Merge pull request #140 from adknowledgeportal/clear-ad-updates

updated and added new attributes for CLEAR-AD individual human template

Author: MasterPastures

AD.model.csv

@@ -44,3 +44,10 @@ 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 Study of Aging (MCSA),,,,,False,cohort,,,,string,clinical
+Mayo Clinic Brain Bank (MCBB),,,,,False,cohort,,,,string,clinical
+Michigan ADRC (MADC),,,,,False,cohort,,,,string,clinical
+Knight ADRC,,,,,False,cohort,,,,string,clinical
+1Florida ADRC (1FL ADRC),,,,,False,cohort,,,,string,clinical
+Emory ADRC,,,,,False,cohort,,,,string,clinical
+Indiana ADRC (IADRC),,,,,False,cohort,,,,string,clinical

AD.model.jsonld

@@ -51,3 +51,11 @@ traumatic brain injury,A form of acquired brain injury which occurs when a sudde
 type 2 diabetes mellitus,A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity.,,,,,diagnosis,,http://purl.obolibrary.org/obo/MONDO_0005148,,string,clinical
 vascular dementia,A dementia that involves impairments in cognitive function caused by problems in blood vessels that feed the brain.,,,,,diagnosis,,http://purl.obolibrary.org/obo/DOID_8725,,string,clinical
 Williams Syndrome,"A genetic syndrome caused by mulitple gene deletions from a region of chromosome 7, and characterized by distinctive facial appearance, mild-to-moderate developmental delay, cheerfulness, cardiovascular abnormalities, and infantile hypercalcemia",,,,,diagnosis,,https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20Metathesaurus&code=C0175702,,string,clinical
+Subjective Memory Concern,,,,,,diagnosis,,,,string,clinical
+Other,,,,,,diagnosis,,,,string,clinical
+Unknown,,,,,,diagnosis,,,,string,clinical
+Dyslipidemia,,,,,,diagnosis,,,,string,clinical
+Hypertension,,,,,,diagnosis,,,,string,clinical
+Cardiovascular Disease,,,,,,diagnosis,,,,string,clinical
+Metabolic Syndrome,,,,,,diagnosis,,,,string,clinical
+Posterior Cortical Atrophy,,,,,,diagnosis,,,,string,clinical

modules/clinical/cohort.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-pH,A scale used to specify the acidity or basicity of an aqueous or other liquid solution,,,,False,ManifestColumn,,sage.annotations-neuro.pH-0.0.3,,string,clinical
+pH,A scale used to specify the acidity or basicity of an aqueous or other liquid solution. pH for intracellular tissue in the brain,,,,False,ManifestColumn,,sage.annotations-neuro.pH-0.0.3,,string,clinical

modules/clinical/diagnosis.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+hypercholesterolemia, For CLEAR AD. UDSV3 IVP Form A5 Subject Health History Question 5c.  AND OR UDSV3 IVP Form D1 Clinician Diagnosis Question 8., "absent, recent/active, remote/inactive, unknown",,,False,ManifestColumn,,sage.annotations-demographics.hypercholesterolemias-0.0.2,,string,demographics

modules/clinical/pH.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+diabetes, For CLEAR-AD. UDSV3 IVP  Form A5  Subject Health History Questions 5a-5b. AND OR UDSV3 IVP Form D1 Clinician DiagnosisQuestion 2,"absent, recent/active, remote/inactive, type 1, type 2, other, other type, unknown, not assessed or unknown",,,False,ManifestColumn,,sage.annotations-demographics.diabetes-0.0.2,,string,demographics

modules/demographics/Hypercholesterolemia.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-ethnicity,Ethnicity of the donor,,,,False,ManifestColumn,,sage.annotations-demographics.ethnicity-0.0.2,,string,demographics
+ethnicity,Ethnicity of the donor. For CLEAR AD use either Hispanic/Latino or African American,,,,False,ManifestColumn,,sage.annotations-demographics.ethnicity-0.0.2,,string,demographics

modules/demographics/diabetes.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+height,For CLEAR AD. UDSV3 IVP Form B1 Physical Question 1 Numeric XX.X (inches). Use 888 for not assessed.,,,,False,ManifestColumn,,sage.annotations-demographics.height-0.0.2,,string,demographics

modules/demographics/ethnicity.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+hypertension,For CLEAR-AD. UDSV3 IVP Form A5 Subject Health History Question 5b. AND OR UDSV3 IVP Form D1 Clinician Diagnosis Question 6.,"absent, recent/active, remote/inactive, unknown, no, yes, not assessed or unknown",,,False,ManifestColumn,,sage.annotations-demographics.hypertension-0.0.2,,string,demographics