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sparc-methods.ttl
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@prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
@prefix asp: <http://uri.interlex.org/tgbugs/uris/readable/aspect/> .
@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
@prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
@prefix CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix definition: <http://purl.obolibrary.org/obo/IAO_0000115> .
@prefix editorNote: <http://purl.obolibrary.org/obo/IAO_0000116> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix GO: <http://purl.obolibrary.org/obo/GO_> .
@prefix hasInput: <http://purl.obolibrary.org/obo/RO_0002233> .
@prefix hasOutput: <http://purl.obolibrary.org/obo/RO_0002234> .
@prefix hasPart: <http://purl.obolibrary.org/obo/BFO_0000051> .
@prefix hasParticipant: <http://purl.obolibrary.org/obo/RO_0000057> .
@prefix hasRole: <http://purl.obolibrary.org/obo/RO_0000087> .
@prefix HBP_MEM: <http://www.hbp.FIXME.org/hbp_measurement_methods/> .
@prefix ilxtr: <http://uri.interlex.org/tgbugs/uris/readable/> .
@prefix NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_> .
@prefix NIFRID: <http://uri.neuinfo.org/nif/nifstd/readable/> .
@prefix NLX: <http://uri.neuinfo.org/nif/nifstd/nlx_> .
@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix prot: <http://uri.interlex.org/tgbugs/uris/readable/protocol/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix realizes: <http://purl.obolibrary.org/obo/BFO_0000055> .
@prefix replacedBy: <http://purl.obolibrary.org/obo/IAO_0100001> .
@prefix SAO: <http://uri.neuinfo.org/nif/nifstd/sao> .
@prefix SO: <http://purl.obolibrary.org/obo/SO_> .
@prefix sparc: <http://uri.interlex.org/tgbugs/uris/readable/sparc/> .
@prefix tech: <http://uri.interlex.org/tgbugs/uris/readable/technique/> .
@prefix TEMP: <http://uri.interlex.org/temp/uris/> .
@prefix UBERON: <http://purl.obolibrary.org/obo/UBERON_> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<https://raw.githubusercontent.com/SciCrunch/NIF-Ontology/sparc/ttl/sparc-methods.ttl> a owl:Ontology .
### Object Properties
sparc:acidBaseHemostasis a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty ilxtr:hasResult ;
owl:someValuesFrom [ a owl:Restriction ;
owl:onProperty ilxtr:resultAspect ;
owl:someValuesFrom asp:acidBaseHomeostasis ] ] ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource .
sparc:acquisitionData a owl:ObjectProperty ;
replacedBy: prov:generated ;
rdfs:domain sparc:Acquisition ;
rdfs:range sparc:Resource .
sparc:anatomicalOriginOfSample a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty prov:wasDerivedFrom ;
owl:someValuesFrom UBERON:0001062 ] ;
rdfs:domain sparc:TissueSample ;
rdfs:range sparc:AnatomicalLocation ;
rdfs:comment "in all likelihood what we really want to know here is the intended target of dissection, so we need to look at the chain, wasGeneratedBy -> ilxtr:hadConstrainingAspect or more likely ilxtr:hasPrimaryParticipant because "^^xsd:string .
sparc:bloodGasHemostasis a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty ilxtr:hasResult ;
owl:someValuesFrom [ a owl:Restriction ;
owl:onProperty ilxtr:resultAspect ;
owl:someValuesFrom asp:acidBaseHomeostasis ] ] ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource .
sparc:carriedOutAccordingToProtocol a owl:ObjectProperty ;
replacedBy: ilxtr:isConstrainedBy ;
rdfs:domain sparc:Acquisition,
sparc:Anesthesia,
sparc:Experiment,
sparc:Extraction,
sparc:Modulation,
sparc:Procedure,
sparc:Sedation ;
rdfs:range sparc:Protocol .
sparc:carriedOutBy a owl:ObjectProperty ;
replacedBy: ilxtr:hasExecutor ;
rdfs:domain sparc:Experiment ;
rdfs:range sparc:Researcher .
