Merge pull request #161 from adknowledgeportal/CLEAR-AD_update_cohorts

added clear-ad cohorts

Author: MasterPastures

AD.model.csv

@@ -477,6 +477,7 @@ UPBB,University of Pennsylvania School of Medicine Brain Bank,,,,False,cohort,,h
 UPenn,"The University of Pennsylvania Alzheimer's Disease Core Center (ADCC), Penn Udall Center and the Center for Neurodegenerative Disease Research (CNDR)",,,,False,cohort,,"https://pathology.med.upenn.edu/research/centers-and-institutes/udall-center-for-parkinsons-research, https://www.med.upenn.edu/cndr/",,string,clinical
 UW ADRC,University of Washington Alzheimer's Disease Research Center,,,,False,cohort,,http://depts.washington.edu/mbwc/adrc,,string,clinical
 WHICAP,"The Washington-Heights/Inwood Columbia Aging Project (WHICAP) is a community-based longitudinal study, recruiting elderly subjects from Northern Manhattan. Cohorts were established in 1992, 1999, and 2009. Subjects are evaluated every two years.",,,,False,cohort,,https://www.neurology.columbia.edu/research/research-centers-and-programs/alzheimers-disease-research-center-adrc/investigators/investigator-resources,,string,clinical
+Mayo Clinic ADRC (Mayo ADRC),,,,,False,cohorts,,,,string,clinical
 both fixed and frozen tissue,Conservation method is both fixed and frozen tissue,,,,,conservationMethod,,CLEAR-AD,,string,clinical
 fixed tissues only,Conservation method is fixed tissues only,,,,,conservationMethod,,CLEAR-AD,,string,clinical
 frozen tissue only,Conservation method is frozen tissue only,,,,,conservationMethod,,CLEAR-AD,,string,clinical
@@ -878,7 +879,7 @@ 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,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 ADRC (Mayo ADRC),MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP, Mayo Clinic Study of Aging (MCSA),Mayo Clinic Brain Bank (MCBB),Michigan ADRC (MADC),Knight ADRC, 1Florida ADRC (1FL ADRC),Emory ADRC, Indiana ADRC (IADRC)",,,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,MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP, Mayo Clinic Study of Aging (MCSA),Mayo Clinic Brain Bank (MCBB),Mayo Clinic ADRC (Mayo ADRc),Michigan ADRC (MADC),Knight ADRC, 1Florida ADRC (1FL ADRC),Emory ADRC, Indiana ADRC (IADRC)",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
 collectionMethod,For CLEAR-AD.Blood samples that are collected in heparin tubes will be sent directly to NCRAD for them to extract and store PBMCs for eventual generation of iPSCs.,"PAXgene Blood Tube, EDTA Purple Top Tube, Heparin (NaHep) Green Top Tubes,other, not collected",,,False,ManifestColumn,,sage.annotations-experimentalData.collectionMethod-0.0.11,,string,biospecimen
 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, AGMP, 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

AD.model.jsonld

@@ -10156,9 +10156,6 @@
                 {
                     "@id": "bts:MARS-WI"
                 },
-                {
-                    "@id": "bts:MayoClinicADRC(MayoADRC)"
-                },
                 {
                     "@id": "bts:MC"
                 },
@@ -10219,6 +10216,9 @@
                 {
                     "@id": "bts:MayoClinicBrainBank(MCBB)"
                 },
+                {
+                    "@id": "bts:MayoClinicADRC(MayoADRc)"
+                },
                 {
                     "@id": "bts:MichiganADRC(MADC)"
                 },
@@ -10906,11 +10906,11 @@
         {
             "@id": "bts:MayoClinicADRC(MayoADRC)",
             "@type": "rdfs:Class",
-            "rdfs:comment": "Mayo Clinic Brain Bank",
+            "rdfs:comment": "TBD",
             "rdfs:label": "MayoClinicADRC(MayoADRC)",
             "rdfs:subClassOf": [
                 {
-                    "@id": "bts:Cohort"
+                    "@id": "bts:Cohorts"
                 }
             ],
             "schema:isPartOf": {
@@ -10920,6 +10920,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Cohorts",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Cohorts",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "cohorts",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:MayoClinicBrainBank(MCBB)",
             "@type": "rdfs:Class",
@@ -19184,6 +19201,23 @@
             "sms:required": "sms:true",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:MayoClinicADRC(MayoADRc)",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "MayoClinicADRC(MayoADRc)",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Cohort"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Mayo Clinic ADRC (Mayo ADRc)",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:CollectionMethod",
             "@type": "rdfs:Class",

modules/clinical/cohort.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-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 ADRC (Mayo ADRC),MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP, Mayo Clinic Study of Aging (MCSA),Mayo Clinic Brain Bank (MCBB),Michigan ADRC (MADC),Knight ADRC, 1Florida ADRC (1FL ADRC),Emory ADRC, Indiana ADRC (IADRC)",,,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,MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP, Mayo Clinic Study of Aging (MCSA),Mayo Clinic Brain Bank (MCBB),Mayo Clinic ADRC (Mayo ADRc),Michigan ADRC (MADC),Knight ADRC, 1Florida ADRC (1FL ADRC),Emory ADRC, Indiana ADRC (IADRC)",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
 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
@@ -46,6 +46,7 @@ UW ADRC,University of Washington Alzheimer's Disease Research Center,,,,False,co
 WHICAP,"The Washington-Heights/Inwood Columbia Aging Project (WHICAP) is a community-based longitudinal study, recruiting elderly subjects from Northern Manhattan. Cohorts were established in 1992, 1999, and 2009. Subjects are evaluated every two years.",,,,False,cohort,,https://www.neurology.columbia.edu/research/research-centers-and-programs/alzheimers-disease-research-center-adrc/investigators/investigator-resources,,string,clinical
 Mayo Clinic Study of Aging (MCSA),,,,,False,cohort,,,,string,clinical
 Mayo Clinic Brain Bank (MCBB),,,,,False,cohort,,,,string,clinical
+Mayo Clinic ADRC (Mayo ADRC),,,,,False,cohorts,,,,string,clinical
 Michigan ADRC (MADC),,,,,False,cohort,,,,string,clinical
 Knight ADRC,,,,,False,cohort,,,,string,clinical
 1Florida ADRC (1FL ADRC),,,,,False,cohort,,,,string,clinical