# baseURI: https://datamodel.terra.bio/TerraCoreValueSets # imports: http://www.w3.org/2004/02/skos/core# # imports: https://datamodel.terra.bio/imports/CL_subset # imports: https://datamodel.terra.bio/imports/UBERON_subset # prefix: TerraCoreValueSets @prefix : . @prefix TerraCoreValueSets: . @prefix TerraDCAT_ap: . @prefix obo: . @prefix owl: . @prefix rdf: . @prefix rdfs: . @prefix skos: . @prefix xsd: . a owl:Ontology ; owl:imports skos: ; owl:imports ; owl:imports ; owl:versionInfo "Created with TopBraid Composer" ; . TerraCoreValueSets:AmnioticFluid a TerraCoreValueSets:AmnioticFluidType ; rdfs:label "Amniotic fluid" ; . TerraCoreValueSets:AmnioticFluidType a owl:Class ; rdfs:label "Amniotic fluid" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0000173 ; . TerraCoreValueSets:Assembly a TerraCoreValueSets:AssemblyModality ; rdfs:label "Assembly" ; . TerraCoreValueSets:AssemblyModality a owl:Class ; rdfs:label "Assembly" ; rdfs:subClassOf TerraCoreValueSets:GenomicModality ; . TerraCoreValueSets:BCell a TerraCoreValueSets:BCellType ; rdfs:label "B cell" ; . TerraCoreValueSets:BCellType a owl:Class ; rdfs:label "B cell" ; rdfs:subClassOf TerraCoreValueSets:PrimaryCellType ; owl:equivalentClass obo:CL_0000236 ; . TerraCoreValueSets:BioSampleType a owl:Class ; rdfs:label "BioSampleType" ; rdfs:subClassOf TerraCoreValueSets:SampleType ; skos:definition "A classification of samples taken from organisms based on the type of material collected and grouped into primary, cell line and derived type." ; . TerraCoreValueSets:Blood a owl:Class ; rdfs:label "Blood" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0000178 ; . TerraCoreValueSets:BodyFluid a owl:Class ; rdfs:label "Body fluid" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; . TerraCoreValueSets:BreastMilk a TerraCoreValueSets:BreastMilkType ; rdfs:label "Breast milk" ; . TerraCoreValueSets:BreastMilkType a owl:Class ; rdfs:comment "Should this be simply Milk with hasAnatomicalSite of Mammary Glands? See https://biology.stackexchange.com/questions/39291/are-there-any-non-mammalian-species-known-that-lactate and http://purl.obolibrary.org/obo/UBERON_0001913" ; rdfs:label "Breast milk" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass rdfs:Resource ; . TerraCoreValueSets:BuffyCoat a TerraCoreValueSets:BuffyCoatType ; rdfs:label "BuffyCoat" ; . TerraCoreValueSets:BuffyCoatType a owl:Class ; rdfs:label "Buffy coat" ; rdfs:subClassOf TerraCoreValueSets:Blood ; . TerraCoreValueSets:CTScanModality a owl:Class ; rdfs:label "CT scan" ; rdfs:subClassOf TerraCoreValueSets:MedicalImagingModality ; . TerraCoreValueSets:CellFreeDNA a TerraCoreValueSets:CellFreeDNAType ; rdfs:label "Cell free DNA" ; . TerraCoreValueSets:CellFreeDNAType a owl:Class ; rdfs:label "Cell-free DNA" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; . TerraCoreValueSets:CellLine a TerraCoreValueSets:CellLineType ; rdfs:label "Cell line" ; . TerraCoreValueSets:CellLineType a owl:Class ; rdfs:comment "Will likely create instances for specific cell lines, but no concrete use case available yet. Also this should map to \"cell line\" in the Cell Line Ontology. " ; rdfs:label "Cell Line" ; rdfs:subClassOf TerraCoreValueSets:BioSampleType ; . TerraCoreValueSets:CerebrospinalFluid a TerraCoreValueSets:CerebrospinalFluidType ; rdfs:label "Cerebrospinal fluid" ; . TerraCoreValueSets:CerebrospinalFluidType a owl:Class ; rdfs:label "Cerebrospinal