical
MARS,The Minority Aging Research Study,,,,False,cohort,,https://www.rushu.rush.edu/research/departmental-research/minority-aging-research-study,,string,clinical
MARS-WI,The MARS: Microbiome in Alzheimer’s Risk Study at the University of Wisconsin,,,,False,cohort,,https://www.adrc.wisc.edu/mars-study,,string,clinical
Mayo Clinic,Mayo Clinic Brain Bank,,,,False,cohort,,https://www.mayo.edu/research/departments-divisions/department-neuroscience-florida/biorepositories/mayo-clinic-brain-bank,,string,clinical
MC,"Mayo Clinic (NOT brain bank, living)",,,,False,cohort,,https://www.mayo.edu/research/clinical-trials/cls-20308924#participating,,string,clinical
MCJ,Mayo Clinic Jacksonville,,,,False,cohort,,https://www.mayo.edu/research/florida,,string,clinical
MCR,Mayo Clinic Rochester,,,,False,cohort,,https://www.mayo.edu/research/minnesota,,string,clinical
MIND,MIND Trial to Prevent Alzheimer's,,,,False,cohort,,https://mind-diet-trial.org/,,string,clinical
MSBB,Mount Sinai/JJ Peters VA Medical Center Brain Bank,,,,False,cohort,,https://icahn.mssm.edu/research/nih-brain-tissue-repository,,string,clinical
NYBB,New York Brain Bank at Columbia University,,,,False,cohort,,http://www.columbianeuroresearch.org/taub/res-investigation.html,,string,clinical
Pitt ADRC,University of PIttsburgh Alzheimer's Disease Research Center,,,,False,cohort,,https://www.adrc.pitt.edu/,,string,clinical
POINTER,Protect Brain Health Through Lifestyle Intervention to Reduce Risk,,,,False,cohort,,https://www.alz.org/us-pointer/home.asp,,string,clinical
RADC,Rush Alzheimer's Disease Center,,,,False,cohort,,https://www.rushu.rush.edu/research/departmental-research/rush-alzheimers-disease-center,,string,clinical
ROSMAP,Religious Orders Study/Memory and Aging Project from Rush University ,,,,False,cohort,,"https://www.rushu.rush.edu/research/departmental-research/religious-orders-study, https://www.rushu.rush.edu/research/departmental-research/memory-and-aging-project",,string,clinical
SMRI,Stanley Medical Research Institute,,,,False,cohort,,https://www.stanleyresearch.org/,,string,clinical
Tulsa LIBR-1000, Tulsa Univ and Laureate Institute for Brain Research,,,,False,cohort,,https://utulsa.edu/news/libr-mental-health/,,string,clinical
UFL, University of Florida Neuromedicine Human Brain and Tissue Bank (UF HBTB),,,,False,cohort,,https://ctrnd.med.ufl.edu/research/brain-bank/,,string,clinical
UK Biobank,UK Biobank,,,,False,cohort,,https://www.ukbiobank.ac.uk/,,string,clinical
UPBB,University of Pennsylvania School of Medicine Brain Bank,,,,False,cohort,,https://www.med.upenn.edu/adrc/datasharing.html,,string,clinical
Expand Down Expand Up @@ -849,7 +855,7 @@ chromatinAmount,Amount in ug of chromatin used for an assay,,,,False,ManifestCol
chromatinAmountUnits,Units of measure for the amount of chromatin used for an assay,,,,False,ManifestColumn,,sage.annotations-immunoAssays.chromatinAmountUnits-0.0.2,,string,sequencing
chromosome,A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information; number or designation of the particular chromosome that the data is associated with.,"1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, mitochondrial",,,False,ManifestColumn,,sage.annotations-experimentalData.chromosome-0.0.4,,string,sequencing
climbID,Identifying string linked to an animal in Climb database,,,,True,ManifestColumn,,sage.annotations-neuro.climbID-0.0.1,,string,MODEL-AD
cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,ADRC,Banner,BEAM,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,MARS-WI,Mayo Clinic,MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
conservationMethod,The conservation method,"noConservation, fixed tissues only, frozen tissue only, both fixed and frozen tissue, missing or unknown",,,True,ManifestColumn,,sage-annotations-clinical.conservationMethod-0.0.2,string,,clinical
consortium,The name of the consortium,"CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP
contrastAgent,Substance administered during an imaging procedure that allows delineation of internal structures.,,,,False,ManifestColumn,,sage.annotations-experimentalData.contrastAgent-0.0.2,,string,imaging
Expand Down
192 changes: 149 additions & 43 deletions AD.model.jsonld
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10123,30 +10123,10 @@
}
},
{
"@id": "bts:Banner",
"@type": "rdfs:Class",
"rdfs:comment": "Banner Sun Health Research Institute's Brain and Body Donation Program",
"rdfs:label": "Banner",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
},
{
