Github Action: Updated dictionary term files and term pages

Author: github-actions[bot]

_data/ManifestColumn.csv

@@ -37,7 +37,7 @@ databaseVersion,"The version of the database. Provide a value OR provide one of
 databaseWeblink,"An internet address that may provide details of a database or software search, as well as for labs that generate their own search method (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 diagnosisStatus,"Whether the individual has been diagnosed with a condition or disease (physical and/or cognitive), \True"" indicates the individual has been diagnosed""","FALSE,TRUE",STRING,ManifestColumn,ManifestColumn
 digestionMethod,"The type of digestion (ex. in-solution, in-gel)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
-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",STRING,ManifestColumn,ManifestColumn
+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",STRING,ManifestColumn,ManifestColumn
 dnaBatchID,"DNA isolation batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 dnaBatchSize,The number of samples. Provide a value or Unknown Not collected Not applicable Not specified,,STRING,ManifestColumn,ManifestColumn
 dnaBatchSizeUnit,The unit of measurement for number of samples in a batch,"AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,other,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml,Unknown,Not collected,Not applicable,Not specified",STRING,ManifestColumn,ManifestColumn
@@ -122,7 +122,7 @@ specimenSource,Indicate the biological area of the specimen,,STRING,ManifestColu
 specimenType,Type of biological material comprising the Specimen,"blood,Cerebrospinal Fluid (CSF),Not applicable,Not collected,Not specified,organoid,plasma,saliva,serum,sputum,stool,swabs,tissue,Unknown,urine",STRING,ManifestColumn,ManifestColumn
 stage,Stage of the experimental design.,"Discovery,Not applicable,Not collected,Not specified,Other,Replication,Unknown",STRING,ManifestColumn,ManifestColumn
 statisticalModel,"A brief description of the statistical model used to determine association significance. It is important to distinguish studies that would otherwise appear identical (e.g., the same trait analyzed using additive, dominant, and recessive models). Example - additive model",,STRING,ManifestColumn,ManifestColumn
-studyCode,"Unique identifier for the study, assigned by the DCC","ILO,LC,LG,LLFS",STRING,ManifestColumn,ManifestColumn
+studyCode,"Unique identifier for the study, assigned by the DCC","CDCP,ILO,LC,LG,LLFS,Other",STRING,ManifestColumn,ManifestColumn
 studyKey,The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA),,STRING,ManifestColumn,ManifestColumn
 summaryFile,The name of any summary statistics file uploaded to Synapse. Example - example.tsv,,STRING,ManifestColumn,ManifestColumn
 summaryStatisticsAssembly,Genome assembly for the summary statistics. Example - GRCh38,,STRING,ManifestColumn,ManifestColumn

_data/assay_phenotype_human_template.csv

@@ -5,9 +5,9 @@ speciesGroup,The taxonomic ranking including both species and subspecies the ind
 Component,,False,,,,,
 Filename,,False,STRING,,,,
 diagnosis,Indicate the disease or condition.,False,STRING,,sage.annotations-experimentalData.diagnosis-0.0.12,ManifestColumn,"AD-DS, Affective Disorder, Alzheimer Disease, Alzheimer disease with psychosis, amyotrophic lateral sclerosis, anxiety, Autism Spectrum Disorder, Bipolar Disorder, Bladder Cancer, Brain Cancer, Breast Cancer, Cervical Cancer, Colon Cancer, control, corticobasal degeneration disorder, CS-DS, dementia, dystonia, essential tremor, Fibrocystic Breast Disease, frontotemporal dementia, gliosis, hypoxia, Juvenile Myelomonocytic Leukemia, Leukemia, Lewy body disease, Longevity, Lung Cancer, Major Depressive Disorder, MCI-DS, mild cognitive impairment, multiple system atrophy, Neurofibromatosis 1, Neurofibromatosis 2, no cognitive impairment, Not Applicable, obesity, obsessive compulsive disorder, Ovary Cancer, Pancreatic Cancer, Parkinson's disease, pathological aging, progressive supranuclear palsy, Prostate Cancer, Schizophrenia, Skin Cancer, Substance Related Disorder, Tourette Syndrome, traumatic brain injury, type 2 diabetes mellitus, vascular dementia, Williams Syndrome"
-ethnicity,Ethnicity of individual,True,STRING,,sage.annotations-demographics.ethnicity-0.0.2,ManifestColumn,"Hispanic or Latino,Not Hispanic or Latino,Prefer not to answer,Not Applicable"
-race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,ManifestColumn,"American Indian or Alaska Native,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Prefer not to answer,White"
+ethnicity,Ethnicity of individual,True,STRING,,sage.annotations-demographics.ethnicity-0.0.2,ManifestColumn,"Hispanic or Latino,Not Hispanic or Latino,Not applicable,Not collected,Other ethnicity,Prefer not to answer,Unknown"
+race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,ManifestColumn,"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"
 sex,The biological sex of the individual,True,STRING,,sage.annotations-experimentalData.sex-0.0.2,ManifestColumn,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown"
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",True,STRING,,,ManifestColumn,
-cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"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"
+cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"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"
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",True,STRING,,sage.annotations-experimentalData.individualID-0.0.2,ManifestColumn,

_data/assay_proteomics_template.csv

@@ -4,7 +4,7 @@ databaseName,"The name of the search database (nr, SwissProt or est_human, and/o
 databaseSource,"The name of the organization, project, or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).",True,STRING,,,ManifestColumn,
 databaseWeblink,"An internet address that may provide details of a database or software search, as well as for labs that generate their own search method (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 digestionMethod,"The type of digestion (ex. in-solution, in-gel)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
-digestionReagent,Enzymes or reagents used for digestion.,True,STRING,,,ManifestColumn,"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"
+digestionReagent,Enzymes or reagents used for digestion.,True,STRING,,,ManifestColumn,"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"
 enrichment,"Protocol or reagent used for enrichment (ex. Fe3+NTA-Agarose (Qiagen)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 enrichmentStrategy,Type of peptide or protein enrichment,True,STRING,,,ManifestColumn,"Acetylome Proteome,Glycoproteome,Lipidome,Metabolome,Not applicable,Not available,Not collected,Not specified,Phosphoproteome,Ubiquitylome,Unknown"
 experimentType,"The type of experiment used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,

_data/cohort.csv

@@ -1,74 +1,15 @@
 Key,Key Description,columnType,Source,Parent
-ABC-DS,,STRING,,ManifestColumn
- ACT,,STRING,,ManifestColumn
- ADNI,,STRING,,ManifestColumn
- Banner,,STRING,,ManifestColumn
- BEB-Miller,,STRING,,ManifestColumn
- BLSA,,STRING,,ManifestColumn
- CHDWB,,STRING,,ManifestColumn
-CHS,,STRING,,ManifestColumn
- CLINCOR,,STRING,,ManifestColumn
- DiCAD,,STRING,,ManifestColumn
- EHBS,,STRING,,ManifestColumn
- Emory ADRC,,STRING,,ManifestColumn
- Framingham,,STRING,,ManifestColumn
- HABC,,STRING,,ManifestColumn
- HBTRC,,STRING,,ManifestColumn
- HPGP,,STRING,,ManifestColumn
- HUP,,STRING,,ManifestColumn
- LBP,,STRING,,ManifestColumn
- MARS,,STRING,,ManifestColumn
- MAYO,,STRING,,ManifestColumn
- MC,,STRING,,ManifestColumn
- MCJ,,STRING,,ManifestColumn
- MCR,,STRING,,ManifestColumn
- MSBB,,STRING,,ManifestColumn
- MrOS,,STRING,,ManifestColumn
- NYBB,,STRING,,ManifestColumn
- Pitt ADRC,,STRING,,ManifestColumn
- RADC,,STRING,,ManifestColumn
- ROSMAP,,STRING,,ManifestColumn
- SMRI,,STRING,,ManifestColumn
- SOF,,STRING,,ManifestColumn
- UK Biobank,,STRING,,ManifestColumn
- UPBB,,STRING,,ManifestColumn
- UPenn,,STRING,,ManifestColumn
- UW ADRC,,STRING,,ManifestColumn
-ABC-DS,,STRING,,ManifestColumn
-ACT,,STRING,,ManifestColumn
-ADNI,,STRING,,ManifestColumn
-Banner,,STRING,,ManifestColumn
-BEB-Miller,,STRING,,ManifestColumn
-Biggs Institute Brain Bank,,STRING,,ManifestColumn
-BLSA,,STRING,,ManifestColumn
-CHDWB,,STRING,,ManifestColumn
-CLINCOR,,STRING,,ManifestColumn
-Columbia ADRC,,STRING,,ManifestColumn
-DiCAD,,STRING,,ManifestColumn
-EFIGA,,STRING,,ManifestColumn
-EHBS,,STRING,,ManifestColumn
-Emory ADRC,,STRING,,ManifestColumn
-FBS,,STRING,,ManifestColumn
-Framingham,,STRING,,ManifestColumn
-HBCC,,STRING,,ManifestColumn
-HBTRC,,STRING,,ManifestColumn
-HPGP,,STRING,,ManifestColumn
-HUP,,STRING,,ManifestColumn
-LBP,,STRING,,ManifestColumn
-MARS,,STRING,,ManifestColumn
-Mayo Clinic,,STRING,,ManifestColumn
-MC,,STRING,,ManifestColumn
-MCJ,,STRING,,ManifestColumn
-MCR,,STRING,,ManifestColumn
-MSBB,,STRING,,ManifestColumn
-NYBB,,STRING,,ManifestColumn
-Pitt ADRC,,STRING,,ManifestColumn
-RADC,,STRING,,ManifestColumn
-ROSMAP,,STRING,,ManifestColumn
-SMRI,,STRING,,ManifestColumn
-UFL,,STRING,,ManifestColumn
-UK Biobank,,STRING,,ManifestColumn
-UPBB,,STRING,,ManifestColumn
-UPenn,,STRING,,ManifestColumn
-UW ADRC,,STRING,,ManifestColumn
-WHICAP,,STRING,,ManifestColumn
+Arivale Scientific Wellness Study (SWS),,STRING,,ManifestColumn
+ Cardiovascular Health Study (CHS),,STRING,,ManifestColumn
+ Centenarian,,STRING,,ManifestColumn
+ Denmark Family,,STRING,,ManifestColumn
+ Not applicable,,STRING,,ManifestColumn
+ Not collected,,STRING,,ManifestColumn
+ Not specified,,STRING,,ManifestColumn
+ Other,,STRING,,ManifestColumn
+ Study of Osteoporotic Fractures (SOF),,STRING,,ManifestColumn
+ SuperAgers Family Study,,STRING,,ManifestColumn
+ The Health Aging and Body Composition Studay (HealthABC),,STRING,,ManifestColumn
+ The Osteoporotic Fractures in Men (MrOS) Study,,STRING,,ManifestColumn
+ Unknown,,STRING,,ManifestColumn
+ US Family,,STRING,,ManifestColumn

_data/demographics.csv

@@ -1,5 +1,5 @@
 Key,Key Description,Valid Values,columnType,Parent,module
-ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Prefer not to answer,Not Applicable",STRING,ManifestColumn,demographics
+ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Not applicable,Not collected,Other ethnicity,Prefer not to answer,Unknown",STRING,ManifestColumn,demographics
 familyStudyParticipant,Indicates whether or not a file has data from a human participant involved in a family study (ex. LLFS),"Yes, No, Not Assigned",STRING,ManifestColumn,demographics
-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",STRING,ManifestColumn,demographics
+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",STRING,ManifestColumn,demographics
 sex,The biological sex of the individual,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown",STRING,ManifestColumn,demographics

_data/digestionReagent.csv

@@ -12,6 +12,7 @@ Lys-C,,STRING,,ManifestColumn
 Lys-C/P,,STRING,,ManifestColumn
 No cleavage,,STRING,,ManifestColumn
 NoEnzyme,,STRING,,ManifestColumn
+Not applicable,,STRING,,ManifestColumn
 Not available,,STRING,,ManifestColumn
 Not collected,,STRING,,ManifestColumn
 Not specified,,STRING,,ManifestColumn

_data/ethnicity.csv

@@ -1,5 +1,8 @@
 Key,Key Description,columnType,Source,Parent
 Hispanic or Latino,,STRING,,ManifestColumn
 Not Hispanic or Latino,,STRING,,ManifestColumn
+Not applicable,,STRING,,ManifestColumn
+Not collected,,STRING,,ManifestColumn
+Other ethnicity,,STRING,,ManifestColumn
 Prefer not to answer,,STRING,,ManifestColumn
-Not Applicable,,STRING,,ManifestColumn
+Unknown,,STRING,,ManifestColumn

_data/individual.csv

@@ -1,6 +1,6 @@
 Key,Key Description,Valid Values,columnType,Parent,module
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",,STRING,ManifestColumn,individual
-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",STRING,ManifestColumn,individual
+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",STRING,ManifestColumn,individual
 hasADLs,The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs),"Yes, No",STRING,ManifestColumn,individual
 hasCASI,The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI),"Yes, No",STRING,ManifestColumn,individual
 hasCDR,The datafile and/or individualID includes cognitive variables and/or scores from the The Clinical Dementia Rating (CDR),"Yes, No",STRING,ManifestColumn,individual