@prefix : . @prefix cl: . @prefix go: . @prefix qb: . @prefix ro: . @prefix bfo: . @prefix dct: . @prefix iao: . @prefix obi: . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix af-c: . @prefix af-e: . @prefix af-m: . @prefix af-p: . @prefix af-q: . @prefix af-r: . @prefix af-x: . @prefix foaf: . @prefix rdfs: . @prefix skos: . @prefix af-rl: . @prefix af-cur: . @base . rdf:type owl:Ontology ; owl:versionIRI ; owl:imports , ; dct:contributor ; dct:issued "2025-12-16T12:00:00Z"^^xsd:dateTime ; dct:license ; dct:modified "2025-06-25T12:00:00Z"^^xsd:dateTime ; dct:publisher ; dct:rights , ; dct:rightsHolder ; dct:title "AFO Quantitative Polymerase Chain Reaction (qPCR) Domain Ontology (REC/2025/12)" ; owl:priorVersion ; owl:versionInfo "REC/2025/12" . ################################################################# # Classes ################################################################# ### http://purl.allotrope.org/ontologies/process#AFP_0003775 af-p:AFP_0003775 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "standard curve" , "standard curve experiment" ; skos:definition "A standard curve qPCR experiment is an experiment using qPCR that measures prepared samples and standards to determine absolute DNA target quantity in samples. [Allotrope]" ; skos:prefLabel "standard curve qPCR experiment" . ### http://purl.allotrope.org/ontologies/process#AFP_0003776 af-p:AFP_0003776 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "relative standard curve" , "relative standard curve experiment" ; skos:definition "A relative standard curve qPCR experiment is an experiment using qPCR that measures relative quantity by comparison of diluted samples and known target DNA. [Allotrope]" ; skos:prefLabel "relative standard curve qPCR experiment" . ### http://purl.allotrope.org/ontologies/process#AFP_0003777 af-p:AFP_0003777 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "comparative CT experiment" , "comparative cycle threshold qPCR experiment" , "∆∆CT" ; skos:definition "A comparative CT experiment is an experiment using qPCR that determines relative target quantity in samples. Samples are compared to a normalized target quantity to determine relative quantity of the sample. [Allotrope]" ; skos:prefLabel "comparative CT qPCR experiment" ; skos:scopeNote "comparative CT" . ### http://purl.allotrope.org/ontologies/process#AFP_0003778 af-p:AFP_0003778 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "melt curve" , "melt curve experiment" ; skos:definition "A melt curve qPCR experiment is an experiment using qPCR that identifies non-specific PCR amplification by evaluating the melting temperature of the DNA target. [Allotrope]" ; skos:prefLabel "melt curve qPCR experiment" . ### http://purl.allotrope.org/ontologies/process#AFP_0003779 af-p:AFP_0003779 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "genotyping" , "genotyping experiment" ; skos:definition "A genotyping qPCR experiment is an experiment using qPCR that identifies known mutations in a DNA Sample. DNA primers are used to target and identify specific alleles in a sample. [Allotrope]" ; skos:prefLabel "genotyping qPCR experiment" . ### http://purl.allotrope.org/ontologies/process#AFP_0003780 af-p:AFP_0003780 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003784 ; skos:altLabel "presence/absence" , "presence/absence experiment" ; skos:definition "A presence/absence qPCR experiment is an experiment using qPCR that identifies if DNA targets are present in samples. [Allotrope]" ; skos:prefLabel "presence/absence qPCR experiment" . ### http://purl.allotrope.org/ontologies/process#AFP_0003784 af-p:AFP_0003784 rdf:type owl:Class ; rdfs:subClassOf af-p:AFP_0003842 ; skos:definition "A qPCR experiment is a PCR experiment that uses qPCR to achieve its goals. [Allotrope]" ; skos:prefLabel "qPCR experiment" . ### http://purl.allotrope.org/ontologies/result#AFR_0002235 af-r:AFR_0002235 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002277 , af-r:AFR_0002278 ; skos:definition "An automatic cycle threshold enabled setting is a control setting that sets whether the cycle threshold determination is automated or manual. [Allotrope]" ; skos:prefLabel "automatic cycle threshold enabled setting" . ### http://purl.allotrope.org/ontologies/result#AFR_0002236 af-r:AFR_0002236 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0001243 , af-r:AFR_0002278 ; skos:altLabel "cycle threshold value setting" ; skos:definition "A cycle threshold value setting is a setting that sets the threshold value used for automatic qPCR cycle threshold determination. [Allotrope]" ; skos:prefLabel "cycle threshold value setting (qPCR)" . ### http://purl.allotrope.org/ontologies/result#AFR_0002238 af-r:AFR_0002238 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002278 ; skos:definition "A baseline determination start cycle setting is a PCR setting that specifies the start cycle for baseline determination. [Allotrope]" ; skos:prefLabel "baseline determination start cycle setting" . ### http://purl.allotrope.org/ontologies/result#AFR_0002239 af-r:AFR_0002239 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002278 ; skos:definition "A baseline determination end cycle setting is a PCR setting that specifies the end cycle for baseline determination. [Allotrope]" ; skos:prefLabel "baseline determination end cycle setting" . ### http://purl.allotrope.org/ontologies/result#AFR_0002246 af-r:AFR_0002246 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002279 ; skos:altLabel "cycle threshold result" ; skos:definition "A cycle threshold result is an qPCR assay result that records the cycle at which the threshold was