fluid" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0001359 ; . TerraCoreValueSets:ChromatinAccessibilityModality a owl:Class ; rdfs:label "DNA Chromatin Accessibility" ; rdfs:subClassOf TerraCoreValueSets:EpigenomicModality ; . TerraCoreValueSets:ContactMaps3D a TerraCoreValueSets:ContactMaps3DModality ; rdfs:label "3D Contact Maps" ; . TerraCoreValueSets:ContactMaps3DModality a owl:Class ; rdfs:label "3D Contact Maps" ; rdfs:subClassOf TerraCoreValueSets:EpigenomicModality ; . TerraCoreValueSets:DNABinding a TerraCoreValueSets:DNABindingModality ; rdfs:label "DNA Binding" ; . TerraCoreValueSets:DNABindingModality a owl:Class ; rdfs:label "DNA Binding" ; rdfs:subClassOf TerraCoreValueSets:EpigenomicModality ; . TerraCoreValueSets:DNAChromatinAccessibility a TerraCoreValueSets:ChromatinAccessibilityModality ; rdfs:label "DNA Chromatin Accessibility" ; . TerraCoreValueSets:DNAMethylation a TerraCoreValueSets:DNAMethylationModality ; rdfs:label "DNA Methylation" ; . TerraCoreValueSets:DNAMethylationModality a owl:Class ; rdfs:label "DNA Methylation" ; rdfs:subClassOf TerraCoreValueSets:EpigenomicModality ; . TerraCoreValueSets:DataModality a owl:Class ; rdfs:comment "This term attempts to characterize entities in terms of its channel of biological investigation. For example, activities that produce such results include assays, analysis pipelines, lab tests, and imaging -- x-ray, CT-scan, or microscopy as well as the data these activities generate." ; rdfs:label "Data Modality" ; rdfs:subClassOf obo:IAO_0000030 ; skos:altLabel "Biological Data Type" ; skos:altLabel "Data Category" ; skos:definition "Data modality describes the biological nature of the information gathered as the result of an Activity, independent of the technology or methods used to produce the information." ; . TerraCoreValueSets:DerivedType a owl:Class ; rdfs:label "DerivedType" ; rdfs:subClassOf TerraCoreValueSets:BioSampleType ; . TerraCoreValueSets:Electrocardiogram a TerraCoreValueSets:ElectrocardiogramModality ; rdfs:label "Electrocardiogram" ; skos:altLabel "ECG" ; skos:altLabel "EKG" ; . TerraCoreValueSets:ElectrocardiogramModality a owl:Class ; rdfs:comment "Is this an Imaging technology or should we have a category for lab tests and consider this a Lab Test or is it a type of assay?" ; rdfs:label "Electrocardiogram" ; rdfs:subClassOf TerraCoreValueSets:MedicalImagingModality ; . TerraCoreValueSets:Electrophysiology a TerraCoreValueSets:ElectrophysiologyModality ; rdfs:label "Electrophysiology" ; . TerraCoreValueSets:ElectrophysiologyModality a owl:Class ; rdfs:label "Electrophysiology" ; rdfs:subClassOf TerraCoreValueSets:ImagingModality ; . TerraCoreValueSets:Epigenomic a TerraCoreValueSets:EpigenomicModality ; rdfs:label "Epigenomic" ; . TerraCoreValueSets:EpigenomicModality a owl:Class ; rdfs:label "Epigenomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the epigenome." ; . TerraCoreValueSets:Erythrocyte a TerraCoreValueSets:ErythrocyteType ; rdfs:label "Erythrocyte" ; . TerraCoreValueSets:ErythrocyteType a owl:Class ; rdfs:label "Erythrocyte" ; rdfs:subClassOf TerraCoreValueSets:Blood ; skos:altLabel "RBC" ; skos:altLabel "Red blood cell" ; . TerraCoreValueSets:Exome a TerraCoreValueSets:ExomeModality ; rdfs:label "Exome" ; skos:altLabel "WES" ; . TerraCoreValueSets:ExomeModality a owl:Class ; rdfs:label "Exome" ; rdfs:subClassOf TerraCoreValueSets:GenomicModality ; skos:altLabel "WES" ; . TerraCoreValueSets:Genomic a TerraCoreValueSets:GenomicModality ; rdfs:label "Genomic" ; . TerraCoreValueSets:GenomicModality a owl:Class ; rdfs:label "Genomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the genome." ; . TerraCoreValueSets:Genotyping a TerraCoreValueSets:GenotypingModality ; rdfs:label "Genotyping" ; . TerraCoreValueSets:GenotypingModality a owl:Class ; rdfs:comment "Definition from Genotyping (operation_3196) in edamontology.org. Need to add this as an equivalent class. Note that this is often performed by calling SNPs from assays. It it intended to differentiate from larger scale genomic sequencing -- exome, genome." ; rdfs:label "Genotyping" ; rdfs:subClassOf TerraCoreValueSets:GenomicModality ; skos:definition "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." ; . TerraCoreValueSets:HistoneModificationLocation a TerraCoreValueSets:HistoneModificationLocationModality ; rdfs:label "Histone Modification Location" ; . TerraCoreValueSets:HistoneModificationLocationModality a owl:Class ; rdfs:label "Histone Modification Location" ; rdfs:subClassOf TerraCoreValueSets:DNABindingModality ; . TerraCoreValueSets:Imaging a TerraCoreValueSets:ImagingModality ; rdfs:label "Imaging" ; . TerraCoreValueSets:ImagingModality a owl:Class ; rdfs:label "Imaging" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; . TerraCoreValueSets:InducedPluripotentStemCellType a owl:Class ; rdfs:label "Induced pluripotent stem cells" ; rdfs:subClassOf TerraCoreValueSets:DerivedType ; . TerraCoreValueSets:InvitroDifferentiatedCellType a owl:Class ; rdfs:label "In vitro differentiated cells" ; rdfs:subClassOf TerraCoreValueSets:DerivedType ; . TerraCoreValueSets:Leukocyte a TerraCoreValueSets:LeukocyteType ; rdfs:label "Leukocyte" ; . TerraCoreValueSets:LeukocyteType a owl:Class ; rdfs:label "Leukocyte" ; rdfs:subClassOf TerraCoreValueSets:Blood ; skos:altLabel "White blood cell" ; . TerraCoreValueSets:Lymphocyte a TerraCoreValueSets:LymphocyteType ; rdfs:label "Lymphocyte" ; . TerraCoreValueSets:LymphocyteType a owl:Class ; rdfs:label "Lymphocyte" ; rdfs:subClassOf TerraCoreValueSets:PrimaryCellType ; owl:equivalentClass obo:CL_0000542 ; . TerraCoreValueSets:MRI a TerraCoreValueSets:MRIModality ; rdfs:label "MRI" ; skos:altLabel "Magnetic resonance imaging" ; . TerraCoreValueSets:MRIModality a owl:Class ; rdfs:label "MRI" ; rdfs:subClassOf TerraCoreValueSets:MedicalImagingModality ; . TerraCoreValueSets:MedicalImaging a TerraCoreValueSets:MedicalImagingModality ; rdfs:label "Medical Imaging" ; . TerraCoreValueSets:MedicalImagingModality a owl:Class ; rdfs:label "Medical Imaging" ; rdfs:subClassOf TerraCoreValueSets:ImagingModality ; . TerraCoreValueSets:Metabolomic a owl:Class ; rdfs:label "Metabolomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the metabolome." ; . TerraCoreValueSets:MetagenomicModality a owl:Class ; rdfs:label "Metagenomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; . TerraCoreValueSets:MicroRNACounts a TerraCoreValueSets:TranscriptomicTargetedModality ; rdfs:label "microRNA Counts" ; skos:altLabel "miRNA counts" ; . TerraCoreValueSets:Microbiome a owl:Class ; rdfs:label "Microbiome" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the microbiome." ; . TerraCoreValueSets:Microscopy a TerraCoreValueSets:MicroscopyModality ; rdfs:label "Microscopy" ; . TerraCoreValueSets:MicroscopyModality a owl:Class ; rdfs:label "Microscopy" ; rdfs:subClassOf TerraCoreValueSets:ImagingModality ; . TerraCoreValueSets:MolecularSample a TerraCoreValueSets:MolecularSampleType ; rdfs:label "MolecularSample" ; . TerraCoreValueSets:MolecularSampleType a owl:Class ; rdfs:label "MolecularSampleType" ; rdfs:subClassOf TerraCoreValueSets:SampleType ; skos:definition "A classification of molecular sample types." ; . TerraCoreValueSets:Monocyte a TerraCoreValueSets:MonocyteType ; rdfs:label "Monocyte" ; . TerraCoreValueSets:MonocyteType a owl:Class ; rdfs:label "Monocyte" ; rdfs:subClassOf TerraCoreValueSets:PrimaryCellType ; owl:equivalentClass obo:CL_0000576 ; . TerraCoreValueSets:OrganoidType a owl:Class ; rdfs:label "Organoid" ; rdfs:subClassOf TerraCoreValueSets:DerivedType ; . TerraCoreValueSets:PeripheralBloodMononuclearCell a TerraCoreValueSets:PeripheralBloodMononuclearCellType ; rdfs:label "PeripheralBloodMononuclearCell" ; . TerraCoreValueSets:PeripheralBloodMononuclearCellType a owl:Class ; rdfs:label "Peripheral blood mononuclear cell" ; rdfs:subClassOf TerraCoreValueSets:Blood ; skos:altLabel "PBMC" ; . TerraCoreValueSets:Plasma a TerraCoreValueSets:PlasmaType ; rdfs:label "Plasma" ; . TerraCoreValueSets:PlasmaType a owl:Class ; rdfs:label "Plasma" ; rdfs:subClassOf TerraCoreValueSets:Blood ; owl:equivalentClass obo:UBERON_0001969 ; . TerraCoreValueSets:Platelet a TerraCoreValueSets:PlateletType ; rdfs:label "Platelet" ; . TerraCoreValueSets:PlateletType a owl:Class ; rdfs:label "Platelet" ; rdfs:subClassOf TerraCoreValueSets:Blood ; owl:equivalentClass obo:CL_0000233 ; . TerraCoreValueSets:PrimaryCell a TerraCoreValueSets:PrimaryCellType ; rdfs:label "Primary cell" ; . TerraCoreValueSets:PrimaryCellType a owl:Class ; rdfs:label "PrimaryCell" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; . TerraCoreValueSets:PrimaryCulture a TerraCoreValueSets:PrimaryCultureType ; rdfs:label "Primary culture" ; . TerraCoreValueSets:PrimaryCultureType a owl:Class ; rdfs:label "Primary culture" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; owl:equivalentClass obo:CL_0000001 ; . TerraCoreValueSets:PrimaryType a owl:Class ; rdfs:label "PrimaryType" ; rdfs:subClassOf TerraCoreValueSets:BioSampleType ; . TerraCoreValueSets:Proteomic a owl:Class ; rdfs:label "Proteomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the proteome." ; . TerraCoreValueSets:RNABinding a TerraCoreValueSets:RNABindingModality ; rdfs:label "RNA Binding" ; . TerraCoreValueSets:RNABindingModality a owl:Class ; rdfs:label "RNA Binding" ; rdfs:subClassOf TerraCoreValueSets:EpigenomicModality ; . TerraCoreValueSets:RnaSeq a TerraCoreValueSets:TranscriptomicNonTargeted ; rdfs:label "RNASeq" ; . TerraCoreValueSets:Saliva a TerraCoreValueSets:SalivaType ; rdfs:label "Saliva" ; . TerraCoreValueSets:SalivaType a owl:Class ; rdfs:label "Saliva" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0001836 ; . TerraCoreValueSets:SampleType a owl:Class ; rdfs:label "SampleType" ; rdfs:subClassOf obo:IAO_0000030 ; skos:definition "A classification of samples based on the type of material collected and grouped by subclass." ; . TerraCoreValueSets:Semen a TerraCoreValueSets:SemenType ; rdfs:label "Semen" ; . TerraCoreValueSets:SemenType a owl:Class ; rdfs:label "Semen" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0001968 ; . TerraCoreValueSets:Serum a TerraCoreValueSets:SerumType ; rdfs:label "Serum" ; . TerraCoreValueSets:SerumType