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set metaboliteType validation rule as "list like" #107

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Sep 23, 2024
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2 changes: 1 addition & 1 deletion AD.model.csv
Original file line number Diff line number Diff line change
Expand Up @@ -924,7 +924,7 @@ meanCoverage,Total number of bases covered by ATAC-seq reads/size of genome,,,,F
meanGCContent,Mean GC content per sample,,,,False,ManifestColumn,,sage.annotations-qc.meanGCContent-0.0.2,,number,sequencing
medianGenes,The median number of genes detected (with nonzero UMI counts) across all cell-associated barcodes,,,,False,ManifestColumn,,sage.annotations-qc.medianGenes-0.0.2,,number,sequencing
medianUMIs,The median number of total Unique Molecular Identifier (UMI) counts across all cell-associated barcodes,,,,False,ManifestColumn,,sage.annotations-qc.medianUMIs-0.0.2,,number,sequencing
metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,,string,metabolomics
metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,list like error,string,metabolomics
metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","analytical covariates, assay metadata, biospecimen, data dictionary, ID mapping, individual, manifest, protocol",,,False,ManifestColumn,,sage.annotations-experimentalData.metadataType-0.0.4,,string,ADKP
MICR,Microinfarcts,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.MICR-0.0.2,string,,clinical
microchipID,Identifying string of p-chip implanted in the animal being studied,,,,False,ManifestColumn,,sage.annotations-neuro.microchipID-0.0.1,,string,MODEL-AD
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4 changes: 3 additions & 1 deletion AD.model.jsonld
Original file line number Diff line number Diff line change
Expand Up @@ -19684,7 +19684,9 @@
],
"sms:displayName": "metaboliteType",
"sms:required": "sms:false",
"sms:validationRules": []
"sms:validationRules": [
"list like error"
]
},
{
"@id": "bts:Acylcarnitines",
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2 changes: 1 addition & 1 deletion modules/metabolomics/metaboliteType.csv
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,,string,metabolomics
metaboliteType,Class of metabolite.,"acylcarnitines, acylglycerols, amino acids, ApoA1, ApoE, bile acids, biogenic amines, carbohydrates, catecholamine, ceramides, cholesterol, cofactors and vitamins, drugs, eicosanoids, endocannabinoids, fatty acids, glycerides, glycerolipid, glycerophospholipid, ketones, lipids, lipoproteins, lysophosphatidylcholine, lysophospholipids, nucleotides, oxylipins, peptides, phosphatidylcholine, phosphatidylethonalamines, phospholipids, plasmalogens, sphingolipids, steroids, sterols, sugars, TCA cycle metabolites, triglycerides, untargeted metabolomics, xenobiotics",,,False,ManifestColumn,,sage.annotations-experimentalData.metaboliteType-0.0.5,list like error,string,metabolomics
acylcarnitines,acylcarnitine,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/C116917,,string,metabolomics
acylglycerols,"Glycerides, more correctly known as acylglycerols, are esters formed from glycerol and fatty acids that are very hydrophobic. ",,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D005989,,string,metabolomics
amino acids,Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.,,,,,metaboliteType,,http://purl.bioontology.org/ontology/MESH/D000596,,string,metabolomics
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