@prefix : . @prefix dc: . @prefix px: . @prefix dct: . @prefix obo: . @prefix owl: . @prefix rdf: . @prefix sio: . @prefix xml: . @prefix xsd: . @prefix foaf: . @prefix rdfs: . @prefix skos: . @prefix uniprot: . @prefix unimod: . @base . rdf:type owl:Ontology ; owl:imports ; dc:creator "Yuki Moriya" ; dc:description "jPOST RDF ontology" ; dct:license ; rdfs:label "jPOST RDF Ontology" ; owl:versionInfo 0.15 . ################################################################# # Object Properties ################################################################# ### http://rdf.jpostdb.org/ontology/jpost.owl#cellLine :cellLine rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; rdfs:range :CellLine ; dc:description "Property that describes the cell line of sample." ; rdfs:label "cell line" . ### http://rdf.jpostdb.org/ontology/jpost.owl#disease :disease rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; dc:description "Property that describes the disease of sample." ; rdfs:label "disease" . ### http://rdf.jpostdb.org/ontology/jpost.owl#diseaseClass :diseaseClass rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; dc:description "Property that describes the disease class of sample." ; rdfs:label "disease class" . ### http://rdf.jpostdb.org/ontology/jpost.owl#enzyme :enzyme rdf:type owl:ObjectProperty ; rdfs:domain :EnzymeAndModification ; rdfs:range :Enzyme ; dc:description "Property that describes the used enzyme to convert proteins into peptides" ; rdfs:label "enzyme" . ### http://rdf.jpostdb.org/ontology/jpost.owl#fixedModification :fixedModification rdf:type owl:ObjectProperty ; rdfs:domain :EnzymeAndModification ; rdfs:range :FixedModification ; dc:description "Property that describes the amino acid mass modifications applied universally." ; rdfs:label "fixed modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasDatabaseSequence :hasDatabaseSequence rdf:type owl:ObjectProperty ; rdfs:domain :Protein ; rdfs:comment "has protein sequence entry in database." ; rdfs:label "has database sequence" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasDataset :hasDataset rdf:type owl:ObjectProperty ; rdfs:range :Dataset ; rdfs:comment "jPOST project has a dataset." ; rdfs:label "has dataset" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasEnzymeAndModification :hasEnzymeAndModification rdf:type owl:ObjectProperty ; rdfs:domain :Profile ; rdfs:range :EnzymeAndModification ; rdfs:label "has enzyme/modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasFractionation :hasFractionation rdf:type owl:ObjectProperty ; rdfs:domain :Profile ; rdfs:range :Fractionation ; rdfs:label "has fractionation" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasFractionationType :hasFractionationType rdf:type owl:ObjectProperty ; rdfs:domain :Fractionation ; rdfs:range :FractionationType ; rdfs:label "has fractionation type" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasIndistinguishablePeptide :hasIndistinguishablePeptide rdf:type owl:ObjectProperty ; rdfs:domain :UniquePeptide ; rdfs:range :UniquePeptide ; rdfs:label "has indistinguishable peptide at MS level" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasLeadingProtein :hasLeadingProtein rdf:type owl:ObjectProperty ; rdfs:domain :Protein ; rdfs:range :Protein ; rdfs:label "has leading protein" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasModification :hasModification rdf:type owl:ObjectProperty ; rdfs:domain :Peptide ; rdfs:range unimod:UNIMOD_0 ; rdfs:range obo:MOD_00000 ; rdfs:comment "amino acid sequence has a modification." ; rdfs:label "has modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasMsMode :hasMsMode rdf:type owl:ObjectProperty ; rdfs:domain :Profile ; rdfs:range :MsMode ; rdfs:label "has LC/MS/MS mode" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPeptide :hasPeptide rdf:type owl:ObjectProperty ; rdfs:domain [ rdf:type owl:Class ; owl:unionOf ( :Dataset :PeptideEvidence ) ] ; rdfs:range :Peptide ; rdfs:comment "Dataset and peptide evidence has a peptide." ; rdfs:label "has peptide" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPeptideEvidence :hasPeptideEvidence rdf:type owl:ObjectProperty ; rdfs:domain :Protein ; rdfs:range :PeptideEvidence ; rdfs:label "has peptide evidence" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPlex :hasPlex rdf:type owl:ObjectProperty ; rdfs:domain :Profile ; rdfs:range :Plex ; rdfs:label "has plex" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasProfile :hasProfile