Clear-ad-template-updates-jan2025

AD.model.csv

@@ -451,7 +451,7 @@ HUP,Hospital of the University of Pennsylvania autopsy service,,,,False,cohort,,
 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
+Mayo Clinic ADRC (Mayo ADRC),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
@@ -862,7 +862,7 @@ 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,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
+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",,,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, 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
 contrastAgent,Substance administered during an imaging procedure that allows delineation of internal structures.,,,,False,ManifestColumn,,sage.annotations-experimentalData.contrastAgent-0.0.2,,string,imaging
@@ -874,11 +874,12 @@ CVD_ATH_ANY,Atherosclerosis (dichotomous),"No CVD_ATH_ANY, Mild or Moderate or S
 CVD_CAA,Cerebral Amyloid Angiopathy (CAA),"No CVD_CAA, Mild, Moderate, Severe, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.CVD_CAA-0.0.2,string,,clinical
 CVD_CAA_ANY,Cerebral Amyloid Angiopathy (CAA) (dichotomous),"No CVD_CAA_ANY, Mild or Moderate or Severe, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.CVD_CAA_ANY-0.0.2,string,,clinical
 CVD_S,Cerebrovascular Disease (simplified). Composite variable indicating whether at least one of the contributing indicators (CVD_ATH_ANY CVD_ART_ANY CVD_CAA_ANY) are 1 else if at least one contributing indicator was evaluated as 0 CVD_S is 0 only missing if all indicators are missing.,"No CVD_S, Presence, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.CVD_S-0.0.2,string,,clinical
+dataContributionGroup,This describes the identifier assigned to a data contributor,"ADNI,MCSA,MCBB,MC ADRC,Emory,Duke,Baker Heart & Diabetes Institute,IADRC,Knight ADRC",,,False,ManifestColumn,,,,,
 dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","dataMatrix, metadata, normalized, processed, raw, residualized",,,False,ManifestColumn,,sage.annotations-experimentalData.dataSubtype-0.0.3,,string,experimentalData
 dataType,Types of input/output data in bioinformatics pipelines,"Volume, Weight, Pharmacokinetic Study, genomicVariants, behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, metagenomics, epigenetics, pharmacology",,,False,ManifestColumn,,sage.annotations-experimentalData.dataType-0.0.3,,string,experimentalData
 dateBirth,Individual date of birth,,,,True,ManifestColumn,,sage.annotations-demographics.dateBirth-0.0.2,,string,mouse
 dateDeath,Individual date of death,,,,False,ManifestColumn,,sage.annotations-demographics.dateDeath-0.0.2,,string,mouse
-diagnosis,A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.,"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, 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",,,False,ManifestColumn,,sage.annotations-experimentalData.diagnosis-0.0.12,,string,clinical
+diagnosis,A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.,"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, 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,Subjective Memory Concern, Other, Unknown, Dyslipidemia, Hypertension, Cardiovascular Disease, Metabolic Syndrome, Posterior Cortical Atrophy",,,False,ManifestColumn,,sage.annotations-experimentalData.diagnosis-0.0.12,,string,clinical
 diagnosisCriteria,"If a diagnosis is provided, the criteria it is based on",,,,False,ManifestColumn,,sage.annotations-experimentalData.diagnosisCriteria-0.0.2,,string,clinical
 differentiationMethod,The general strategy by which a reprogrammed or pluripotent cell is differentiated into a target cell.,"directed differentiation, Ngn2 induction",,,False,ManifestColumn,,sage.annotations-experimentalData.differentiationMethod-0.0.2,,string,biospecimen
 directionalBSseqLibrary,Indicates whether or not the bisulfiteSeq library is directional,"TRUE, FALSE",,,False,ManifestColumn,,sage.annotations-ngs.directionalBSseqLibrary-0.0.2,,boolean,sequencing
@@ -904,7 +905,7 @@ HEMOR,Hemorrhages,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-ann
 HS_L,Hippocampal sclerosis (with laterality),"No HS_L, Unilateral, Bilateral, Present Location UK, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.HS_L-0.0.2,string,,clinical
 HS_S,Hippocampal sclerosis (with simplified),"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.HS_S-0.0.2,string,,clinical
 individualID,Identifying string linked to the individual or animal being studied,,,,False,ManifestColumn,,sage.annotations-experimentalData.individualID-0.0.2,required^^#FileAnnotationTemplate,string,individual
-individualIdSource,Database or repository to which individual ID maps,"ABN, ABR, ADNI, AIBS, BannerSun, BEB_Miller, Caltech, Clotomics_PAIKEA_MSSM, DongLab, Einstein, Emory, Geschwind, HBSFRC, HBTRC, JAX, LIBD, LivingBrainProject_MSSM, MayoBrainBank, Mayo Clinic, MSSM, NDRI, Newcastle, NICHD, NIMH-HBCC, Novogenix, NYBB, Oxford, Penn, PGP, Pitt, Pritzker, Rush, Sestan, SMRI, StemExpress, TAA, UCI_TMF, UCSF, UM-BTB, UW-CDL, Vaccarino, XCell Science, Yale, IU",,,False,ManifestColumn,,sage.annotations-experimentalData.individualIdSource-0.0.17,required^^#IndividualHumanMetadataTemplate,string,individual
+individualIdSource,Database or repository to which individual ID maps,"ABN, ABR, ADNI, AIBS, BannerSun, BEB_Miller, Caltech, Clotomics_PAIKEA_MSSM, DongLab, Einstein, Emory, Geschwind, HBSFRC, HBTRC, JAX, LIBD, LivingBrainProject_MSSM, MayoBrainBank, Mayo Clinic, MSSM, NDRI, Newcastle, NICHD, NIMH-HBCC, Novogenix, NYBB, Oxford, Penn, PGP, Pitt, Pritzker, Rush, Sestan, SMRI, StemExpress, TAA, UCI_TMF, UCSF, UM-BTB, UW-CDL, Vaccarino, XCell Science, Yale, IU, Mayo Clinic, University of Miami, University of Florida, Washington University, Michigan University",,,False,ManifestColumn,,sage.annotations-experimentalData.individualIdSource-0.0.17,required^^#IndividualHumanMetadataTemplate,string,individual
 INFA,Infarcts and lacunes. Reports of anoxic ischemic injury will not be considered within the infarcts and lacunes lesions,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.INFA-0.0.2,string,,clinical
 INT,Interval between last exam and death (unit in months). Use missing or unknown if not available,,,,True,ManifestColumn,,sage-annotations-clinical.INT-0.0.2,string,,clinical
 ionMode,"Ionization polarity (positive, negative, polar)",,,,False,ManifestColumn,,sage.annotations-experimentalData.ionMode-0.0.2,,string,mass spectrometry