"@id": "bts:Study"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Banner",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:BEB-Miller",
"@id": "bts:ADRC",
"@type": "rdfs:Class",
"rdfs:comment": "University of Miami Miller School of Medicine Brain Endowment Bank",
"rdfs:label": "BEB-Miller",
"rdfs:comment": "Alzheimer Disease Research Centers",
"rdfs:label": "ADRC",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
Expand All @@ -10155,7 +10135,7 @@
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "BEB-Miller",
"sms:displayName": "ADRC",
"sms:required": "sms:false",
"sms:validationRules": []
},
Expand All @@ -10182,9 +10162,15 @@
{
"@id": "bts:ADNI"
},
{
"@id": "bts:ADRC"
},
{
"@id": "bts:Banner"
},
{
"@id": "bts:BEAM"
},
{
"@id": "bts:BEB-Miller"
},
Expand Down Expand Up @@ -10239,6 +10225,9 @@
{
"@id": "bts:MARS"
},
{
"@id": "bts:MARS-WI"
},
{
"@id": "bts:MayoClinic"
},
Expand All @@ -10251,6 +10240,9 @@
{
"@id": "bts:MCR"
},
{
"@id": "bts:MIND"
},
{
"@id": "bts:MSBB"
},
Expand All @@ -10260,6 +10252,9 @@
{
"@id": "bts:PittADRC"
},
{
"@id": "bts:POINTER"
},
{
"@id": "bts:RADC"
},
Expand All @@ -10269,6 +10264,9 @@
{
"@id": "bts:SMRI"
},
{
"@id": "bts:TulsaLIBR-1000"
},
{
"@id": "bts:UFL"
},
Expand All @@ -10292,6 +10290,63 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Banner",
"@type": "rdfs:Class",
"rdfs:comment": "Banner Sun Health Research Institute's Brain and Body Donation Program",
"rdfs:label": "Banner",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
},
{
"@id": "bts:Study"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Banner",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:BEAM",
"@type": "rdfs:Class",
"rdfs:comment": "Brain Energy for Amyloid transformation In Alzheimer's disease (BEAM) study",
"rdfs:label": "BEAM",
"rdfs:subClassOf": [
{
"@id": "bts:Study"
},
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "BEAM",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:BEB-Miller",
"@type": "rdfs:Class",
"rdfs:comment": "University of Miami Miller School of Medicine Brain Endowment Bank",
"rdfs:label": "BEB-Miller",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "BEB-Miller",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:BiggsInstituteBrainBank",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -10602,6 +10657,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MARS-WI",
"@type": "rdfs:Class",
"rdfs:comment": "The MARS: Microbiome in Alzheimer’s Risk Study at the University of Wisconsin",
"rdfs:label": "MARS-WI",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "MARS-WI",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MayoClinic",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -10673,6 +10745,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MIND",
"@type": "rdfs:Class",
"rdfs:comment": "MIND Trial to Prevent Alzheimer's",
"rdfs:label": "MIND",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "MIND",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:MSBB",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -10730,6 +10819,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POINTER",
"@type": "rdfs:Class",
"rdfs:comment": "Protect Brain Health Through Lifestyle Intervention to Reduce Risk",
"rdfs:label": "POINTER",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POINTER",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:RADC",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -10774,10 +10880,10 @@
"rdfs:label": "SMRI",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
"@id": "bts:IndividualIdSource"
},
{
"@id": "bts:IndividualIdSource"
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
Expand All @@ -10787,6 +10893,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:TulsaLIBR-1000",
"@type": "rdfs:Class",
"rdfs:comment": "Tulsa Univ and Laureate Institute for Brain Research",
"rdfs:label": "TulsaLIBR-1000",
"rdfs:subClassOf": [
{
"@id": "bts:Cohort"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Tulsa LIBR-1000",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:UFL",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -32110,23 +32233,6 @@
"sms:displayName": "ATP6V1A_kd",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:BEAM",
"@type": "rdfs:Class",
"rdfs:comment": "Brain Energy for Amyloid transformation In Alzheimer's disease (BEAM) study",
"rdfs:label": "BEAM",
"rdfs:subClassOf": [
{
"@id": "bts:Study"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "BEAM",
"sms:required": "sms:false",
"sms:validationRules": []
}
],
"@id": "http://schema.biothings.io/#0.1"
Expand Down
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