passed. [Allotrope]" ; skos:prefLabel "cycle threshold result (qPCR)" . ### http://purl.allotrope.org/ontologies/result#AFR_0002247 af-r:AFR_0002247 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002279 ; skos:definition "A normalized reporter result is a qPCR assay result that specifies the fluorescent signal of the reporter dye normalized to the signal of the passive reference dye. [Allotrope]" ; skos:prefLabel "normalized reporter result" . ### http://purl.allotrope.org/ontologies/result#AFR_0002248 af-r:AFR_0002248 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002279 ; skos:definition "A baseline corrected reporter result is a qPCR assay result that specifies the normalized reporter result minus the baseline signal of the instrument. [Allotrope]" ; skos:prefLabel "baseline corrected reporter result" . ### http://purl.allotrope.org/ontologies/result#AFR_0002309 af-r:AFR_0002309 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0000992 , af-r:AFR_0002279 , qb:DataSet , [ rdf:type owl:Restriction ; owl:onProperty [ owl:inverseOf af-x:AFX_0002737 ] ; owl:someValuesFrom af-r:AFR_0002247 ] ; rdfs:isDefinedBy ; skos:altLabel "Rn data cube" ; skos:definition "A normalized reporter data cube is a data cube that represents a plot of normalized reporter result against cycle. [Allotrope]" ; skos:prefLabel "normalized reporter data cube" . ### http://purl.allotrope.org/ontologies/result#AFR_0002310 af-r:AFR_0002310 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0000992 , af-r:AFR_0002279 , qb:DataSet , [ rdf:type owl:Restriction ; owl:onProperty [ owl:inverseOf af-x:AFX_0002737 ] ; owl:someValuesFrom af-r:AFR_0002248 ] ; skos:altLabel "ΔRn data cube" ; skos:definition "A baseline corrected reporter data cube is a data cube that represents a plot of baseline corrected reporter result against cycle. [Allotrope]" ; skos:prefLabel "baseline corrected reporter data cube" . ### http://purl.allotrope.org/ontologies/result#AFR_0002899 af-r:AFR_0002899 rdf:type owl:Class ; rdfs:subClassOf af-c:AFC_0000160 , iao:_0000310 , [ rdf:type owl:Restriction ; owl:onProperty ro:_0002351 ; owl:someValuesFrom af-r:AFR_0002890 ] ; skos:definition "A qPCR aggregate document is a document that aggregates qPCR documents. [Allotrope]" ; skos:prefLabel "qPCR aggregate document" . ### http://purl.allotrope.org/ontologies/result#AFR_0002900 af-r:AFR_0002900 rdf:type owl:Class ; rdfs:subClassOf iao:_0000310 , [ rdf:type owl:Restriction ; owl:onProperty iao:_0000136 ; owl:someValuesFrom af-p:AFP_0003282 ] ; skos:definition "A qPCR document is a document that encompasses the information associated with some qPCR experiment. [Allotrope]" ; skos:prefLabel "qPCR document" . ### http://purl.allotrope.org/ontologies/result#AFR_0002908 af-r:AFR_0002908 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0002034 ; skos:definition "A genotyping qPCR method identifier is an identifier that identifies the method used for some genotyping qPCR experiment. [Allotrope]" ; skos:prefLabel "genotyping qPCR method identifier" . ### http://purl.allotrope.org/ontologies/result#AFR_0002909 af-r:AFR_0002909 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0001243 ; skos:definition "A genotyping qPCR method setting is a control setting that specifies the threshold of some genotyping qPCR experiment. [Allotrope]" ; skos:prefLabel "genotyping qPCR method setting" . ### http://purl.allotrope.org/ontologies/result#AFR_0002910 af-r:AFR_0002910 rdf:type owl:Class ; owl:equivalentClass [ owl:intersectionOf ( af-r:AFR_0000207 [ rdf:type owl:Restriction ; owl:onProperty af-x:AFX_0002734 ; owl:someValuesFrom af-p:AFP_0003779 ] ) ; rdf:type owl:Class ] ; af-x:AFX_0002798 "true"^^xsd:boolean ; skos:altLabel "genotyping qPCR assay result" , "genotyping qualitative PCR result" , "genotyping qualitative polymerase chain reaction result" ; skos:definition "A genotyping qPCR result is an assay result that is output of a genotyping qPCR experiment. [Allotrope]" ; skos:prefLabel "genotyping qPCR result" . ### http://purl.allotrope.org/ontologies/result#AFR_0002911 af-r:AFR_0002911 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0000992 , af-r:AFR_0002279 , qb:DataSet ; skos:definition "A reporter data cube is a data cube that represents a plot of reporter dye result against cycle. [Allotrope]" ; skos:prefLabel "reporter data cube" . ### http://purl.allotrope.org/ontologies/result#AFR_0002912 af-r:AFR_0002912 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0000992 , af-r:AFR_0002279 , qb:DataSet ; skos:definition "A passive reference dye data cube is a data cube that represents a plot of passive reference dye result against cycle. [Allotrope]" ; skos:prefLabel "passive reference dye data cube" . ### http://purl.allotrope.org/ontologies/result#AFR_0002913 af-r:AFR_0002913 rdf:type owl:Class ; rdfs:subClassOf af-r:AFR_0000992 , af-r:AFR_0002279 , qb:DataSet ; skos:definition "A melting curve data cube is a data cube that represents a plot of fluorescence against temperature. [Allotrope]" ; skos:prefLabel "melting curve data cube" . ################################################################# # Individuals ################################################################# ### http://www.allotrope.org rdf:type owl:NamedIndividual , foaf:Organization ; foaf:name "Allotrope Foundation" . ### http://purl.allotrope.org/voc/attribution rdf:type owl:NamedIndividual , dct:RightsStatement ; dct:description """ These taxonomies contain material or may constitute derivative works of material which may be subject to copyright by one of the following organizations. 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