Merge pull request #96 from eliteportal/oct30_model_updates

Oct30_model_updates

Author: melissarklein

EL.data.model.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-digestionReagent,Enzymes or reagents used for digestion.,"2-iodobenzoate,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Glutamyl endopeptidase,Leukocyte elastase,Lys-C,Lys-C/P,No cleavage,NoEnzyme,Not available,Not collected,Not specified,PepsinA,Proline endopeptidase,TrypChymo,Trypsin,Trypsin/P,Unknown,Unspecific cleavage,V8-DE,V8-E",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomics Data Commons, ,Proteomics
+digestionReagent,Enzymes or reagents used for digestion.,"2-iodobenzoate,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Glutamyl endopeptidase,Leukocyte elastase,Lys-C,Lys-C/P,No cleavage,NoEnzyme,Not applicable,Not available,Not collected,Not specified,PepsinA,Proline endopeptidase,TrypChymo,Trypsin,Trypsin/P,Unknown,Unspecific cleavage,V8-DE,V8-E",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomics Data Commons, ,Proteomics

EL.data.model.jsonld

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62690https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045, ,"Individual_Human,Individual_non_Human,Phenotype_human"
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62690https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045, ,"Individual_non_Human,Phenotype_human"

modules/ManifestColumn/digestionReagent.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyCode,"Unique identifier for the study, assigned by the DCC","ILO,LC,LG,LLFS",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human"
+studyCode,"Unique identifier for the study, assigned by the DCC","CDCP,ILO,LC,LG,LLFS,Other",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human"

modules/ManifestColumn/speciesGroup.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Prefer not to answer,Not Applicable",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicity-0.0.2,demographics,False,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249", ,"Individual_Human,Phenotype_human"
+ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Not applicable,Not collected,Other ethnicity,Prefer not to answer,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicity-0.0.2,demographics,False,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249", ,"Individual_Human,Phenotype_human"

modules/ManifestColumn/studyCode.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-race,Race of individual,"American Indian or Alaska Native,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Prefer not to answer,White",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.race-0.0.2,demographics,True,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249, https://jamanetwork.com/pages/inclusive-language, https://thesaurus.cancer.gov/ncitbrowser/pages/home.jsf?version=23.04d", ,"Individual_Human,Phenotype_human"
+race,Race of individual,"American Indian or Alaska Native,Ashkenazi Jewish,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Not collected,Not applicable,Other race,Prefer not to answer,Unknown,White",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.race-0.0.2,demographics,True,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249, https://jamanetwork.com/pages/inclusive-language, https://thesaurus.cancer.gov/ncitbrowser/pages/home.jsf?version=23.04d", ,"Individual_Human,Phenotype_human"

modules/demographics/ethnicity.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-cohort,Name of the cohort the individual belongs to,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,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,,ManifestColumn,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",individual,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human,Phenotype_human"
+cohort,Name of the cohort the individual belongs to,"Arivale Scientific Wellness Study (SWS), Cardiovascular Health Study (CHS), Centenarian, Denmark Family, Not applicable, Not collected, Not specified, Other, Study of Osteoporotic Fractures (SOF), SuperAgers Family Study, The Health Aging and Body Composition Studay (HealthABC), The Osteoporotic Fractures in Men (MrOS) Study, Unknown, US Family",,,False,ManifestColumn,,ManifestColumn,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",individual,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human,Phenotype_human"