sparc:concentrationOfChemicalInSolution a owl:ObjectProperty ;
replacedBy: asp:concentration ;
rdfs:domain sparc:ChemicalInSolution ;
rdfs:range sparc:Measurement .
sparc:environmentForTissueDerivatives a owl:ObjectProperty ;
replacedBy: ilxtr:processHasContext,
prov:atLocation ;
rdfs:domain sparc:ExperimentOnTissueDerivatives .
sparc:environmentLogsForLiveOrganism a owl:ObjectProperty ;
replacedBy: prov:generated ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource ;
rdfs:comment "the named individual should also ilxtr:hasPrimaryParticipant NCBITaxon:1 and ilxtr:hasConstrainingAspect asp:aliveness" .
sparc:experimentCarriedOutInEnvironment a owl:ObjectProperty ;
replacedBy: ilxtr:processHasContext,
prov:atLocation ;
rdfs:domain sparc:Experiment ;
rdfs:range sparc:Environment ;
rdfs:comment "prov:atLocation is probably the correct one because processHasContext would be an invariant across all executions of the technique" .
sparc:experimentCarriedOutOn a owl:FunctionalProperty,
owl:ObjectProperty ;
replacedBy: ilxtr:hasPrimaryParticipant ;
rdfs:domain sparc:Experiment ;
rdfs:range sparc:Specimen .
sparc:experimentCarriedOutProcedure a owl:FunctionalProperty,
owl:ObjectProperty ;
replacedBy: hasPart: ;
rdfs:domain sparc:Experiment ;
rdfs:range sparc:Procedure .
sparc:experimentHasEthicalApprovalDocument a owl:ObjectProperty ;
rdfs:domain sparc:Experiment ;
rdfs:range sparc:Resource ;
rdfs:comment "TODO this should probably be hasEthicsApprovalDocument and domain should be ilxtr:protocol not an experiment or technique, because IACUCs and IRBs must review the actual protocol artifact. By associating specific protocol instances with techniques we will then be able to show people which techniques have approved protocols." .
sparc:experimentHasSubjectUnderAnesthesia a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:anaesthesia ] ;
rdfs:domain sparc:AnimalExperiment,
sparc:ClinicalExperiment ;
rdfs:range sparc:Anesthesia ;
rdfs:comment "used on a named individual experiment (composite techniqe) this is just myExperiment: hasPart: tech:anaesthesia" ;
editorNote: "Should be inferred" .
sparc:experimentHasSubjectUnderSedation a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:sedation ] ;
rdfs:subPropertyOf owl:topObjectProperty ;
rdfs:domain sparc:AnimalExperiment,
sparc:ClinicalExperiment ;
rdfs:range sparc:Sedation ;
editorNote: "Should be inferred" .
sparc:extractionGeneratedOutputSpecimen a owl:ObjectProperty ;
replacedBy: ilxtr:hasPrimaryOutput ;
rdfs:domain sparc:Extraction ;
rdfs:range sparc:CellCulture,
sparc:StemCells,
sparc:TissueSample ;
rdfs:comment "could also be replaced by hasOutput, worth considering that this could be modelled with a restriction so that named individuals simply list hasPrimaryOutput mytissuesample, but this seems to be conflating the spec of the expeirment with its execution trace..." .
sparc:fMRIHasStimulusFile a owl:ObjectProperty ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range sparc:Resource .
sparc:generalMRISequenceHasImagedBodyPart a owl:ObjectProperty ;
rdfs:subPropertyOf owl:topObjectProperty ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range sparc:AnatomicalLocation .
sparc:growthTemperature a owl:ObjectProperty ;
replacedBy: asp:temperature,
tech:cellCulture ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range sparc:Measurement .
sparc:hasGeneratedLogFile a owl:ObjectProperty ;
replacedBy: prov:generated ;
rdfs:domain sparc:Acquisition,
sparc:Anesthesia,
sparc:Experiment,
sparc:Extraction,
sparc:Modulation,
sparc:Procedure,
sparc:Sedation ;
rdfs:range sparc:Resource .
sparc:hasMember a owl:ObjectProperty ;
rdfs:domain sparc:Organization ;
rdfs:range sparc:Researcher .
sparc:hemodynamicHemostasis a owl:ObjectProperty ;
replacedBy: ilxtr:hasAspect,
[ a owl:Restriction ;
owl:onProperty ilxtr:hasResult ;
owl:someValuesFrom [ a owl:Restriction ;
owl:onProperty ilxtr:resultAspect ;
owl:someValuesFrom asp:hemodynamicHomeostasis ] ] ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource ;
rdfs:comment "for the data entry side of this, this could simply be obtained by filling in ilxtr:hasAspect without the need to be overly specific, the result would then have ilxtr:resultAspect which would match, otherwise we will wind up with the usual cartesian explosion of terms in our schema" .
sparc:isInputSpecimenForExtraction a owl:FunctionalProperty,
owl:ObjectProperty ;
replacedBy: ilxtr:hasPrimaryInput ;
rdfs:domain sparc:Specimen ;
rdfs:range sparc:Extraction .
sparc:memberOf a owl:ObjectProperty ;
rdfs:domain sparc:Researcher ;
rdfs:range sparc:Organization .
sparc:perfusionProtocol a owl:ObjectProperty ;
replacedBy: tech:perfusion ;
rdfs:domain sparc:TissueSample ;
rdfs:range sparc:Protocol .
sparc:procedureCarriedOutAcquisition a owl:ObjectProperty ;
replacedBy: ilxtr:hasPrimaryAspectMeasured,
[ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:measuring ] ;
rdfs:domain sparc:Procedure ;
rdfs:range sparc:Acquisition ;
rdfs:comment "in the new model this relationship doesn't exist because measurements/acquisitions are simply treated as any other technique, the other possibility here is probably just to use hasPart:" .
sparc:procedureCarriedOutAnalysis a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:analysis ] ;
rdfs:domain sparc:Procedure ;
rdfs:range sparc:Analysis ;
rdfs:comment "this could also be hasPart: -> hasRole: some analysis, analysis is essentially an asserted intention of the activity which can be orthogonal to things like using statistical or computational methods which could be employed for some other end" .
sparc:procedureCarriedOutModulation a owl:ObjectProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:activityModulation ] ;
rdfs:domain sparc:Procedure ;
rdfs:range sparc:Modulation .
sparc:procedureTriggeredCorollaryExperiments a owl:ObjectProperty ;
rdfs:domain sparc:Procedure ;
rdfs:range sparc:Experiment .
sparc:procedureTriggeredExtraction a owl:ObjectProperty ;
rdfs:subPropertyOf owl:topObjectProperty ;
rdfs:domain sparc:Procedure ;
rdfs:range sparc:Extraction .
sparc:protocolDescribedInResource a owl:ObjectProperty ;
rdfs:domain sparc:Protocol ;
rdfs:range sparc:Resource .
sparc:protocolToAssessBlockEfficacy a owl:ObjectProperty ;
rdfs:domain sparc:BioelectronicNerveBlockingModulation ;
rdfs:range sparc:Protocol .
sparc:radiologicalImagingProtocolHasFeatures a owl:ObjectProperty ;
rdfs:domain sparc:RadiologicalImagingProtocol ;
rdfs:range sparc:FunctionalMRIFeatures,
sparc:GeneralMRISequence .
sparc:radiologicalImagingProtocolHasProtocol a owl:ObjectProperty ;
rdfs:subPropertyOf owl:topObjectProperty ;
rdfs:domain sparc:RadiologicalImagingProtocol ;
rdfs:range sparc:Protocol .
sparc:radioloigcalAcquisitionHasImagingProtocol a owl:ObjectProperty ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range sparc:RadiologicalImagingProtocol .
sparc:respiratoryHemostasis a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource .
sparc:solutionBathVolume a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionBuffer a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:ChemicalInSolution .
