SBPAX3 SGMP Example 4 in N3

This is an example of adding kinetic data to BioPAX using SBPAX3 for glucose transport kinetics (GLUT4) based on data from Signaling Gateway Molecule Pages. Their BioPAX Level 3 export was taken, some sample fragments extracted, some URIs adjusted, some SBO terms guessed, and their data added using SBPAX3. Original data is here.

@prefix :       . @prefix rdfs:   . @prefix ex:     . @prefix bp:     . @prefix owl:    . @prefix xsd:    . @prefix sgmp:   . @prefix sbx3:   . @prefix rdf:    . @prefix uome-list: .

sgmp:PublicationXref_447648 a      bp:PublicationXref ; bp:author "Gliemann J"^^xsd:string, "Whitesell RR"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "447648"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Kinetic parameters of transport of 3-O-methylglucose and glucose in adipocytes."^^xsd:string ; bp:year "1979"^^xsd:int.

sgmp:RelationshipXref_GO_0005215 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005215"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_3140043.

ex:zerothOrderRateConstantTerm a      sbx3:SBVocabulary ; bp:term "forward zeroth order rate constant, continuous case" ; bp:xref ex:zerothOrderRateConstantSBORef.

ex:zerothOrderRateConstant4 a      sbx3:SBMeasurable ; sbx3:hasNumber "80000.0"^^xsd:double ; sbx3:hasUnit uome-list:PerMinute ; sbx3:sbTerm ex:zerothOrderRateConstantTerm.

sgmp:SequenceSite_6298 a      bp:SequenceSite ; bp:positionStatus "EQUAL"^^xsd:string ; bp:sequencePosition "57"^^xsd:int.

sgmp:PublicationXref_8457198 a      bp:PublicationXref ; bp:author "Takeda J"^^xsd:string, "Thomas HM"^^xsd:string , "Gould GW"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "8457198"^^xsd:string ; bp:source "Biochem J"^^xsd:string ; bp:title "Differential targeting of glucose transporter isoforms heterologously expressed in Xenopus oocytes."^^xsd:string ; bp:year "1993"^^xsd:int.

sgmp:PublicationXref_2645527 a      bp:PublicationXref ; bp:author "Mueckler M"^^xsd:string, "Strube M"^^xsd:string , "James DE"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "2645527"^^xsd:string ; bp:source "Nature"^^xsd:string ; bp:title "Molecular cloning and characterization of an insulin-regulatable glucose transporter."^^xsd:string ; bp:year "1989"^^xsd:int.

sgmp:Provenance_SGMP a      bp:Provenance ; bp:displayName "SGMP"^^xsd:string ; bp:standardName "Signaling Gateway Molecule Pages"^^xsd:string.

sgmp:RelationshipXref_GO_0005355 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005355"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_3140045.

sgmp:RelationshipTypeVocabulary_3140043 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: IEA"^^xsd:string ; bp:term "transporter activity"^^xsd:string.

ex:zerothOrderRateLawSBORef a      bp:UnificationXref ; bp:comment "mass action rate law for zeroth order irreversible reactions, continuous scheme" ; bp:db  "SBO" ; bp:id  "0000047".

sgmp:UnificationXref_BAB03251 a      bp:UnificationXref ; bp:db  "DDBJ"^^xsd:string ; bp:id  "BAB03251"^^xsd:string ; bp:idVersion "1"^^xsd:string.

ex:zerothOrderRateLaw2b a      sbx3:SBEntity ; sbx3:sbSubEntity ex:zerothOrderRateConstant4 ; sbx3:sbTerm ex:zerothOrderRateLawTerm.

ex:zerothOrderRateLawTerm a      sbx3:SBVocabulary ; bp:term "mass action rate law for zeroth order irreversible reactions, continuous scheme" ; bp:xref ex:zerothOrderRateLawSBORef.

sgmp:CellularLocationVocabulary_GO_0005886 a      bp:CellularLocationVocabulary ; bp:term "plasma membrane"^^xsd:string ; bp:xref sgmp:UnificationXref_GO_0005886.

sgmp:RelationshipXref_GO_0005360 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005360"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_3140046.

sgmp:RelationshipXref_GO_0005351 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005351"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_3140044.

sgmp:BioSource_Musmusculus a      bp:BioSource ; bp:displayName "Mouse"^^xsd:string ; bp:standardName "Mus musculus"^^xsd:string ; bp:xref sgmp:UnificationXref_10090.

sgmp:PublicationXref_1599406 a      bp:PublicationXref ; bp:author "Clark AE"^^xsd:string, "Kozka IJ"^^xsd:string , "Holman GD"^^xsd:string , "Denton RM"^^xsd:string , "Palfreyman RW"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "1599406"^^xsd:string ; bp:source "Biochem J"^^xsd:string ; bp:title "Kinetic resolution of the separate GLUT1 and GLUT4 glucose transport activities in 3T3-L1 cells."^^xsd:string ; bp:year "1992"^^xsd:int.

