merge updated diagnosis valid values

AD.model.csv

@@ -898,7 +898,7 @@ dataType,Types of input/output data in bioinformatics pipelines,"Volume, Weight,
 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
 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
-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
+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,Late Mild Cognitive Impairment,Early Mild Cognitive Impairment,Subjective Memory Complaints,Possible AD,Probable AD,Early Onset AD,AD with vascular component,Atypical AD Logopenic progressive Aphasia",,,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

AD.model.jsonld

@@ -13981,6 +13981,30 @@
                 },
                 {
                     "@id": "bts:PosteriorCorticalAtrophy"
+                },
+                {
+                    "@id": "bts:LateMildCognitiveImpairment"
+                },
+                {
+                    "@id": "bts:EarlyMildCognitiveImpairment"
+                },
+                {
+                    "@id": "bts:SubjectiveMemoryComplaints"
+                },
+                {
+                    "@id": "bts:PossibleAD"
+                },
+                {
+                    "@id": "bts:ProbableAD"
+                },
+                {
+                    "@id": "bts:EarlyOnsetAD"
+                },
+                {
+                    "@id": "bts:ADwithvascularcomponent"
+                },
+                {
+                    "@id": "bts:AtypicalADLogopenicprogressiveAphasia"
                 }
             ],
             "sms:displayName": "diagnosis",
@@ -19731,6 +19755,142 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:LateMildCognitiveImpairment",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "LateMildCognitiveImpairment",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Late Mild Cognitive Impairment",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:EarlyMildCognitiveImpairment",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "EarlyMildCognitiveImpairment",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Early Mild Cognitive Impairment",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:SubjectiveMemoryComplaints",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "SubjectiveMemoryComplaints",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Subjective Memory Complaints",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:PossibleAD",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "PossibleAD",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Possible AD",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:ProbableAD",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "ProbableAD",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Probable AD",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:EarlyOnsetAD",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "EarlyOnsetAD",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Early Onset AD",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:ADwithvascularcomponent",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "ADwithvascularcomponent",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "AD with vascular component",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:AtypicalADLogopenicprogressiveAphasia",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "AtypicalADLogopenicprogressiveAphasia",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Diagnosis"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Atypical AD Logopenic progressive Aphasia",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:DiagnosisCriteria",
             "@type": "rdfs:Class",

modules/clinical/diagnosis.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-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
+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,Late Mild Cognitive Impairment,Early Mild Cognitive Impairment,Subjective Memory Complaints,Possible AD,Probable AD,Early Onset AD,AD with vascular component,Atypical AD Logopenic progressive Aphasia",,,False,ManifestColumn,,sage.annotations-experimentalData.diagnosis-0.0.12,,string,clinical
 AD-DS,Alzheimer's disease in Down Syndrome,,,,,diagnosis,,https://alz-journals.onlinelibrary.wiley.com/doi/full/10.1002/dad2.12044,,string,clinical
 Affective Disorder,Change in mood is the main underlying feature of these disorders.,,,,,diagnosis,,Sage Bionetworks,,string,clinical
 Alzheimer Disease,"(AD) - Alzheimer disease is a neurodegenerative disorder characterized by progressive dementia, loss of cognitive abilities, and deposition of fibrillar amyloid proteins as intraneuronal neurofibrillary tangles, extracellular amyloid plaques and vascular amyloid deposits.",,,,,diagnosis,,https://www.ebi.ac.uk/ols/ontologies/cco/terms?iri=http%3A%2F%2Fidentifiers.org%2Fomim%2F104300,,string,clinical