sparc:solutionChemicalComposition a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:ChemicalInSolution ;
rdfs:comment "the domain here does not seem correct?" ;
editorNote: "redundant?" .
sparc:solutionCO2PartialPressure a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionFlowRate a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionOsmolality a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionOxygenPartialPressure a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionPH a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:solutionTemperature a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentForTissueDerivatives ;
rdfs:domain sparc:ExperimentOnTissueDerivatives ;
rdfs:range sparc:Measurement .
sparc:spatialLocationOfModulator a owl:ObjectProperty ;
rdfs:domain sparc:Modulation ;
rdfs:range sparc:AnatomicalLocation .
sparc:spatialLocationOfSensor a owl:ObjectProperty ;
rdfs:domain sparc:Acquisition ;
rdfs:range sparc:AnatomicalLocation .
sparc:temperatureHemostasis a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource .
sparc:tissuePreparationCarriedOutForMicroscopyAcquisition a owl:ObjectProperty ;
rdfs:domain sparc:TissuePreparationForMicroscopy ;
rdfs:range sparc:MicroscopyAcquisition .
sparc:tissuePreparationHasStep a owl:ObjectProperty ;
rdfs:domain sparc:TissuePreparationForMicroscopy ;
rdfs:range sparc:TissuePreparationSteps .
sparc:tissueSampleForTissuePreparationForMicroscopy a owl:ObjectProperty ;
rdfs:domain sparc:TissueSample ;
rdfs:range sparc:TissuePreparationForMicroscopy .
sparc:volumeHemostasis a owl:ObjectProperty ;
rdfs:subPropertyOf sparc:environmentLogsForLiveOrganism ;
rdfs:domain sparc:ExperimentOnLiveOrganism ;
rdfs:range sparc:Resource .
### Annotation Properties
replacedBy: a owl:AnnotationProperty .
### Data Properties
sparc:administrationDose a owl:DatatypeProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string .
sparc:administrationFrequency a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string .
sparc:administrationRoute a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string .
sparc:administrationStartTime a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:administrationStopTime a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:administrationVehicle a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia,
sparc:Sedation ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:anesthesiaWasSourcedFrom a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Anesthesia ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:animalHasGeneticVariation a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string ;
editorNote: "all example data is on wild type" .
sparc:animalSubjectHasWeight a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalExperiment,
sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:animalSubjectIsOfGenus a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:animalSubjectIsOfSpecies a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:animalSubjectIsOfStrain a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:animalSupplier a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:bioreactor a owl:DatatypeProperty ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:cameraSettings a owl:DatatypeProperty ;
rdfs:domain sparc:MicroscopyAcquisition ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:cameraType a owl:DatatypeProperty ;
rdfs:domain sparc:MicroscopyAcquisition ;
rdfs:range xsd:string .
sparc:cellLine a owl:DatatypeProperty ;
rdfs:domain sparc:CellCulture ;
rdfs:range xsd:string ;
rdfs:comment "RRID:CVCL_" ;
editorNote: "no cell culture data sets" .
sparc:cellSelectionProcessForAcquisition a owl:DatatypeProperty ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:characterisiticsOfACStimulation a owl:DatatypeProperty ;
rdfs:domain sparc:BioelectronicNerveBlockingModulation ;
rdfs:range xsd:string ;
editorNote: "there are references to electrical stimulation but AC vs DC is never explicitly mentioned" .
sparc:characteristicsOfDCStimulation a owl:DatatypeProperty ;
rdfs:domain sparc:BioelectronicNerveBlockingModulation ;
rdfs:range xsd:string ;
editorNote: "there are references to electrical stimulation but AC vs DC is never explicitly mentioned" .
sparc:characteristicsOfEnergyDelivered a owl:DatatypeProperty ;
rdfs:domain sparc:IREnergyModulation,
sparc:ThermalEnergyModulation ;
rdfs:range xsd:string ;
editorNote: "no data sets" .
sparc:characteristicsOfInterfaceToBiologicalTarget a owl:DatatypeProperty ;
rdfs:domain sparc:Modulation ;
rdfs:range xsd:string ;
editorNote: "usage unclear" .
sparc:characteristicsOfOpticalMappingSystem a owl:DatatypeProperty ;
rdfs:domain sparc:OpticalAcquisition ;
rdfs:range xsd:string ;
editorNote: "no data sets" .
sparc:characteristicsOfStimulation a owl:DatatypeProperty ;
rdfs:domain sparc:ElectricalModulation ;
rdfs:range xsd:string .
sparc:charactersiticsOfPreamplifierAndAmplifier a owl:DatatypeProperty ;
rdfs:domain sparc:ChemicalAcquisition,
sparc:ElectricalAcquisition,
sparc:MechanicalAcquisition ;
editorNote: "models are listed but specs are not provided" .
sparc:compositionCellularAndAcellular a owl:DatatypeProperty ;
rdfs:domain sparc:EngineeredTissue ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:conversionAD a owl:DatatypeProperty ;
rdfs:domain sparc:ChemicalAcquisition,
sparc:ElectricalAcquisition,
sparc:MechanicalAcquisition ;
rdfs:range xsd:string ;
editorNote: "usage unclear" .
sparc:criteriaForStimulusEfficacy a owl:DatatypeProperty ;
rdfs:domain sparc:ElectricalModulation ;
rdfs:range xsd:string ;
editorNote: "I think the statistical significance statement is what we are going for here?" .
sparc:descriptionAndCharacteristicsOfSensor a owl:DatatypeProperty ;
rdfs:domain sparc:ChemicalAcquisition,
sparc:ElectricalAcquisition,
sparc:MechanicalAcquisition ;
rdfs:range xsd:string .
sparc:deviceHasMagnetFieldStrength a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:deviceHasManufacturer a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:deviceHasMRReceiveCoilSequence a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:deviceHasReceiveCoilName a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:deviceHasReceiveCoilType a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:deviceHasSoftwareVersion a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:emailAddress a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:Researcher ;
rdfs:range xsd:string ;
editorNote: "trivial, included in structured data that was not annotated, and intentionally excluded for privacy reasons" .
sparc:energyDeliveryDeviceUtilized a owl:DatatypeProperty ;
rdfs:domain sparc:IREnergyModulation,
sparc:ThermalEnergyModulation ;
rdfs:range xsd:string .
sparc:experimentHasOverallDesign a owl:DatatypeProperty ;
rdfs:domain sparc:Experiment ;
rdfs:range xsd:string ;
editorNote: "usage unclear, there are some potential candidates but I'm not sure what level of detail or depth is desired" .
sparc:experimentHasSummary a owl:DatatypeProperty ;
rdfs:domain sparc:Experiment ;
rdfs:range xsd:string .
sparc:experimentHasTitle a owl:DatatypeProperty ;
rdfs:domain sparc:Experiment ;
rdfs:range xsd:string .
sparc:firstName a owl:DatatypeProperty ;
rdfs:domain sparc:Researcher ;
rdfs:range xsd:string .
sparc:growthMedia a owl:DatatypeProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasInput: ;
owl:someValuesFrom ilxtr:cultureMedia ] ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
rdfs:comment "we can't quite model it this way because cell lines can in theory be grown in many different media and it is not a relationship between the line and the media, but rather between the line, the technique, and the media, for a single instance in a data oriented view this would make sense, but we need to enable the cartesian product here" ;
editorNote: "no cell culture data sets" .
sparc:growthStimulation a owl:DatatypeProperty ;
replacedBy: hasInput: ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
rdfs:comment "example?" ;
editorNote: "no cell culture data sets" .
sparc:growthSubstrate a owl:DatatypeProperty ;
replacedBy: hasInput: ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:growthSupplements a owl:DatatypeProperty ;
replacedBy: hasInput: ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
rdfs:comment "note to self: the reason to shift to the technique centric approach is because otherwise we end up having to assert that entities have properties that would seem to be intrinsic whereas they are accidental by virtue of the environment they have been exposed to -- there may be some change that is induced in the cells as a result of those accidents, but those need to be independent from the accidentals" ;
editorNote: "no cell culture data sets" .
sparc:growthTime a owl:DatatypeProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty ilxtr:hasConstrainingAspect ;
owl:someValuesFrom asp:duration ] ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:CellCulture,
sparc:EngineeredTissue,
sparc:StemCells ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:hardwareBasedDataProcessing a owl:DatatypeProperty ;
rdfs:domain sparc:Acquisition ;
rdfs:range xsd:string .
sparc:hasAcquisitionMatrixDimensions a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasBiologicalSex a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:hasBodyMassIndex a owl:DatatypeProperty,
owl:FunctionalProperty ;
replacedBy: asp:BMI,
ilxtr:hasAspect ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range owl:real ;
rdfs:comment "these are results of measurements, if we annotate the data with aspect + value that should be sufficient, we can 'pun' the aspects as edges, or we can generate an edge that is the intersection of the aspect with the implementation used to measure it see comment on ilxtr:hasResult" ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasClinicalInformation a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasDateAndTimeStamp a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:domain sparc:Acquisition,
sparc:Anesthesia,
sparc:Experiment,
sparc:Extraction,
sparc:Measurement,
sparc:Procedure,
sparc:Sedation ;
rdfs:range xsd:string .
sparc:hasDesignType a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasDiseaseInformation a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasDrugInformation a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasEchoTime a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasFamilyHistory a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasFieldOfViewSequence a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasFileName a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:domain sparc:Resource ;
rdfs:range xsd:string ;
editorNote: "in data file registry" .
sparc:hasFlipAngle a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasGender a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasImageOrientationWRTPatient a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasImagePosition a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasInPlanePhaseEncodingDirection a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasInversionTime a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasNumberOfBlocks a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasNumberOfDummyScans a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasNumberOfSlices a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasNumberOfVolumesCollected a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasORCIDId a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:domain sparc:Researcher ;
rdfs:range xsd:string ;
editorNote: "not in data that we have" .
sparc:hasParallelReductionFactorInPlane a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasParallelReductionFactorOutOfPlane a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasPatientOrientation a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasPhenotypicSex a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:hasPixelBandwidth a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasPulseSequenceName a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasRepetitionTime a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasSliceThickness a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfGeneralMRISequence ;
rdfs:domain sparc:GeneralMRISequence ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasSubjectPerformTask a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:hasTotalDuration a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfFunctionalMRI ;
rdfs:domain sparc:FunctionalMRIFeatures ;
rdfs:range xsd:string ;
editorNote: "TODO" .
sparc:howModulatorAffixedToBiologicalTarget a owl:DatatypeProperty ;
rdfs:domain sparc:Modulation ;
rdfs:range xsd:string ;
editorNote: "there are multiple references to modulators and sensors but no explanation of how" .
sparc:howSensorAffixedToBiologicalTarget a owl:DatatypeProperty ;
rdfs:domain sparc:Acquisition,
sparc:ChemicalAcquisition,
sparc:ElectricalAcquisition,
sparc:MechanicalAcquisition ;
rdfs:range xsd:string ;
editorNote: "there are SensorModulators out there ..." .
sparc:husbandryDetails a owl:DatatypeProperty ;
replacedBy: ilxtr:wasParticipantIn ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:imageResolution a owl:DatatypeProperty ;
rdfs:domain sparc:MicroscopyAcquisition ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:indicesForAssessmentOfViability a owl:DatatypeProperty ;
rdfs:domain sparc:TissueSample ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:isDiseaseModelOf a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:isOfAge a owl:DatatypeProperty,
owl:FunctionalProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:AnimalSubject,
sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:isOfDevelopmentalStage a owl:DatatypeProperty,
owl:FunctionalProperty ;
replacedBy: ilxtr:hasDevelopmentalStage ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
rdfs:comment "hasDevelopmentalStage can be used for many many things, and should be modelled as an objectProperty to control the values, data properties on strings invariably lead to unhappyness because they are deadends that allow no additional information to be attached to the term, for example, how the value was determined" ;
editorNote: "have not found data related to human subjects in examples" .
sparc:isOfEthnicity a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:isOfFileType a owl:DatatypeProperty,
owl:FunctionalProperty ;
replacedBy: dc:format ;
rdfs:domain sparc:Resource ;
rdfs:range xsd:string ;
rdfs:comment "the domain here is incorrect, because many, many resources are not file-like the range should be mimetypes, butacross many initiatives there still isn't a good solution for enforcing that via data types" .
sparc:isOfHandedness a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:isOfRace a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfHumanSubject ;
rdfs:domain sparc:HumanSubject ;
rdfs:range xsd:string ;
editorNote: "have not found data related to human subjects in examples" .
sparc:isolationProcedureForOrgan a owl:DatatypeProperty ;
replacedBy: ilxtr:isConstrainedBy,
prov:wasGeneratedBy ;
rdfs:domain sparc:TissueSample ;
rdfs:range xsd:string .
sparc:lastName a owl:DatatypeProperty,
owl:FunctionalProperty ;
replacedBy: foaf:familyName ;
rdfs:domain sparc:Researcher ;
rdfs:range xsd:string ;
rdfs:comment "I highly reccomend not using this at all, and only using orcids since dealing with names is a complete nightmare" .
sparc:methodOfEuthanasia a owl:DatatypeProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty prov:wasGeneratedBy ;
owl:someValuesFrom [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom tech:euthanasia ] ] ;
rdfs:subPropertyOf sparc:propertiesOfAnimalSubject ;
rdfs:domain sparc:AnimalSubject ;
rdfs:range xsd:string .
sparc:microscopeSettings a owl:DatatypeProperty ;
rdfs:domain sparc:MicroscopyAcquisition ;
rdfs:range xsd:string ;
editorNote: "could not find in example protocols and data" .
sparc:nameOfChemicalInSolution a owl:DatatypeProperty ;
replacedBy: [ a owl:Restriction ;
owl:onProperty hasParticipant: ;
owl:someValuesFrom [ a owl:Restriction ;
owl:onProperty hasPart: ;
owl:someValuesFrom CHEBI:24431 ] ] ;
rdfs:domain sparc:ChemicalInSolution ;
rdfs:range xsd:string ;
rdfs:comment "I'm translating this into the underlying model of the solutions that will need to be created. The scheme that we use for describing solutions for the curators/experimentalists will be much simpler." .
sparc:nameOfInstitution a owl:DatatypeProperty ;
rdfs:domain sparc:Organization ;
rdfs:range xsd:string .
sparc:nameOfRadiologicalDevice a owl:DatatypeProperty ;
rdfs:subPropertyOf sparc:propertiesOfRadiologicalAcquisition ;
rdfs:domain sparc:RadiologcalAcquistion ;
rdfs:range xsd:string .
sparc:organismSubjectHasGenotype a owl:DatatypeProperty ;
rdfs:subPropertyOf owl:topDataProperty ;
rdfs:domain sparc:OrganismSubject ;
rdfs:range xsd:string .
sparc:originOfSample a owl:DatatypeProperty ;
rdfs:domain sparc:CellCulture,
sparc:StemCells ;
rdfs:range xsd:string ;
editorNote: "no cell culture data sets" .
sparc:passage a owl:DatatypeProperty ;
rdfs:domain sparc:CellCulture,
sparc:StemCells ;
rdfs:range xsd:string ;
rdfs:comment "I have no idea what this means" ;
editorNote: "no cell culture data sets" .
sparc:propertiesOfAnimalSubject a owl:DatatypeProperty ;
rdfs:domain sparc:AnimalSubject ;
editorNote: "Parent class." .
sparc:propertiesOfFunctionalMRI a owl:DatatypeProperty ;
rdfs:domain sparc:FunctionalMRIFeatures ;
editorNote: "Parent class." .
sparc:propertiesOfGeneralMRISequence a owl:DatatypeProperty ;
rdfs:domain sparc:GeneralMRISequence ;
editorNote: "Parent class." .