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add lipidomics to data type #120

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add lipidomics to data type #120

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48c9647
add lipidomics to data type
ameliakallaher Oct 4, 2024
79241c7
Merge 48c964775d34967e6148397691910e68e8304439 into da80a23cd33a2a1b0…
ameliakallaher Oct 4, 2024
ff775ba
GitHub Action: assemble *.model.csv from modules directory
ameliakallaher Oct 4, 2024
b588f1c
GitHub Action: convert *.model.csv to *.model.jsonld
ameliakallaher Oct 4, 2024
985f36a
added 18 valid values to treatmentType
ameliakallaher Oct 4, 2024
2515493
Merge 985f36a3e4186b6ad2157262fdd9eb1b7185d930 into da80a23cd33a2a1b0…
ameliakallaher Oct 4, 2024
6a4b843
GitHub Action: assemble *.model.csv from modules directory
ameliakallaher Oct 4, 2024
1062c35
GitHub Action: convert *.model.csv to *.model.jsonld
ameliakallaher Oct 4, 2024
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20 changes: 19 additions & 1 deletion AD.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -872,7 +872,7 @@ CVD_CAA,Cerebral Amyloid Angiopathy (CAA),"No CVD_CAA, Mild, Moderate, Severe, m
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
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
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, lipidomics",,,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
Expand Down Expand Up @@ -1631,9 +1631,27 @@ Abeta42 oligomer,The stable oligomeric preparation of an amyloid beta peptide th
clozapine,A second generation antipsychotic used in the treatment of psychiatric disorders like schizophrenia.,,,,,treatmentType,,http://purl.obolibrary.org/obo/CHEBI_3766,,string,experimentalData
control,A group used as a standard of comparison in a control experiment.,,,,,treatmentType,,http://purl.obolibrary.org/obo/NCIT_C28143,,string,experimentalData
cuprizone,Cuprizon is an organooxygen compound and an organonitrogen compound. It is functionally related to an alpha-amino acid. Copper chelator that inhibits monoamine oxidase and causes liver and brain damage.,,,,,treatmentType,,https://pubchem.ncbi.nlm.nih.gov/compound/Cuprizone,,string,experimentalData
FU 1,Visit schedule Diet 2 Post B F/U,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
FU 1 PRE 2,Visit schedule Diet 1 between treatment A and treatment B,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
FU 2,Visit schedule Diet 1 final visit,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
FU 2 PRE 1,Visit schedule Diet 2 between treatment A and B,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
haloperidol,A compound composed of a central piperidine structure with hydroxy and p-chlorophenyl substituents at position 4 and an N-linked p-fluorobutyrophenone moiety,,,,,treatmentType,,http://purl.obolibrary.org/obo/CHEBI_5613,,string,experimentalData
levetiracetam,"A pyrrolidinone and carboxamide that is N-methylpyrrolidin-2-one in which one of the methyl hydrogens is replaced by an aminocarbonyl group, while another is replaced by an ethyl group (the S enantiomer). An anticonvulsant, it is used for the treatment of epilepsy in both human and veterinary medicine.",,,,,treatmentType,,http://purl.obolibrary.org/obo/CHEBI_6437,,string,experimentalData
placebo,A negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance,,,,,treatmentType,,http://purl.obolibrary.org/obo/OBI_0000169,,string,experimentalData
POST 1 keto,POST 1-keto,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POST 2 aha,POST 2-aha,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTA COG_aha,Post treatment A Cog labs. A= American Heart diet,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTA COG_keto,Post treatment A Cog labs keto diet,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTA LP_keto,Post treatment A Lumbar puncture,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTB COG_aha,Post treatment B Cog labs American Heart,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTB COG_keto,Post treatment B Cog labs. B = keto diet,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTB FU,Final follow up visit,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
POSTB LP_aha,Post treatment B Lumbar puncture,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
PRE 1,Diet schedule 1 first visit,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
PRE 2,Visit schedule Diet 2 first visit,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
PREA COG,Pre treatment A Cog labs,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
PREA LP,Pre treatment A Lumbar puncture,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
PREB COG,Pre treatment B Cog labs,,,,,treatmentType,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796564/,,string,experimentalData
verubecestat,Investigational oral beta-site amyloid precursor protein cleaving enzyme (BACE1 or beta secretase) inhibitor,,,,,treatmentType,,https://pubchem.ncbi.nlm.nih.gov/compound/Verubecestat,,string,experimentalData
missing or unknown,WBVD is missing or unknown,,,,,WBVD,,DiverseCohorts,,string,clinical
