SBPAX3 SGMP Example 2b in N3

This is an example of adding kinetic data to BioPAX using SBPAX3 for positive cooperativity enzyme kinetics (Phosphodiesterase 2A, cGMP stimulated) 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: .

ex:hillRateLawSBORef a      bp:UnificationXref ; bp:comment "unmodulated reversible Hill-type rate law" ; bp:db  "SBO" ; bp:id  "0000431".

ex:catalyticRateConstantSBORef a      bp:UnificationXref ; bp:comment "catalytic rate constant" ; bp:db  "SBO" ; bp:id  "0000320".

sgmp:RelationshipXref_GO_0030553 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0030553"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_4000982.

sgmp:UnificationXref_NP_001008548 a      bp:UnificationXref ; bp:db  "RefSeq"^^xsd:string ; bp:id  "NP_001008548"^^xsd:string ; bp:idVersion "1"^^xsd:string.

ex:pseudoDissociationConstantSBORef a      bp:UnificationXref ; bp:comment "pseudo-dissociation constant" ; bp:db  "SBO" ; bp:id  "0000194".

sgmp:CellularLocationVocabulary_GO_0005622 a      bp:CellularLocationVocabulary ; bp:term "intracellular"^^xsd:string ; bp:xref sgmp:UnificationXref_GO_0005622.

sgmp:RelationshipXref_GO_0004114 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0004114"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_4000977.

sgmp:Protein_Afcs_A001750_GO_0005622 a      bp:Protein ; bp:cellularLocation sgmp:CellularLocationVocabulary_GO_0005622 ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "Pde2a"^^xsd:string ; bp:entityReference sgmp:ProteinReference_A001750 ; bp:standardName "Phosphodiesterase 2A, cGMP stimulated"^^xsd:string.

ex:pseudoDissociationConstantTerm a      sbx3:SBVocabulary ; bp:term "pseudo-dissociation constant" ; bp:xref ex:pseudoDissociationConstantSBORef.

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

sgmp:PublicationXref_6276403 a      bp:PublicationXref ; bp:author "Mumby MC"^^xsd:string, "Beavo JA"^^xsd:string , "Martins TJ"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "6276403"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Purification and characterization of a cyclic GMP-stimulated cyclic nucleotide phosphodiesterase from bovine tissues."^^xsd:string ; bp:year "1982"^^xsd:int.

ex:hillRateLawTerm a      sbx3:SBVocabulary ; bp:term "unmodulated reversible Hill-type rate law" ; bp:xref ex:hillRateLawSBORef.

ex:hillCoefficientSBORef a      bp:UnificationXref ; bp:comment "Hill coefficient" ; bp:db  "SBO" ; bp:id  "0000190".

ex:pseudoDissociationConstant2b a      sbx3:SBMeasurable ; sbx3:hasNumber "10.0"^^xsd:double ; sbx3:hasUnit uome-list:Micromolar ; sbx3:sbTerm ex:pseudoDissociationConstantTerm.

sgmp:State_31197 a      bp:Complex ; bp:cellularLocation sgmp:CellularLocationVocabulary_GO_0005622 ; bp:component sgmp:Protein_Afcs_A001750_GO_0005622, sgmp:SmallMolecule_35 ; bp:displayName "PDE2A-cGMP"^^xsd:string ; bp:xref sgmp:PublicationXref_19828435, sgmp:PublicationXref_6276403 , sgmp:PublicationXref_6313664 , sgmp:PublicationXref_12271124 , sgmp:PublicationXref_6263632.

sgmp:PublicationXref_12271124 a      bp:PublicationXref ; bp:author "Wu AY"^^xsd:string, "Martinez SE"^^xsd:string , "Tang XB"^^xsd:string , "Turley S"^^xsd:string , "Glavas NA"^^xsd:string , "Beavo JA"^^xsd:string , "Hol WG"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "12271124"^^xsd:string ; bp:source "Proc Natl Acad Sci U S A"^^xsd:string ; bp:title "The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding."^^xsd:string ; bp:year "2002"^^xsd:int.

sgmp:SmallMolecule_81 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "GMP"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_81 ; bp:standardName "GMP"^^xsd:string.

ex:hillCoefficient2b a      sbx3:SBMeasurable ; sbx3:hasNumber "1.3"^^xsd:double ; sbx3:hasUnit uome-list:Dimensionless ; sbx3:sbTerm ex:hillCoefficientTerm.

ex:hillCoefficientTerm a      sbx3:SBVocabulary ; bp:term "Hill coefficient" ; bp:xref ex:hillCoefficientSBORef.

ex:hillRateLaw2b a      sbx3:SBEntity ; sbx3:sbSubEntity ex:catalyticRateConstant2b, ex:maximalVelocity2b , ex:pseudoDissociationConstant2b , ex:hillCoefficient2b ; sbx3:sbTerm ex:hillRateLawTerm.

ex:maximalVelocity2b a      sbx3:SBMeasurable ; sbx3:hasNumber "120.0"^^xsd:double ; sbx3:hasUnit uome-list:MicromolePerMilligramMinute ; sbx3:sbTerm ex:maximalVelocityTerm.

sgmp:RelationshipXref_GO_0016787 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0016787"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_4000980.

sgmp:SmallMolecule_35 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "cGMP (cyclic GMP)"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_35 ; bp:standardName "cGMP (cyclic GMP)"^^xsd:string.

sgmp:UnificationXref_81 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "81"^^xsd:string.

sgmp:RelationshipXref_GO_0030552 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0030552"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_4000981.

sgmp:BiochemicalReaction_4285 a      bp:BiochemicalReaction ; bp:displayName "cGMP (cyclic GMP) -> GMP"^^xsd:string ; bp:left sgmp:SmallMolecule_35 ; bp:right sgmp:SmallMolecule_81.

ex:maximalVelocityTerm a      sbx3:SBVocabulary ; bp:term "maximal velocity" ; bp:xref ex:maximalVelocitySBORef.

sgmp:RelationshipTypeVocabulary_4000980 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: IEA"^^xsd:string ; bp:term "hydrolase activity"^^xsd:string.

sgmp:PublicationXref_19828435 a      bp:PublicationXref ; bp:author "Dillman KS"^^xsd:string, "Forman MD"^^xsd:string , "Fennell KF"^^xsd:string , "Pandit J"^^xsd:string , "Menniti FS"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "19828435"^^xsd:string ; bp:source "Proc Natl Acad Sci U S A"^^xsd:string ; bp:title "Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct."^^xsd:string ; bp:year "2009"^^xsd:int.

ex:catalyticRateConstant2b a      sbx3:SBMeasurable ; sbx3:hasNumber "210.5"^^xsd:double ; sbx3:hasUnit uome-list:PerSecond ; sbx3:sbTerm ex:catalyticRateConstantTerm.

sgmp:UnificationXref_GO_0005622 a      bp:UnificationXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005622"^^xsd:string.

sgmp:Reaction_31197_4285 a      bp:Catalysis ; sbx3:sbSubEntity ex:hillRateLaw2b ; bp:catalysisDirection "LEFT-TO-RIGHT"^^xsd:string ; bp:controlType "ACTIVATION"^^xsd:string ; bp:controlled sgmp:BiochemicalReaction_4285 ; bp:controller sgmp:State_31197 ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "cGMP (cyclic GMP) -> GMP"^^xsd:string.

sgmp:PublicationXref_6313664 a      bp:PublicationXref ; bp:author "Vaughan M"^^xsd:string, "Manganiello VC"^^xsd:string , "Yamamoto T"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "6313664"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Purification and characterization of cyclic GMP-stimulated cyclic nucleotide phosphodiesterase from calf liver. Effects of divalent cations on activity."^^xsd:string ; bp:year "1983"^^xsd:int.

sgmp:UnificationXref_35 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "35"^^xsd:string.

sgmp:SmallMoleculeReference_35 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_35.

sgmp:SmallMoleculeReference_81 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_81.

sgmp:ProteinReference_A001750 a      bp:ProteinReference ; bp:organism sgmp:BioSource_Musmusculus ; bp:sequence "MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPQPCADSLQDALLSLGAVIDIAGLRQAARDALSAVLPKVETVYTYLLDGESRLVCEDPPHELPQEGKIREAVISQKRLSCNGLGPSDLLGKPLARLVAPLAPDMQVLVIPLLDKETGSVAAVILVHCGQLSDSEEQSLQVVEKHALVALRRVQALQQRRPEAVQNTSVDASEDQKDEKGYTDHDRKILQLCGELFDLDATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTMGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMKVSDDEYTKLLHDGIQPVAAIDSNFANFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELSNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNRQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPVNGCCSLEG"^^xsd:string ; bp:xref sgmp:RelationshipXref_GO_0004114, sgmp:RelationshipXref_GO_0000166 , sgmp:RelationshipXref_GO_0016787 , sgmp:RelationshipXref_GO_0047555 , sgmp:RelationshipXref_GO_0030553 , sgmp:RelationshipXref_GO_0003824 , sgmp:RelationshipXref_GO_0030552 , sgmp:UnificationXref_NP_001008548 , sgmp:RelationshipXref_GO_0042803 , sgmp:RelationshipXref_GO_0004118 , sgmp:RelationshipXref_GO_0008081 , sgmp:RelationshipXref_GO_0046872.

sgmp:PublicationXref_6263632 a      bp:PublicationXref ; bp:author "Jastorff B"^^xsd:string, "Erneux C"^^xsd:string , "Baraniak J"^^xsd:string , "Dumont JE"^^xsd:string , "Stec WJ"^^xsd:string , "Petridis G"^^xsd:string , "Abbad EG"^^xsd:string , "Couchie D"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "6263632"^^xsd:string ; bp:source "Eur J Biochem"^^xsd:string ; bp:title "Specificity of cyclic GMP activation of a multi-substrate cyclic nucleotide phosphodiesterase from rat liver."^^xsd:string ; bp:year "1981"^^xsd:int.

sgmp:RelationshipXref_GO_0008081 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0008081"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_4000979.

ex:maximalVelocitySBORef a      bp:UnificationXref ; bp:comment "maximal velocity" ; bp:db  "SBO" ; bp:id  "0000324".

ex:catalyticRateConstantTerm a      sbx3:SBVocabulary ; bp:term "catalytic rate constant" ; bp:xref ex:catalyticRateConstantSBORef.