a owl:Class ; rdfs:label "Serum" ; rdfs:subClassOf TerraCoreValueSets:Blood ; owl:equivalentClass obo:UBERON_0001977 ; . TerraCoreValueSets:SpatialTranscriptomicModality a owl:Class ; rdfs:label "Spatial Transcriptomics" ; rdfs:subClassOf TerraCoreValueSets:Transcriptomic ; . TerraCoreValueSets:Stool a TerraCoreValueSets:StoolType ; rdfs:label "Stool" ; . TerraCoreValueSets:StoolType a owl:Class ; rdfs:label "Stool" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; owl:equivalentClass obo:UBERON_0001988 ; . TerraCoreValueSets:SynovialFluid a TerraCoreValueSets:SynovialFluidType ; rdfs:label "Synovial fluid" ; . TerraCoreValueSets:SynovialFluidType a owl:Class ; rdfs:label "Synovial fluid" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0001090 ; . TerraCoreValueSets:TCell a TerraCoreValueSets:TCellType ; rdfs:label "T cell" ; . TerraCoreValueSets:TCellType a owl:Class ; rdfs:label "T cell" ; rdfs:subClassOf TerraCoreValueSets:PrimaryCellType ; owl:equivalentClass obo:CL_0000084 ; . TerraCoreValueSets:Tissue a TerraCoreValueSets:TissueType ; rdfs:label "Tissue" ; . TerraCoreValueSets:TissueType a owl:Class ; rdfs:label "Tissue" ; rdfs:subClassOf TerraCoreValueSets:PrimaryType ; . TerraCoreValueSets:TranscriptionFactorLocation a TerraCoreValueSets:TranscriptionFactorLocationModality ; rdfs:label "Transcription Factor Location" ; . TerraCoreValueSets:TranscriptionFactorLocationModality a owl:Class ; rdfs:label "Transcription Factor Location" ; rdfs:subClassOf TerraCoreValueSets:DNABindingModality ; . TerraCoreValueSets:Transcriptomic a owl:Class ; rdfs:label "Transcriptomic" ; rdfs:subClassOf TerraCoreValueSets:DataModality ; skos:definition "A property that indicates this entity is related to the biological investigation of the transcriptome." ; . TerraCoreValueSets:TranscriptomicNonTargeted a owl:Class ; rdfs:label "Transcriptomic NonTargeted" ; rdfs:subClassOf TerraCoreValueSets:Transcriptomic ; skos:altLabel "Transcriptomic NonTargeted" ; . TerraCoreValueSets:TranscriptomicTargetedModality a owl:Class ; rdfs:label "Transcriptomic Targeted" ; rdfs:subClassOf TerraCoreValueSets:Transcriptomic ; . TerraCoreValueSets:Urine a TerraCoreValueSets:UrineType ; rdfs:label "Urine" ; . TerraCoreValueSets:UrineType a owl:Class ; rdfs:label "Urine" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0001088 ; . TerraCoreValueSets:VaginalFluid a TerraCoreValueSets:VaginalFluidType ; rdfs:label "Vaginal fluid" ; . TerraCoreValueSets:VaginalFluidType a owl:Class ; rdfs:label "Vaginal fluid" ; rdfs:subClassOf TerraCoreValueSets:BodyFluid ; owl:equivalentClass obo:UBERON_0036243 ; skos:altLabel "Vaginal swab" ; . TerraCoreValueSets:WholeBlood a TerraCoreValueSets:WholeBloodType ; rdfs:label "Whole blood" ; . TerraCoreValueSets:WholeBloodType a owl:Class ; rdfs:label "Whole blood" ; rdfs:subClassOf TerraCoreValueSets:Blood ; owl:equivalentClass obo:UBERON_0000178 ; . TerraCoreValueSets:WholeGenome a TerraCoreValueSets:WholeGenomeModality ; rdfs:label "Whole Genome" ; skos:altLabel "WGS" ; . TerraCoreValueSets:WholeGenomeModality a owl:Class ; rdfs:label "Whole genome" ; rdfs:subClassOf TerraCoreValueSets:GenomicModality ; skos:altLabel "WGS" ; . TerraCoreValueSets:XRay a TerraCoreValueSets:XRayModality ; rdfs:label "XRay" ; . TerraCoreValueSets:XRayModality a owl:Class ; rdfs:label "X ray" ; rdfs:subClassOf TerraCoreValueSets:MedicalImagingModality ; skos:altLabel "X-ray" ; .