sgmp:ModificationFeature_G_6298 a      bp:ModificationFeature ; bp:featureLocation sgmp:SequenceSite_6298 ; bp:modificationType sgmp:SequenceModificationVocabulary_G.

sgmp:RelationshipXref_GO_0022891 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0022891"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_3140047.

sgmp:SmallMoleculeReference_75 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_75.

sgmp:PublicationXref_6749843 a      bp:PublicationXref ; bp:author "Mikulecky DC"^^xsd:string, "May JM"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "6749843"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "The simple model of adipocyte hexose transport. Kinetic features, effect of insulin, and network thermodynamic computer simulations."^^xsd:string ; bp:year "1982"^^xsd:int.

sgmp:Transporter_transport_21385_1822 a      bp:Transport ; sbx3:sbSubEntity ex:zerothOrderRateLaw2b ; bp:comment "CommonDirection: IN"^^xsd:string, "The affinity of GLUT4 for glucose is in the sub physiological range (2-5 mM)."^^xsd:string ; bp:conversionDirection "LEFT-TO-RIGHT"^^xsd:string ; bp:left sgmp:SmallMolecule_75, sgmp:State_26425 ; bp:right sgmp:SmallMolecule_75 ; bp:xref sgmp:PublicationXref_7025902, sgmp:PublicationXref_1599406 , sgmp:PublicationXref_447648 , sgmp:PublicationXref_6749843 , sgmp:PublicationXref_8457198.

ex:zerothOrderRateConstantSBORef a      bp:UnificationXref ; bp:comment "forward zeroth order rate constant, continuous case" ; bp:db  "SBO" ; bp:id  "0000048".

sgmp:PublicationXref_7025902 a      bp:PublicationXref ; bp:author "Holman GD"^^xsd:string, "Taylor LP"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "7025902"^^xsd:string ; bp:source "Biochim Biophys Acta"^^xsd:string ; bp:title "Symmetrical kinetic parameters for 3-O-methyl-D-glucose transport in adipocytes in the presence and in the absence of insulin."^^xsd:string ; bp:year "1981"^^xsd:int.

sgmp:ProteinReference_A001046 a      bp:ProteinReference ; bp:organism sgmp:BioSource_Musmusculus ; bp:sequence "MPSGFQQIGSDDGEPPRQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQKVIEQSYNATWLGRQGPGGPDSIPQGTLTTLWALSVAIFSVGGMISSFLIGIISQWLGRKRAMLANNVLAVLGGALMGLANAAASYEILILGRFLIGAYSGLTSGLVPMYVGEIAPTHLRGALGTLNQLAIVIGILVAQVLGLESMLGTATLWPLLLALTVLPALLQLILLPFCPESPRYLYIIRNLEGPARKSLKRLTGWADVSDALAELKDEKRKLERERPMSLLQLLGSRTHRQPLIIAVVLQLSQQLSGINAVFYYSTSIFESAGVGQPAYATIGAGVVNTVFTLVSVLLVERAGRRTLHLLGLAGMCGCAILMTVALLLLERVPAMSYVSIVAIFGFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGFSNWTCNFIVGMGFQYVADAMGPYVFLLFAVLLLGFFIFTFLKVPETRGRTFDQISAAFRRTPSLLEQEVKPSTELEYLGPDEND"^^xsd:string ; bp:xref sgmp:RelationshipXref_GO_0022891, sgmp:RelationshipXref_GO_0005355 , sgmp:RelationshipXref_GO_0005215 , sgmp:UnificationXref_BAB03251 , sgmp:RelationshipXref_GO_0005360 , sgmp:RelationshipXref_GO_0005351.

sgmp:UnificationXref_75 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "75"^^xsd:string.

sgmp:RelationshipTypeVocabulary_3140044 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: IEA"^^xsd:string ; bp:term "sugar:hydrogen symporter activity"^^xsd:string.

sgmp:SmallMolecule_75 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "Glc"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_75 ; bp:standardName "glucose"^^xsd:string.

sgmp:UnificationXref_10090 a      bp:UnificationXref ; bp:db  "Taxonomy"^^xsd:string ; bp:id  "10090"^^xsd:string.

sgmp:SequenceModificationVocabulary_G a      bp:SequenceModificationVocabulary ; bp:term "Glycosylation"^^xsd:string.

sgmp:RelationshipTypeVocabulary_3140046 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: TAS"^^xsd:string ; bp:term "insulin-responsive hydrogen:glucose symporter activity"^^xsd:string.

sgmp:State_26425 a      bp:Protein ; bp:cellularLocation sgmp:CellularLocationVocabulary_GO_0005886 ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "Slc2a4 G"^^xsd:string ; bp:entityReference sgmp:ProteinReference_A001046 ; bp:feature sgmp:ModificationFeature_G_6298 ; bp:standardName "GLUT4"^^xsd:string ; bp:xref sgmp:PublicationXref_2645527.

sgmp:UnificationXref_GO_0005886 a      bp:UnificationXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005886"^^xsd:string.