rdf:type owl:ObjectProperty ; rdfs:domain [ rdf:type owl:Class ; owl:unionOf ( :Dataset :RawData ) ] ; rdfs:range :Profile ; rdfs:label "has profile" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasProtein :hasProtein rdf:type owl:ObjectProperty ; rdfs:domain :Dataset ; rdfs:range :Protein ; rdfs:comment "Dataset has a protein." ; rdfs:label "has protein" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPsm :hasPsm rdf:type owl:ObjectProperty ; rdfs:range :PeptideSpectrumMatch ; rdfs:comment "Peptide has a PSM" ; rdfs:label "has PSM" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasRawData :hasRawData rdf:type owl:ObjectProperty ; rdfs:range :RawData ; rdfs:comment "jPOST project has a LC-MS/MS raw data." ; rdfs:label "has raw data" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasSample :hasSample rdf:type owl:ObjectProperty ; rdfs:domain :Profile ; rdfs:range :Sample ; rdfs:label "has sample" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasSequence :hasSequence rdf:type owl:ObjectProperty ; rdfs:domain [ rdf:type owl:Class ; owl:unionOf ( :Peptide :Protein ) ] ; rdfs:comment "has amino acid sequence." ; rdfs:label "has sequence" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasSpectrum :hasSpectrum rdf:type owl:ObjectProperty ; rdfs:range :Spectrum ; rdfs:comment "PSM has a spectrum" ; rdfs:label "has spectrum" . ### http://rdf.jpostdb.org/ontology/jpost.owl#inPlex :inPlex rdf:type owl:ObjectProperty ; rdfs:domain :RelativeQuantitativeValue ; rdfs:range :Plex ; rdfs:label "in plex" . ### http://rdf.jpostdb.org/ontology/jpost.owl#inProteinGroup :inProteinGroup rdf:type owl:ObjectProperty ; rdfs:domain :Protein ; rdfs:range :ProteinGroup ; rdfs:comment "Pataset in a protein group." ; rdfs:label "in protein group" . ### http://rdf.jpostdb.org/ontology/jpost.owl#inRawData :inRawData rdf:type owl:ObjectProperty ; rdfs:range :RawData ; rdfs:comment "Peptide in a LC-MS/MS raw data." ; rdfs:label "in raw data" . ### http://rdf.jpostdb.org/ontology/jpost.owl#instrument :instrument rdf:type owl:ObjectProperty ; rdfs:domain [ rdf:type owl:Class ; owl:unionOf ( :Dataset :MsMode ) ] ; dc:description "Property that describes instrument on which the data has been generated." ; rdfs:label "instrument" . ### http://rdf.jpostdb.org/ontology/jpost.owl#instrumentMode :instrumentMode rdf:type owl:ObjectProperty ; rdfs:domain :MsMode ; rdfs:range :InstrumentMode ; dc:description "Property that describes the mode of mass spectrometer." ; rdfs:label "instrument mode" . ### http://rdf.jpostdb.org/ontology/jpost.owl#instrumentPurpose :instrumentPurpose rdf:type owl:ObjectProperty ; rdfs:domain :MsMode ; rdfs:range :InstrumentPurpose ; dc:description "Property that describes the purpose of mass spectrometry." ; rdfs:label "instrument purpose" . ### http://rdf.jpostdb.org/ontology/jpost.owl#modificationClass :modificationClass rdf:type owl:ObjectProperty ; rdfs:range :ModificationClass ; dc:description "Property that describes the modification type." ; rdfs:label "modification class" . ### http://rdf.jpostdb.org/ontology/jpost.owl#organ :organ rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; rdfs:range :Organ ; dc:description "Property that describes the organ of sample." ; rdfs:label "organ" . ### http://rdf.jpostdb.org/ontology/jpost.owl#quantificationPlatform :quantificationPlatform rdf:type owl:ObjectProperty ; rdfs:domain :MsMode ; rdfs:range :QuantificationPlatform ; dc:description "Property that describes the platform of quantification method." , "Property that describes the quantification method." ; rdfs:label "quantification method" , "quantification platform" . ### http://rdf.jpostdb.org/ontology/jpost.owl#representativePsm :representativePsm rdf:type owl:ObjectProperty ; rdfs:domain :PeptideSpectrumMatch ; rdfs:range xsd:boolean ; dc:description "Representative PSM flag in a peptide sequence-level" ; rdfs:label "representative PSM" . ### http://rdf.jpostdb.org/ontology/jpost.owl#sampleType :sampleType rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; rdfs:range :SampleType ; dc:description "Property that describes the sample type of sample." ; rdfs:label "sample type" . ### http://rdf.jpostdb.org/ontology/jpost.owl#species :species rdf:type owl:ObjectProperty ; rdfs:domain [ rdf:type owl:Class ; owl:unionOf ( :Dataset :EnzymeAndModification :Sample ) ] ; dc:description "Property that describes the species from which the data has been generated." ; rdfs:label "species" . ### http://rdf.jpostdb.org/ontology/jpost.owl#tissue :tissue rdf:type owl:ObjectProperty ; rdfs:domain :Sample ; rdfs:range :Tissue ; dc:description "Property that describes the tissue of sample." ; rdfs:label "tissue" . ### http://rdf.jpostdb.org/ontology/jpost.owl#variableModification :variableModification rdf:type owl:ObjectProperty ; rdfs:domain :EnzymeAndModification ; rdfs:range :VariableModification ; dc:description "Property that describes the possible amino acid mass modifications." ; rdfs:label "variable modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#detectedSiteBySearchEngine :detectedSiteBySearchEngine rdf:type owl:ObjectProperty ; rdfs:domain unimod:UNIMOD_0 ; dc:description "Property that describes the detected modification site by search engine, in the ambiguous modification site." ; rdfs:label "detected site by search engine" . ################################################################# # Data properties ################################################################# ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPostResidue :hasPostResidue rdf:type owl:DatatypeProperty ; rdfs:domain :PeptideEvidence ; rdfs:range xsd:string ; rdfs:comment "post residue of matched region" ; rdfs:label "has post residue" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasPreResidue :hasPreResidue rdf:type owl:DatatypeProperty ; rdfs:domain :PeptideEvidence ; rdfs:range xsd:string ; rdfs:comment "pre residue of matched region" ; rdfs:label "has pre residue" . ### http://rdf.jpostdb.org/ontology/jpost.owl#modificationSite :modificationSite rdf:type owl:DatatypeProperty ; rdfs:range xsd:string ; dc:description "Property that describes the amino acid mass modifications site." ; rdfs:label "modification site" . ### http://rdf.jpostdb.org/ontology/jpost.owl#fractions :fractions rdf:type owl:DatatypeProperty ; rdfs:domain :FractionationType ; rdfs:range xsd:integer ; dc:description "Property describes the number of fractions." ; rdfs:label "fractions" . ### http://rdf.jpostdb.org/ontology/jpost.owl#replicates :replicates rdf:type owl:DatatypeProperty ; rdfs:domain :FractionationType ; rdfs:range xsd:integer ; dc:description "Property describes the number of replicates." ; rdfs:label "replicates" . ### http://rdf.jpostdb.org/ontology/jpost.owl#plex :plex rdf:type owl:DatatypeProperty ; rdfs:domain :MsMode ; rdfs:range xsd:integer ; dc:description "Property that describes the number of plex." ; rdfs:label "plex number" . ### http://rdf.jpostdb.org/ontology/jpost.owl#hasCorrespondingConfirmedSite :hasCorrespondingConfirmedSite rdf:type owl:ObjectProperty ; rdfs:domain unimod:UNIMOD_0 ; rdfs:range xsd:boolean ; dc:description "Property that describes the existence of corresponding confirmed site in other PSMs." ; rdfs:label "has corresponding confirmed site" . ################################################################# # Classes ################################################################# ### http://rdf.jpostdb.org/ontology/jpost.owl#AbsoluteAuantitativeValue :AbsoluteAuantitativeValue rdf:type owl:Class ; rdfs:subClassOf :QuantitativeValue ; rdfs:label "" , "Absolute quantitative value" . ### http://rdf.jpostdb.org/ontology/jpost.owl#CalculatedMassToCharge :CalculatedMassToCharge rdf:type owl:Class ; rdfs:subClassOf :MassToCharge ; dc:description "Calculated monoisotopic mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum." ; rdfs:label "Calculated mass-to-charge ratio" . ### http://rdf.jpostdb.org/ontology/jpost.owl#CellLine :CellLine rdf:type owl:Class ; rdfs:subClassOf :Sample ; dc:description "cell line of sample." ; rdfs:label "Cell line" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Dataset :Dataset rdf:type owl:Class ; rdfs:subClassOf :JpostEntry , sio:SIO_000089 ; dc:description "a jPOST entry describing a dataset." ; rdfs:label "jPOST dataset" . ### http://rdf.jpostdb.org/ontology/jpost.owl#DatasetStatistic :DatasetStatistic rdf:type owl:Class ; dct:description "Statistic of proteomics dataset" ; rdfs:label "Dataset statistic" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Disease :Disease rdf:type owl:Class ; rdfs:subClassOf :Sample ; dc:description "disease type of sample." ; rdfs:label "Disease" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Enzyme :Enzyme rdf:type owl:Class ; rdfs:subClassOf :EnzymeAndModification ; dc:description "a used enzyme to convert proteins into peptides." ; rdfs:label "Enzyme" . ### http://rdf.jpostdb.org/ontology/jpost.owl#EnzymeAndModification :EnzymeAndModification rdf:type owl:Class ; rdfs:subClassOf :Profile ; dc:description "metadata of enzymes and modifications." ; rdfs:label "Enzyme/Modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#ExperimentalMassToCharge :ExperimentalMassToCharge rdf:type owl:Class ; rdfs:subClassOf :MassToCharge ; dc:description "Experimental monoisotopic mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum." ; rdfs:label "Experimental mass-to-charge ratio" . ### http://rdf.jpostdb.org/ontology/jpost.owl#FixedModification :FixedModification rdf:type owl:Class ; rdfs:subClassOf px:ModificationType ; dc:description "an amino acid mass modification applied universally." ; rdfs:label "Fixed modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Fractionation :Fractionation rdf:type owl:Class ; rdfs:subClassOf :Profile ; dc:description "metadata of sample fractionation processes." ; rdfs:label "Fractionation" . ### http://rdf.jpostdb.org/ontology/jpost.owl#FractionationType :FractionationType rdf:type owl:Class ; rdfs:subClassOf :Fractionation ; dc:description "fractionation process type, such as subcellular, protein and peptide-level." ; rdfs:label "Fractionation type" . ### http://rdf.jpostdb.org/ontology/jpost.owl#SubcellularFractionation :SubcellularFractionation rdf:type owl:Class ; rdfs:subClassOf :FractionationType ; dc:description "subcellular-level fractionation process." ; rdfs:label "Subcellular fractionation" . ### http://rdf.jpostdb.org/ontology/jpost.owl#ProteinFractionation :ProteinFractionation rdf:type owl:Class ; rdfs:subClassOf :FractionationType ; dc:description "protein-level fractionation process." ; rdfs:label "Protein fractionation" . ### http://rdf.jpostdb.org/ontology/jpost.owl#PeptideFractionation :PeptideFractionation rdf:type owl:Class ; rdfs:subClassOf :FractionationType ; dc:description "peptide-level fractionation process." ; rdfs:label "Peptide fractionation" . ### http://rdf.jpostdb.org/ontology/jpost.owl#InstrumentMode :InstrumentMode rdf:type owl:Class ; rdfs:subClassOf :MsMode ; dc:description "instrument mode of mass spectromerter." ; rdfs:label "Instrument mode" . ### http://rdf.jpostdb.org/ontology/jpost.owl#InstrumentPurpose :InstrumentPurpose rdf:type owl:Class ; rdfs:subClassOf :MsMode ; dc:description "purpose of mass spectrometry." ; rdfs:label "Instrument purpose" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_001 :JPO_001 rdf:type owl:Class ; dc:description "root node for terms relating to the description of jPOST." ; dct:identifier "JPO_001" ; rdfs:label "jPOST controlled vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_002 :JPO_002 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; dc:description "root node for terms relating to the description of instrument modes." ; dct:identifier "JPO_002" ; rdfs:label "Instrument mode vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_003 :JPO_003 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; dc:description "root node for terms relating to the description of instrument purposes." ; dct:identifier "JPO_003" ; rdfs:label "Purpose vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_004 :JPO_004 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; dc:description "root node for terms relating to the description of quntification platforms." ; dct:identifier "JPO_004" ; rdfs:label "Quantification platform vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_005 :JPO_005 rdf:type owl:Class ; rdfs:subClassOf :JPO_002 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_006 :JPO_006 rdf:type owl:Class ; rdfs:subClassOf :JPO_002 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_007 :JPO_007 rdf:type owl:Class ; rdfs:subClassOf :JPO_002 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_008 :JPO_008 rdf:type owl:Class ; rdfs:subClassOf :JPO_002 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_009 :JPO_009 rdf:type owl:Class ; rdfs:subClassOf :JPO_003 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_010 :JPO_010 rdf:type owl:Class ; rdfs:subClassOf :JPO_003 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_011 :JPO_011 rdf:type owl:Class ; rdfs:subClassOf :JPO_003 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_012 :JPO_012 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_013 :JPO_013 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_014 :JPO_014 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_015 :JPO_015 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 ; dct:identifier "JPO_015" ; rdfs:label "Product ion (reporter quantification)" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_016 :JPO_016 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_017 :JPO_017 rdf:type owl:Class ; rdfs:subClassOf :JPO_004 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_018 :JPO_018 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; dc:description "root node for terms relating to the description of sample." ; dct:identifier "JPO_018" ; rdfs:label "Sample vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_019 :JPO_019 rdf:type owl:Class ; rdfs:subClassOf :JPO_018 ; dc:description "non-disease sample." ; dct:identifier "JPO_019" ; rdfs:label "Normal" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_020 :JPO_020 rdf:type owl:Class ; rdfs:subClassOf :JPO_018 ; dc:description "disease sample excludes cancer, nervous system disease, metabolic disease , cardiovascular system disease, infectious disease and immune system disease." ; dct:identifier "JPO_020" ; rdfs:label "Other disease" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_021 :JPO_021 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; dc:description "root node for terms relating to the description of modification class based on unimod." ; dct:identifier "JPO_021" ; rdfs:label "Modification class vocabulary" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_022 :JPO_022 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_023 :JPO_023 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_024 :JPO_024 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_025 :JPO_025 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_026 :JPO_026 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_027 :JPO_027 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_028 :JPO_028 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_029 :JPO_029 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_030 :JPO_030 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_031 :JPO_031 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_032 :JPO_032 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_033 :JPO_033 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_034 :JPO_034 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_035 :JPO_035 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_036 :JPO_036 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_037 :JPO_037 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_038 :JPO_038 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_039 :JPO_039 rdf:type owl:Class ; rdfs:subClassOf :JPO_021 . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_100 :JPO_100 rdf:type owl:Class ; rdfs:subClassOf :JPO_001 ; rdfs:label "Unit"@ja . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_101 :JPO_101 rdf:type owl:Class ; rdfs:subClassOf :JPO_100 ; dc:description "femtomole [obo:UO_0000043] per picoliter [obo:UO_0000103]" ; dct:identifier "JPO_101" ; rdfs:label "Femtomole per picoliter" ; skos:prefLabel "fmol/pl" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JpostEntry :JpostEntry rdf:type owl:Class ; dc:description "root node of jPOST entries." ; rdfs:label "jPOST entry" . ### http://rdf.jpostdb.org/ontology/jpost.owl#JpostScore :JpostScore rdf:type owl:Class ; rdfs:subClassOf :MeasurementValue ; dc:description "jPOST result score for PSM" ; rdfs:label "jPOST score" . ### http://rdf.jpostdb.org/ontology/jpost.owl#UniScore :UniScore rdf:type owl:Class ; rdfs:subClassOf :MeasurementValue ; dc:description "jPOST result score for PSM" ; rdfs:label "Uni score" . ### http://rdf.jpostdb.org/ontology/jpost.owl#MassToCharge :MassToCharge rdf:type owl:Class ; rdfs:subClassOf :MeasurementValue ; dct:description "Mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum." ; rdfs:label "Mass-to-charge ratio" . ### http://rdf.jpostdb.org/ontology/jpost.owl#MatchingType :MatchingType rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a matching ion type of PSM based on the sequence, PTMs and the charge, as a unit for calculating peptide FDR." ; rdfs:label "Matching type" . ### http://rdf.jpostdb.org/ontology/jpost.owl#MeasurementValue :MeasurementValue rdf:type owl:Class ; dct:description "Measurement value for mass spectrometry-based proteomics" ; rdfs:label "Measurement value" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Modification :Modification rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "amin acid mass modification" ; rdfs:label "Modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#AmbiguousModification :AmbiguousModification rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "ambiguous amin acid mass modification" ; rdfs:label "Ambiguous modification" . ### http://rdf.jpostdb.org/ontology/jpost.owl#ModificationClass :ModificationClass rdf:type owl:Class ; rdfs:subClassOf :EnzymeAndModification ; dc:description "A type of amino asid mass modification based on unimod" ; rdfs:label "Modifiaction class" . ### http://rdf.jpostdb.org/ontology/jpost.owl#MsMode :MsMode rdf:type owl:Class ; rdfs:subClassOf :Profile ; dc:description "metadata of MS instrument." ; rdfs:label "MS instrument mode" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfLeadingProtein :NumOfLeadingProtein rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of leading protein (obo:MS_1002401) infered from proteins in a dataset" ; rdfs:label "Number of leading proteins" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfMatchedProteins :NumOfMatchedProteins rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of proteins matched with at least one peptide in a dataset" ; rdfs:label "Number of matched proteins" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfPeptides :NumOfPeptides rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of peptides in a dataset" ; rdfs:label "Number of peptides" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfProteinsWithUniquePeptide :NumOfProteinsWithUniquePeptide rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of proteins matched with at least one unique peptide in a dataset" ; rdfs:label "Number of proteins with unique peptide" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfPsms :NumOfPsms rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of PSMs in a dataset" ; rdfs:label "Number of PSMs" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfRawData :NumOfRawData rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of raw data in a dataset" ; rdfs:label "Number of raw data" . ### http://rdf.jpostdb.org/ontology/jpost.owl#NumOfSpectra :NumOfSpectra rdf:type owl:Class ; rdfs:subClassOf :DatasetStatistic ; dc:description "Number of spectra in a dataset" ; rdfs:label "Number of spectra" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Organ :Organ rdf:type owl:Class ; rdfs:subClassOf :Sample ; dc:description "organ of sample." ; rdfs:label "Organ" . ### http://rdf.jpostdb.org/ontology/jpost.owl#PepArea :PepArea rdf:type owl:Class ; rdfs:subClassOf :QuantitativeValue ; dc:description "area of peptide spectrum for quntification" ; rdfs:label "Peptide area" . ### http://rdf.jpostdb.org/ontology/jpost.owl#PepIntensity :PepIntensity rdf:type owl:Class ; rdfs:subClassOf :QuantitativeValue ; dc:description "intensity of peptide spectrum for quntification" ; rdfs:label "Peptide intensity" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Peptide :Peptide rdf:type owl:Class ; rdfs:subClassOf obo:MS_1000860 , :JpostEntry ; dc:description "a jPOST entry describing a peptide." ; rdfs:label "Peptide" . ### http://rdf.jpostdb.org/ontology/jpost.owl#PeptideEvidence :PeptideEvidence rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing peptide evidence in mzIndentML." ; rdfs:label "Peptide evidence" . ### http://rdf.jpostdb.org/ontology/jpost.owl#PeptideSpectrumMatch :PeptideSpectrumMatch rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a peptide matched to spectrum." ; rdfs:label "Peptide spectrum match" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Plex :Plex rdf:type owl:Class ; rdfs:subClassOf :Profile ; dc:description "plex information of multi-plex experiment" ; rdfs:label "Plex" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Profile :Profile rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "Metadata of a experimental procedure." ; rdfs:label "Profile" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Project :Project rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a project." ; rdfs:label "jPOST project" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Protein :Protein rdf:type owl:Class ; rdfs:subClassOf obo:MS_1000882 , :JpostEntry ; dc:description "a jPOST entry describing a protein." ; rdfs:label "Protein" . ### http://rdf.jpostdb.org/ontology/jpost.owl#ProteinIsoform :ProteinIsoform rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a protein isoform in a dataset." ; rdfs:label "Protein isoform" . ### http://rdf.jpostdb.org/ontology/jpost.owl#ProteinGroup :ProteinGroup rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a protein group" ; rdfs:label "Protein group" . ### http://rdf.jpostdb.org/ontology/jpost.owl#QuantificationPlatform :QuantificationPlatform rdf:type owl:Class ; rdfs:subClassOf :MsMode ; dc:description "platform type for quantification." ; rdfs:label "Quantification platform" . ### http://rdf.jpostdb.org/ontology/jpost.owl#QuantitativeValue :QuantitativeValue rdf:type owl:Class ; rdfs:subClassOf :MeasurementValue ; rdfs:label "Quantitative value" . ### http://rdf.jpostdb.org/ontology/jpost.owl#RawData :RawData rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a raw data of mass spectrometer run." ; rdfs:label "Raw data" . ### http://rdf.jpostdb.org/ontology/jpost.owl#RelativeQuantitativeValue :RelativeQuantitativeValue rdf:type owl:Class ; rdfs:subClassOf :QuantitativeValue ; rdfs:label "Relative quantitative value" . ### http://rdf.jpostdb.org/ontology/jpost.owl#RepresentativeIsoform :RepresentativeIsoform rdf:type owl:Class ; rdfs:subClassOf :JpostEntry ; dc:description "a jPOST entry describing a representative isoform in a dataset." ; rdfs:label "Representative isoform" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Sample :Sample rdf:type owl:Class ; rdfs:subClassOf :Profile ; dc:description "metadata of a sample." ; rdfs:label "Sample" . ### http://rdf.jpostdb.org/ontology/jpost.owl#SampleType :SampleType rdf:type owl:Class ; rdfs:subClassOf :Sample ; dc:description "sample type of sample." ; rdfs:label "Sample type" . ### http://rdf.jpostdb.org/ontology/jpost.owl#SharedPeptide :SharedPeptide rdf:type owl:Class ; rdfs:subClassOf obo:MS_1001175 , :Peptide ; dc:description "Peptide shared in multiple database sequence" ; rdfs:label "Shared peptide" . ### http://rdf.jpostdb.org/ontology/jpost.owl#SharedPeptideAtMsLevel :SharedPeptideAtMsLevel rdf:type owl:Class ; rdfs:subClassOf :SharedSequence ; dc:description "Peptide shared in multiple database sequence at MS level. (not distinguish leucine and isoleucine)" ; rdfs:label "Shared peptide at MS level" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Spectrum :Spectrum rdf:type owl:Class ; rdfs:subClassOf obo:MS_1000442 , :JpostEntry ; dc:description "a jPOST entry describing a spectrum of LC-MS/MS" ; rdfs:label "Spectrum" . ### http://rdf.jpostdb.org/ontology/jpost.owl#Tissue :Tissue rdf:type owl:Class ; rdfs:subClassOf :Sample ; dc:description "tissue of sample." ; rdfs:label "Tissue" . ### http://rdf.jpostdb.org/ontology/jpost.owl#UniquePeptide :UniquePeptide rdf:type owl:Class ; rdfs:subClassOf obo:MS_1001363 , :Peptide ; dc:description "Peptide unique to one database sequence" ; rdfs:label "Unique peptide" . ### http://rdf.jpostdb.org/ontology/jpost.owl#UniquePeptideAtMsLevel :UniquePeptideAtMsLevel rdf:type owl:Class ; rdfs:subClassOf :UniquePeptide ; dc:description "Peptide unique to one database sequence at MS level. (not distinguish leucine and isoleucine)" ; rdfs:label "Unique peptide at MS level" . ### http://rdf.jpostdb.org/ontology/jpost.owl#VariableModification :VariableModification rdf:type owl:Class ; rdfs:subClassOf px:ModificationType ; dc:description "a possible amino acid mass modification." ; rdfs:label "Variable modification" . ### https://raw.githubusercontent.com/PX-RDF/ontology/master/px.owl#ModificationType px:ModificationType rdf:type owl:Class ; rdfs:subClassOf :EnzymeAndModification ; dct:description "Experimental amino acid mass modification type in database search" ; rdfs:label "Modification type" . ################################################################# # Individuals ################################################################# ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_005 :JPO_005 rdf:type owl:NamedIndividual , :InstrumentMode . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_006 :JPO_006 rdf:type owl:NamedIndividual , :InstrumentMode . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_007 :JPO_007 rdf:type owl:NamedIndividual , :InstrumentMode . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_008 :JPO_008 rdf:type owl:NamedIndividual , :InstrumentMode . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_009 :JPO_009 rdf:type owl:NamedIndividual , :InstrumentPurpose . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_010 :JPO_010 rdf:type owl:NamedIndividual , :InstrumentPurpose . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_011 :JPO_011 rdf:type owl:NamedIndividual , :InstrumentPurpose . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_012 :JPO_012 rdf:type owl:NamedIndividual , :QuantificationPlatform . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_013 :JPO_013 rdf:type owl:NamedIndividual , :QuantificationPlatform . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_014 :JPO_014 rdf:type owl:NamedIndividual , :QuantificationPlatform . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_016 :JPO_016 rdf:type owl:NamedIndividual , :QuantificationPlatform . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_017 :JPO_017 rdf:type owl:NamedIndividual , :QuantificationPlatform . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_022 :JPO_022 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_023 :JPO_023 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_024 :JPO_024 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_025 :JPO_025 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_026 :JPO_026 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_027 :JPO_027 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_028 :JPO_028 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_029 :JPO_029 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_030 :JPO_030 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_031 :JPO_031 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_032 :JPO_032 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_033 :JPO_033 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_034 :JPO_034 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_035 :JPO_035 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_036 :JPO_036 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_037 :JPO_037 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_038 :JPO_038 rdf:type owl:NamedIndividual , :ModificationClass . ### http://rdf.jpostdb.org/ontology/jpost.owl#JPO_039 :JPO_039 rdf:type owl:NamedIndividual , :ModificationClass . ################################################################# # Annotations ################################################################# :JPO_005 dc:description "Data-dependent acquisition high resoluiton mode of mass spectrometer." ; dct:identifier "JPO_005" ; rdfs:label "DDA-high res." . :JPO_006 dct:identifier "JPO_006" ; dc:description "Data-dependent acquisition low resoluiton mode of mass spectrometer." ; rdfs:label "DDA-low res." . :JPO_007 dc:description "Data-independent acquisition mode of mass spectrometer." ; rdfs:label "DIA" ; dct:identifier "JPO_007" . :JPO_008 rdfs:label "Target" ; dc:description "Target mode of mass spectrometer." ; dct:identifier "JPO_008" . :JPO_009 rdfs:label "Qualification" ; dct:identifier "JPO_009" . :JPO_010 dct:identifier "JPO_010" ; rdfs:label "Absolute quantification" . :JPO_011 dct:identifier "JPO_011" ; rdfs:label "Relative quantification" . :JPO_012 dct:identifier "JPO_012" ; rdfs:label "Spectra count" . :JPO_013 dct:identifier "JPO_013" ; rdfs:label "Precursor ion label free" . :JPO_014 rdfs:label "Precursor ion stable isotope labeling" ; dct:identifier "JPO_014" . :JPO_016 dct:identifier "JPO_016" ; rdfs:label "Fragment ion (stable isotope labeling)" . :JPO_017 dct:identifier "JPO_017" ; rdfs:label "Fragment ion (label-free)" . :JPO_022 dct:identifier "JPO_022" ; rdfs:label "Post-translational" . :JPO_023 dct:identifier "JPO_023" ; rdfs:label "Co-translational" . :JPO_024 dct:identifier "JPO_024" ; rdfs:label "Pre-translational" . :JPO_025 dct:identifier "JPO_025" ; rdfs:label "Chemical derivative" . :JPO_026 dct:identifier "JPO_026" ; rdfs:label "Artefact" . :JPO_027 dct:identifier "JPO_027" ; rdfs:label "N-linked glycosylation" . :JPO_028 dct:identifier "JPO_028" ; rdfs:label "O-linked glycosylation" . :JPO_029 rdfs:label "Other glycosylation" ; dct:identifier "JPO_029" . :JPO_030 rdfs:label "Synth. pep. protect. gp." ; dct:identifier "JPO_030" . :JPO_031 rdfs:label "Isotopic label" ; dct:identifier "JPO_031" . :JPO_032 dct:identifier "JPO_032" ; rdfs:label "Non-standard residue" . :JPO_033 rdfs:label "Multiple" ; dct:identifier "JPO_033" . :JPO_034 rdfs:label "Other" ; dct:identifier "JPO_034" . :JPO_035 rdfs:label "AA substitution" ; dct:identifier "JPO_035" . :JPO_036 rdfs:label "Cross-link" ; dct:identifier "JPO_036" . :JPO_037 dct:identifier "JPO_037" ; rdfs:label "CID cleavable cross-link" . :JPO_038 rdfs:label "Photo cleavable cross-link" ; dct:identifier "JPO_038" . :JPO_039 rdfs:label "Other cleavable cross-link" ; dct:identifier "JPO_039" . ### Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi