SBPAX3 SGMP Example 2a in N3

This is an example of adding kinetic data to BioPAX using SBPAX3 for Michaelis-Menten enzyme kinetics (Phosphatidylinositol-4-kinase type III beta) 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:UnificationXref_NP_780565 a      bp:UnificationXref ; bp:db  "RefSeq"^^xsd:string ; bp:id  "NP_780565"^^xsd:string ; bp:idVersion "1"^^xsd:string.

ex:maximalVelocity2a a      sbx3:SBMeasurable ; sbx3:hasNumber "0.6"^^xsd:double ; sbx3:hasUnit uome-list:MicromolePerMilligramMinute ; sbx3:sbTerm ex:maximalVelocityTerm.

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

sgmp:UnificationXref_13 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "13"^^xsd:string.

sgmp:RelationshipXref_GO_0016773 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0016773"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_652776.

ex:MichaelisMentenRateLaw2a a      sbx3:SBEntity ; sbx3:sbSubEntity ex:maximalVelocity2a, ex:MichaelisConstant2aPhosphatidylinositol , ex:MichaelisConstant2aATP , ex:catalyticRateConstant2a ; sbx3:sbTerm ex:michaelisMentenKineticsWithTwoSubstratesTerm.

ex:michaelisConstantSBORef a      bp:UnificationXref ; bp:comment "Michaelis constant for substrate" ; bp:db  "SBO" ; bp:id  "0000322".

sgmp:SmallMolecule_151 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "phosphatidylinositol 4-phosphate"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_151 ; bp:standardName "phosphatidylinositol 4-phosphate"^^xsd:string.

sgmp:SmallMolecule_13 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "ADP"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_13 ; bp:standardName "ADP"^^xsd:string.

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

sgmp:State_7793 a      bp:Protein ; bp:cellularLocation sgmp:CellularLocationVocabulary_GO_0000139 ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "Pi4kb"^^xsd:string ; bp:entityReference sgmp:ProteinReference_A001778 ; bp:standardName "Phosphatidylinositol-4-kinase type III beta"^^xsd:string ; bp:xref sgmp:PublicationXref_10567405, sgmp:PublicationXref_10559940 , sgmp:PublicationXref_11704666 , sgmp:PublicationXref_9148941 , sgmp:PublicationXref_10587649.

sgmp:RelationshipTypeVocabulary_652774 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: ISS"^^xsd:string ; bp:term "inositol or phosphatidylinositol kinase activity"^^xsd:string.

ex:MichaelisConstant2aATP a      sbx3:SBMeasurable ; sbx3:hasNumber "400.0"^^xsd:double ; sbx3:hasUnit uome-list:Micromolar ; sbx3:sbSubEntity sgmp:SmallMolecule_26 ; sbx3:sbTerm ex:michaelisConstantTerm.

ex:catalyticRateConstant2a a      sbx3:SBMeasurable ; sbx3:hasNumber "0.9"^^xsd:double ; sbx3:hasUnit uome-list:PerSecond ; sbx3:sbTerm ex:catalyticRateConstantTerm.

ex:michaelisConstantTerm a      sbx3:SBVocabulary ; bp:term "Michaelis constant for substrate" ; bp:xref ex:michaelisConstantSBORef.

sgmp:ProteinReference_A001778 a      bp:ProteinReference ; bp:organism sgmp:BioSource_Musmusculus ; bp:sequence "MGDMVVEPATLKPTSEPTPTPSGNNGGSLLSVITEGVGELSVIDPEVAQKACQEVLEKVKLLHGGVAISSKGTPLELVNGDGVDNEIRCLDDPPAQIREEEDEMGAGVASGTAKGARRRRQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFYFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKLRKLILSDELKPAHRKRELPTLSPAPDTGLSPSKRTHQRSKSDATASISLSSNLKRTASNPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRIRSTRSVENLPECGITHEQRAGSFSTVPNYDNDDEAWSVDDIGELQVELPEVHTNSCDNISQFSVDSITSQESKEPVFIAAGDIRRRLSEQLAHTPTAFKRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTTEFVDVMGGLNGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRSITTKLYDGFQYLTNGIM"^^xsd:string ; bp:xref sgmp:UnificationXref_NP_780565, sgmp:RelationshipXref_GO_0004428 , sgmp:RelationshipXref_GO_0016301 , sgmp:RelationshipXref_GO_0016773 , sgmp:RelationshipXref_GO_0016740.

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

sgmp:UnificationXref_26 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "26"^^xsd:string.

sgmp:SmallMoleculeReference_26 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_26.

sgmp:SmallMolecule_146 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "phosphatidylinositol"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_146 ; bp:standardName "phosphatidylinositol"^^xsd:string.

sgmp:PublicationXref_10567405 a      bp:PublicationXref ; bp:author "Schnieders EA"^^xsd:string, "Takemoto JY"^^xsd:string , "Thorner J"^^xsd:string , "DeWald DB"^^xsd:string , "Hama H"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "10567405"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Direct involvement of phosphatidylinositol 4-phosphate in secretion in the yeast Saccharomyces cerevisiae."^^xsd:string ; bp:year "1999"^^xsd:int.

sgmp:SmallMolecule_26 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "ATP"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_26 ; bp:standardName "ATP"^^xsd:string.

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

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

sgmp:SmallMoleculeReference_146 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_146.

sgmp:RelationshipXref_GO_0004428 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0004428"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_652774.

sgmp:UnificationXref_151 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "151"^^xsd:string.

sgmp:UnificationXref_GO_0000139 a      bp:UnificationXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0000139"^^xsd:string.

ex:michaelisMentenKineticsWithTwoSubstratesSBORef a      bp:UnificationXref ; bp:comment "Michaelis-Menten kinetics for two substrates" ; bp:db  "SBO" ; bp:id  "0000432".

sgmp:Reaction_7793_3632 a      bp:Catalysis ; sbx3:sbSubEntity ex:MichaelisMentenRateLaw2a ; bp:catalysisDirection "LEFT-TO-RIGHT"^^xsd:string ; bp:controlType "ACTIVATION"^^xsd:string ; bp:controlled sgmp:BiochemicalReaction_3632 ; bp:controller sgmp:State_7793 ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "ATP + phosphatidylinositol -> ADP + phosphatidylinositol 4-phosphate"^^xsd:string.

sgmp:RelationshipTypeVocabulary_652775 a      bp:RelationshipTypeVocabulary ; bp:comment "go evidence code: IEA"^^xsd:string ; bp:term "kinase activity"^^xsd:string.

sgmp:CellularLocationVocabulary_GO_0000139 a      bp:CellularLocationVocabulary ; bp:term "Golgi membrane"^^xsd:string ; bp:xref sgmp:UnificationXref_GO_0000139.

sgmp:PublicationXref_10559940 a      bp:PublicationXref ; bp:author "Luini A"^^xsd:string, "Meyers R"^^xsd:string , "Pertile P"^^xsd:string , "Godi A"^^xsd:string , "Di Tullio G"^^xsd:string , "Corda D"^^xsd:string , "De Matteis MA"^^xsd:string , "Iurisci C"^^xsd:string , "Marra P"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "10559940"^^xsd:string ; bp:source "Nat Cell Biol"^^xsd:string ; bp:title "ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex."^^xsd:string ; bp:year "1999"^^xsd:int.

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

sgmp:SmallMoleculeReference_13 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_13.

sgmp:UnificationXref_146 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "146"^^xsd:string.

sgmp:SmallMoleculeReference_151 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_151.

sgmp:RelationshipXref_GO_0016301 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0016301"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_652775.

ex:michaelisMentenKineticsWithTwoSubstratesTerm a      sbx3:SBVocabulary ; bp:term "Michaelis-Menten kinetics for two substrates" ; bp:xref ex:michaelisMentenKineticsWithTwoSubstratesSBORef.

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

ex:MichaelisConstant2aPhosphatidylinositol a      sbx3:SBMeasurable ; sbx3:hasNumber "1000.0"^^xsd:double ; sbx3:hasUnit uome-list:Micromolar ; sbx3:sbSubEntity sgmp:SmallMolecule_146 ; sbx3:sbTerm ex:michaelisConstantTerm.

sgmp:RelationshipXref_GO_0016740 a      bp:RelationshipXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0016740"^^xsd:string ; bp:relationshipType sgmp:RelationshipTypeVocabulary_652777.

sgmp:BiochemicalReaction_3632 a      bp:BiochemicalReaction ; bp:displayName "ATP + phosphatidylinositol -> ADP + phosphatidylinositol 4-phosphate"^^xsd:string ; bp:left sgmp:SmallMolecule_146, sgmp:SmallMolecule_26 ; bp:right sgmp:SmallMolecule_151, sgmp:SmallMolecule_13.

sgmp:PublicationXref_11704666 a      bp:PublicationXref ; bp:author "Jeromin A"^^xsd:string, "Bruns JR"^^xsd:string , "Weisz OA"^^xsd:string , "Ellis MA"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "11704666"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Multiple roles for phosphatidylinositol 4-kinase in biosynthetic transport in polarized Madin-Darby canine kidney cells."^^xsd:string ; bp:year "2002"^^xsd:int.

sgmp:PublicationXref_10587649 a      bp:PublicationXref ; bp:author "Novick P"^^xsd:string, "Walch-Solimena C"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "10587649"^^xsd:string ; bp:source "Nat Cell Biol"^^xsd:string ; bp:title "The yeast phosphatidylinositol-4-OH kinase pik1 regulates secretion at the Golgi."^^xsd:string ; bp:year "1999"^^xsd:int.

sgmp:PublicationXref_9148941 a      bp:PublicationXref ; bp:author "Wong K"^^xsd:string, "Meyers ddR"^^xsd:string , "Cantley LC"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "9148941"^^xsd:string ; bp:source "J Biol Chem"^^xsd:string ; bp:title "Subcellular locations of phosphatidylinositol 4-kinase isoforms."^^xsd:string ; bp:year "1997"^^xsd:int.