No,No whole brain vascular disease,,,,,WBVD,,ADSP,,string,clinical
Expand Down
326 changes: 326 additions & 0 deletions AD.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -13130,6 +13130,9 @@
},
{
"@id": "bts:Pharmacology"
},
{
"@id": "bts:Lipidomics"
}
],
"sms:displayName": "dataType",
Expand Down Expand Up @@ -18573,6 +18576,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Lipidomics",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Lipidomics",
"rdfs:subClassOf": [
{
"@id": "bts:DataType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "lipidomics",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:DateBirth",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -32505,6 +32525,312 @@
"sms:displayName": "ATP6V1A_kd",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FU1",
"@type": "rdfs:Class",
"rdfs:comment": "Visit schedule Diet 2 Post B F/U",
"rdfs:label": "FU1",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "FU 1",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FU1PRE2",
"@type": "rdfs:Class",
"rdfs:comment": "Visit schedule Diet 1 between treatment A and treatment B",
"rdfs:label": "FU1PRE2",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "FU 1 PRE 2",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FU2",
"@type": "rdfs:Class",
"rdfs:comment": "Visit schedule Diet 1 final visit",
"rdfs:label": "FU2",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "FU 2",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:FU2PRE1",
"@type": "rdfs:Class",
"rdfs:comment": "Visit schedule Diet 2 between treatment A and B",
"rdfs:label": "FU2PRE1",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "FU 2 PRE 1",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POST1keto",
"@type": "rdfs:Class",
"rdfs:comment": "POST 1-keto",
"rdfs:label": "POST1keto",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POST 1 keto",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POST2aha",
"@type": "rdfs:Class",
"rdfs:comment": "POST 2-aha",
"rdfs:label": "POST2aha",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POST 2 aha",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTACOGAha",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment A Cog labs. A= American Heart diet",
"rdfs:label": "POSTACOGAha",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTA COG_aha",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTACOGKeto",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment A Cog labs keto diet",
"rdfs:label": "POSTACOGKeto",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTA COG_keto",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTALPKeto",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment A Lumbar puncture",
"rdfs:label": "POSTALPKeto",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTA LP_keto",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTBCOGAha",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment B Cog labs American Heart",
"rdfs:label": "POSTBCOGAha",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTB COG_aha",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTBCOGKeto",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment B Cog labs. B = keto diet",
"rdfs:label": "POSTBCOGKeto",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTB COG_keto",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTBFU",
"@type": "rdfs:Class",
"rdfs:comment": "Final follow up visit",
"rdfs:label": "POSTBFU",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTB FU",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:POSTBLPAha",
"@type": "rdfs:Class",
"rdfs:comment": "Post treatment B Lumbar puncture",
"rdfs:label": "POSTBLPAha",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "POSTB LP_aha",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PRE1",
"@type": "rdfs:Class",
"rdfs:comment": "Diet schedule 1 first visit",
"rdfs:label": "PRE1",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "PRE 1",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PRE2",
"@type": "rdfs:Class",
"rdfs:comment": "Visit schedule Diet 2 first visit",
"rdfs:label": "PRE2",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "PRE 2",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PREACOG",
"@type": "rdfs:Class",
"rdfs:comment": "Pre treatment A Cog labs",
"rdfs:label": "PREACOG",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "PREA COG",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PREALP",
"@type": "rdfs:Class",
"rdfs:comment": "Pre treatment A Lumbar puncture",
"rdfs:label": "PREALP",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "PREA LP",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:PREBCOG",
"@type": "rdfs:Class",
"rdfs:comment": "Pre treatment B Cog labs",
"rdfs:label": "PREBCOG",
"rdfs:subClassOf": [
{
"@id": "bts:TreatmentType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "PREB COG",
"sms:required": "sms:false",
"sms:validationRules": []
}
],
"@id": "http://schema.biothings.io/#0.1"
Expand Down
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