From 26c60d4dff1509bd96b574363e636d43b1f3bad6 Mon Sep 17 00:00:00 2001 From: Samantha Piekos Date: Wed, 17 Jul 2024 00:39:12 -0700 Subject: [PATCH] update tmcf files --- .../biomedical/PharmGKB/tMCFs/chemicals.tmcf | 30 +++++++----- scripts/biomedical/PharmGKB/tMCFs/drugs.tmcf | 47 ++++++++++--------- scripts/biomedical/PharmGKB/tMCFs/genes.tmcf | 22 +++++---- .../biomedical/PharmGKB/tMCFs/phenotypes.tmcf | 10 +++- .../tMCFs/phenotypes_mesh_qualifier.tmcf | 13 +++++ ...pes_mesh_supplementary_concept_record.tmcf | 13 +++++ .../biomedical/PharmGKB/tMCFs/variants.tmcf | 19 ++++++-- 7 files changed, 104 insertions(+), 50 deletions(-) create mode 100644 scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_qualifier.tmcf create mode 100644 scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_supplementary_concept_record.tmcf diff --git a/scripts/biomedical/PharmGKB/tMCFs/chemicals.tmcf b/scripts/biomedical/PharmGKB/tMCFs/chemicals.tmcf index 6d80c43926..7efad45c51 100644 --- a/scripts/biomedical/PharmGKB/tMCFs/chemicals.tmcf +++ b/scripts/biomedical/PharmGKB/tMCFs/chemicals.tmcf @@ -1,13 +1,17 @@ Node: E:chemicals->E1 typeOf: dcs:AnatomicalTherapeuticChemicalCode -dcid: C:chemicals->ATC +dcid: C:chemicals->atcCodes Node: E:chemicals->E2 typeOf: dcs:MeSHConcept -dcid: C:chemicals->MeSH +dcid: C:chemicals->dcid_MeSHConcept Node: E:chemicals->E3 -typeOf: schema:Drug +typeOf: dcs:MeSHDescriptor +dcid: C:chemicals->dcid_MeSHDescriptor + +Node: E:chemicals->E4 +typeOf: dcs:ChemicalCompound dcid: C:chemicals->dcid name: C:chemicals->Name atcCode: E:chemicals->E1 @@ -15,27 +19,27 @@ bindingDBID: C:chemicals->BindingDB chebiID: C:chemicals->ChEBI chemblID: C:chemicals->ChEMBL chemicalAbstractServiceID: C:chemicals->CAS -clinicalAnnotationCount: C:chemicals->Clinical Annotation Count +clinicalAnnotationCount: C:chemicals->clinicalAnnotationCount drugBankID: C:chemicals->DrugBank -drugBankMetaboliteID: C:chemicals->DrugBank Metabolite +drugBankMetaboliteID: C:chemicals->drugBankMetabolite drugBrandMixture: C:chemicals->brandMixture drugGenericName: C:chemicals->genericName drugTradeName: C:chemicals->tradeName drugType: C:chemicals->Type -geneticVariantAnnotationCount: C:chemicals->Variant Annotation Count +geneticVariantAnnotationCount: C:chemicals->variantAnnotationCount humanMetabolomeDatabaseID: C:chemicals->HMDB inChIKey: C:chemicals->InChI medicalSubjectHeadingID: E:chemicals->E2 +medicalSubjectHeadingID: E:chemicals->E3 medicalDictionaryForRegulatoryActivitiesId: C:chemicals->MedDRA -metabolicPathwayCount: C:chemicals->Pathway Count +metabolicPathwayCount: C:chemicals->pathwayCount nationalClinicalTrialNumber: C:chemicals->ClinicalTrials.gov nationalDrugFileReferenceTerminologyCode: C:chemicals->NDF-RT pharmGKBID: C:chemicals->pharmGKBID -pubChemCompoundID: C:chemicals->PubChem Compound -pubChemCompoundID: C:chemicals->PubChem Compound Identifiers -pubChemSubstanceID: C:chemicals->PubChem Substance -rxConceptUniqueId: C:chemicals->RxNorm Identifiers +pubChemCompoundID: C:chemicals->pubChemCID +pubChemSubstanceID: C:chemicals->pubChemSubstance +rxConceptUniqueId: C:chemicals->rxNormID simplifiedMolecularInputLineEntrySystem: C:chemicals->SMILES -topClinicalAnnotationLevel: C:chemicals->Top Clinical Annotation Level +topClinicalAnnotationLevel: C:chemicals->topClinicalAnnotationLevel url: C:chemicals->URL -veryImportantPharmacogeneCount: C:chemicals->VIP Count +veryImportantPharmacogeneCount: C:chemicals->vipCount diff --git a/scripts/biomedical/PharmGKB/tMCFs/drugs.tmcf b/scripts/biomedical/PharmGKB/tMCFs/drugs.tmcf index 2374d58015..449b6b2439 100644 --- a/scripts/biomedical/PharmGKB/tMCFs/drugs.tmcf +++ b/scripts/biomedical/PharmGKB/tMCFs/drugs.tmcf @@ -1,12 +1,16 @@ Node: E:drugs->E1 typeOf: dcs:AnatomicalTherapeuticChemicalCode -dcid: C:drugs->ATC +dcid: C:drugs->atcCodes Node: E:drugs->E2 typeOf: dcs:MeSHConcept -dcid: C:drugs->MeSH +dcid: C:drugs->dcid_MeSHConcept Node: E:drugs->E3 +typeOf: dcs:MeSHDescriptor +dcid: C:drugs->dcid_MeSHDescriptor + +Node: E:drugs->E4 typeOf: schema:Drug dcid: C:drugs->dcid name: C:drugs->Name @@ -17,41 +21,40 @@ chebiID: C:drugs->ChEBI chemblID: C:drugs->ChEMBL chemicalAbstractServiceID: C:drugs->CAS chemSpiderID: C:drugs->ChemSpider -clinicalAnnotationCount: C:drugs->Clinical Annotation Count -dailyMedSetId: C:drugs->FDA Drug Label at DailyMed -dosageGuideline: C:drugs->Dosing Guideline +clinicalAnnotationCount: C:drugs->clinicalAnnotationCount +dailyMedSetId: C:drugs->dailyMedFdaDrugLabel +dosageGuideline: C:drugs->dosingGuideline dosageGuidelineSource: C:drugs->dosingGuidelineSource drugBankID: C:drugs->DrugBank drugBrandMixture: C:drugs->brandMixture drugGenericName: C:drugs->genericName -drugHasPrescribingInfo: C:drugs->FDA Label has Prescribing Info +drugHasPrescribingInfo: C:drugs->hasFdaPrescribingInfo drugHasRxAnnotation: C:drugs->Has Rx Annotation -drugLabelHasDosingInformation: C:drugs->Label Has Dosing Info +drugLabelHasDosingInformation: C:drugs->hasDosingInfo drugTradeName: C:drugs->tradeName drugType: C:drugs->Type -fdaTopPharmacogeneticLevel: C:drugs->Top FDA Label Testing Level -geneticVariantAnnotationCount: C:drugs->Variant Annotation Count +fdaTopPharmacogeneticLevel: C:drugs->topFdaTestingLevel +geneticVariantAnnotationCount: C:drugs->variantAnnotationCount humanMetabolomeDatabaseID: C:drugs->HMDB inChIKey: C:drugs->InChI -iupharLigandID: C:drugs->IUPHAR Ligand -keggCompoundID: C:drugs->KEGG Compound -keggDrugID: C:drugs->KEGG Drug +iupharLigandID: C:drugs->iupharLigand +keggCompoundID: C:drugs->keggCompound +keggDrugID: C:drugs->keggDrug medicalSubjectHeadingID: E:drugs->E2 +medicalSubjectHeadingID: E:drugs->E3 medicalDictionaryForRegulatoryActivitiesId: C:drugs->MedDRA -metabolicPathwayCount: C:drugs->Pathway Count +metabolicPathwayCount: C:drugs->pathwayCount nationalClinicalTrialNumber: C:drugs->ClinicalTrials.gov nationalDrugFileReferenceTerminologyCode: C:drugs->NDF-RT pharmacogeneticAssociation: C:drugs->FDA_PGx_Association pharmGKBID: C:drugs->pharmGKBID -pkgbTags: C:drugs->PharmGKB Tags -pubChemCompoundID: C:drugs->PubChem Compound -pubChemCompoundID: C:drugs->PubChem Compound Identifiers -pubChemSubstanceID: C:drugs->PubChem Substance -rxConceptUniqueId: C:drugs->RxNorm Identifiers +pubChemCompoundID: C:drugs->pubChemCID +pubChemSubstanceID: C:drugs->pubChemSubstance +rxConceptUniqueId: C:drugs->rxNormID rxConceptUniqueId: C:drugs->RxNorm simplifiedMolecularInputLineEntrySystem: C:drugs->SMILES -topClinicalAnnotationLevel: C:drugs->Top Clinical Annotation Level -topCpicLevel: C:drugs->Top CPIC Pairs Level -topPharmacogeneticLevel: C:drugs->Top Any Drug Label Testing Level +topClinicalAnnotationLevel: C:drugs->topClinicalAnnotationLevel +topCpicLevel: C:drugs->topCpicPairsLevel +topPharmacogeneticLevel: C:drugs->topAnyDrugLabelTestingLevel url: C:drugs->URL -veryImportantPharmacogeneCount: C:drugs->VIP Count +veryImportantPharmacogeneCount: C:drugs->vipCount diff --git a/scripts/biomedical/PharmGKB/tMCFs/genes.tmcf b/scripts/biomedical/PharmGKB/tMCFs/genes.tmcf index 1135cdfe62..1e67a2153d 100644 --- a/scripts/biomedical/PharmGKB/tMCFs/genes.tmcf +++ b/scripts/biomedical/PharmGKB/tMCFs/genes.tmcf @@ -3,8 +3,8 @@ typeOf: dcs:GenomicCoordinates dcid: C:genes->genomeCoordDcid38 name: C:genes->genomeCoordName38 chrom: C:genes->Chromosome -chromStart: C:genes->Chromosomal Start - GRCh38 -chromEnd: C:genes->Chromosomal Stop - GRCh38 +chromStart: C:genes->grCh38Start +chromEnd: C:genes->grCh38Stop inGenomeAssembly: C:genes->GenomeAssembly38 Node: E:genes->E2 @@ -12,27 +12,29 @@ typeOf: dcs:GenomicCoordinates dcid: C:genes->genomeCoordDcid37 name: C:genes->genomeCoordName37 chrom: C:genes->Chromosome -chromStart: C:genes->Chromosomal Start - GRCh37 -chromEnd: C:genes->Chromosomal Stop - GRCh37 +chromStart: C:genes->grCh37Start +chromEnd: C:genes->grCh37Stop inGenomeAssembly: C:genes->GenomeAssembly37 Node: E:genes->E3 typeOf: dcs:Gene dcid: C:genes->dcid name: C:genes->Name -alternateGeneSymbol: C:genes->Alternate Symbols -comparativeToxicogenomicsDBID: C:genes->Comparative Toxicogenomics Database +alternateGeneSymbol: C:genes->alternateSymbols +comparativeToxicogenomicsDBID: C:genes->comparativeToxicogenomicsDatabase ensemblID: C:genes->ensemblID ensemblID: C:genes->Ensembl genAtlasID: C:genes->GenAtlas geneCardID: C:genes->GeneCard geneSymbol: C:genes->Symbol -hasCpicDosingGuideline: C:genes->Has CPIC Dosing Guideline -hasGeneticVariantAnnotation: C:genes->Has Variant Annotation +hasCpicDosingGuideline: C:genes->hasCpicDosingGuideline +hasGeneticVariantAnnotation: C:genes->hasVariantAnnotation +hasGenomicCoordinates: E:genes->E1 +hasGenomicCoordinates: E:genes->E2 hgncID: C:genes->hgncID hgncID: C:genes->HGNC -isVeryImportantPharmacogene: C:genes->Is VIP -ncbiGeneID: C:genes->NCBI Gene +isVeryImportantPharmacogene: C:genes->isVIP +ncbiGeneID: C:genes->ncbiGene ncbiGeneID: C:genes->ncbiGeneID pharmGKBID: C:genes->pharmGKBID synonym: C:genes->synonyms diff --git a/scripts/biomedical/PharmGKB/tMCFs/phenotypes.tmcf b/scripts/biomedical/PharmGKB/tMCFs/phenotypes.tmcf index e7a86c252f..d6cfc9b221 100644 --- a/scripts/biomedical/PharmGKB/tMCFs/phenotypes.tmcf +++ b/scripts/biomedical/PharmGKB/tMCFs/phenotypes.tmcf @@ -1,7 +1,13 @@ Node: E:phenotypes->E1 typeOf: dcs:MeSHDescriptor -dcid: C:phenotypes->MeSHDcid -nationalDrugFileReferenceTerminologyCode: C:phenotypes->NDFRT +dcid: C:phenotypes->dcid_mesh +name: C:phenotypes->Name +medicalDictionaryForRegulatoryActivitiesId: C:phenotypes->MedDRA medicalSubjectHeadingID: C:phenotypes->MeSH +mondoID: C:phenotypes->MONDO +nationalDrugFileReferenceTerminologyCode: C:phenotypes->NDFRT +pharmGKBID: C:phenotypes->pharmGKBID snomedCT: C:phenotypes->SnoMedCT +synonym: C:phenotypes->synonyms umlsConceptUniqueID: C:phenotypes->UMLS +url: C:phenotypes->URL diff --git a/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_qualifier.tmcf b/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_qualifier.tmcf new file mode 100644 index 0000000000..906da1fecf --- /dev/null +++ b/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_qualifier.tmcf @@ -0,0 +1,13 @@ +Node: E:phenotypes_mesh_qualifier->E1 +typeOf: dcs:MeSHDescriptor +dcid: C:phenotypes_mesh_qualifier->dcid_mesh +name: C:phenotypes_mesh_qualifier->Name +medicalDictionaryForRegulatoryActivitiesId: C:phenotypes_mesh_qualifier->MedDRA +medicalSubjectHeadingID: C:phenotypes_mesh_qualifier->MeSH +mondoID: C:phenotypes_mesh_qualifier->MONDO +nationalDrugFileReferenceTerminologyCode: C:phenotypes_mesh_qualifier->NDFRT +pharmGKBID: C:phenotypes_mesh_qualifier->pharmGKBID +snomedCT: C:phenotypes_mesh_qualifier->SnoMedCT +synonym: C:phenotypes_mesh_qualifier->synonyms +umlsConceptUniqueID: C:phenotypes_mesh_qualifier->UMLS +url: C:phenotypes_mesh_qualifier->URL diff --git a/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_supplementary_concept_record.tmcf b/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_supplementary_concept_record.tmcf new file mode 100644 index 0000000000..54adb050db --- /dev/null +++ b/scripts/biomedical/PharmGKB/tMCFs/phenotypes_mesh_supplementary_concept_record.tmcf @@ -0,0 +1,13 @@ +Node: E:phenotypes_mesh_supplementary_concept_record->E1 +typeOf: dcs:MeSHDescriptor +dcid: C:phenotypes_mesh_supplementary_concept_record->dcid_mesh +name: C:phenotypes_mesh_supplementary_concept_record->Name +medicalDictionaryForRegulatoryActivitiesId: C:phenotypes_mesh_supplementary_concept_record->MedDRA +medicalSubjectHeadingID: C:phenotypes_mesh_supplementary_concept_record->MeSH +mondoID: C:phenotypes_mesh_supplementary_concept_record->MONDO +nationalDrugFileReferenceTerminologyCode: C:phenotypes_mesh_supplementary_concept_record->NDFRT +pharmGKBID: C:phenotypes_mesh_supplementary_concept_record->pharmGKBID +snomedCT: C:phenotypes_mesh_supplementary_concept_record->SnoMedCT +synonym: C:phenotypes_mesh_supplementary_concept_record->synonyms +umlsConceptUniqueID: C:phenotypes_mesh_supplementary_concept_record->UMLS +url: C:phenotypes_mesh_supplementary_concept_record->URL diff --git a/scripts/biomedical/PharmGKB/tMCFs/variants.tmcf b/scripts/biomedical/PharmGKB/tMCFs/variants.tmcf index aeff129a57..e6c3b0c798 100644 --- a/scripts/biomedical/PharmGKB/tMCFs/variants.tmcf +++ b/scripts/biomedical/PharmGKB/tMCFs/variants.tmcf @@ -1,6 +1,19 @@ Node: E:variants->E1 +typeOf: dcs:Gene +dcid: C:variants->dcid_gene +name: C:variants->geneSymbols +pharmGKBID: C:variants->geneID + +Node: E:variants->E2 typeOf: dcs:GeneticVariant dcid: C:variants->dcid -name: C:variants->Variant Name -pharmGKBID: C:variants->Variant ID -rsID: C:variants->Variant ID +name: C:variants->rsID +clinicalAnnotationCount: C:variants->clinicalAnnotationCount +clinicalAnnotationCountLevel1_2: C:variants->clinicalAnnotationCountLevel1_2 +clinicalGuidelineAnnotationCount: C:variants->guidelineAnnotationCount +drugLabelAnnotationCount: C:variants->labelAnnotationCount +geneSymbol: E:variants->E1 +geneticVariantAnnotationCount: C:variants->variantAnnotationCount +pharmGKBID: C:variants->pharmGKBID +rsID: C:variants->rsID +synonym: C:variants->Synonyms