SBPAX3 SGMP Example 2a in OWL

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.

       0.9   catalytic rate constant   catalytic rate constant</bp:comment> <bp:id>0000320</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <sbx3:sbSubEntity> <sbx3:SBMeasurable rdf:about="http://example.org/sgmp/example2a#maximalVelocity2a"> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#MicromolePerMilligramMinute"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >0.6</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2a#maximalVelocityTerm"> maximal velocity</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2a#maximalVelocitySBORef"> <bp:comment>maximal velocity</bp:comment> <bp:id>0000324</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <sbx3:sbSubEntity> <sbx3:SBMeasurable rdf:about="http://example.org/sgmp/example2a#MichaelisConstant2aPhosphatidylinositol"> <sbx3:sbSubEntity> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_146"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >phosphatidylinositol</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >phosphatidylinositol</bp:displayName> <bp:dataSource> <bp:Provenance rdf:about="http://www.signaling-gateway.org/biopax#Provenance_SGMP"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >SGMP</bp:displayName> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Signaling Gateway Molecule Pages</bp:standardName> </bp:Provenance> </bp:dataSource> <bp:entityReference> <bp:SmallMoleculeReference rdf:about="http://www.signaling-gateway.org/biopax#SmallMoleculeReference_146"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_146"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >146</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >SGMP</bp:db> </bp:UnificationXref> </bp:xref> </bp:SmallMoleculeReference> </bp:entityReference> </bp:SmallMolecule> </sbx3:sbSubEntity> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#Micromolar"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >1000.0</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2a#michaelisConstantTerm"> Michaelis constant for substrate</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2a#michaelisConstantSBORef"> <bp:comment>Michaelis constant for substrate</bp:comment> <bp:id>0000322</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <sbx3:sbSubEntity> <sbx3:SBMeasurable rdf:about="http://example.org/sgmp/example2a#MichaelisConstant2aATP"> <sbx3:sbSubEntity> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_26"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ATP</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ATP</bp:displayName> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:entityReference> <bp:SmallMoleculeReference rdf:about="http://www.signaling-gateway.org/biopax#SmallMoleculeReference_26"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_26"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >26</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >SGMP</bp:db> </bp:UnificationXref> </bp:xref> </bp:SmallMoleculeReference> </bp:entityReference> </bp:SmallMolecule> </sbx3:sbSubEntity> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#Micromolar"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >400.0</sbx3:hasNumber> <sbx3:sbTerm rdf:resource="http://example.org/sgmp/example2a#michaelisConstantTerm"/> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2a#michaelisMentenKineticsWithTwoSubstratesTerm"> Michaelis-Menten kinetics for two substrates</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2a#michaelisMentenKineticsWithTwoSubstratesSBORef"> <bp:comment>Michaelis-Menten kinetics for two substrates</bp:comment> <bp:id>0000432</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBEntity> </sbx3:sbSubEntity> <bp:catalysisDirection rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >LEFT-TO-RIGHT</bp:catalysisDirection> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ATP + phosphatidylinositol -&gt; ADP + phosphatidylinositol 4-phosphate</bp:displayName> <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ACTIVATION</bp:controlType> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:controller> <bp:Protein rdf:about="http://www.signaling-gateway.org/biopax#State_7793"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Pi4kb</bp:displayName> <bp:cellularLocation> <bp:CellularLocationVocabulary rdf:about="http://www.signaling-gateway.org/biopax#CellularLocationVocabulary_GO_0000139"> Golgi membrane</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_GO_0000139"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0000139</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gene Ontology</bp:db> </bp:UnificationXref> </bp:xref> </bp:CellularLocationVocabulary> </bp:cellularLocation> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_10567405"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Takemoto JY</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Hama H</bp:author> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >J Biol Chem</bp:source> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1999</bp:year> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Thorner J</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Schnieders EA</bp:author> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Direct involvement of phosphatidylinositol 4-phosphate in secretion in the yeast Saccharomyces cerevisiae.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >DeWald DB</bp:author> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >10567405</bp:id> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_10587649"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Walch-Solimena C</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Novick P</bp:author> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >10587649</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >The yeast phosphatidylinositol-4-OH kinase pik1 regulates secretion at the Golgi.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Nat Cell Biol</bp:source> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1999</bp:year> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_11704666"> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Weisz OA</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Bruns JR</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Jeromin A</bp:author> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >J Biol Chem</bp:source> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >11704666</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Multiple roles for phosphatidylinositol 4-kinase in biosynthetic transport in polarized Madin-Darby canine kidney cells.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Ellis MA</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >2002</bp:year> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_10559940"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Meyers R</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >De Matteis MA</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Di Tullio G</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1999</bp:year> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Nat Cell Biol</bp:source> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >10559940</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Iurisci C</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Pertile P</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Corda D</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Luini A</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Marra P</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Godi A</bp:author> </bp:PublicationXref> </bp:xref> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Phosphatidylinositol-4-kinase type III beta</bp:standardName> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_9148941"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Wong K</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Meyers ddR</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Cantley LC</bp:author> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >9148941</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Subcellular locations of phosphatidylinositol 4-kinase isoforms.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >J Biol Chem</bp:source> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1997</bp:year> </bp:PublicationXref> </bp:xref> <bp:entityReference> <bp:ProteinReference rdf:about="http://www.signaling-gateway.org/biopax#ProteinReference_A001778"> <bp:sequence rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >MGDMVVEPATLKPTSEPTPTPSGNNGGSLLSVITEGVGELSVIDPEVAQKACQEVLEKVKLLHGGVAISSKGTPLELVNGDGVDNEIRCLDDPPAQIREEEDEMGAGVASGTAKGARRRRQNNSAKQSWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFYFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSDMHISTQRHSRGTKLRKLILSDELKPAHRKRELPTLSPAPDTGLSPSKRTHQRSKSDATASISLSSNLKRTASNPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRIRSTRSVENLPECGITHEQRAGSFSTVPNYDNDDEAWSVDDIGELQVELPEVHTNSCDNISQFSVDSITSQESKEPVFIAAGDIRRRLSEQLAHTPTAFKRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTTEFVDVMGGLNGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRSITTKLYDGFQYLTNGIM</bp:sequence> <bp:organism> <bp:BioSource rdf:about="http://www.signaling-gateway.org/biopax#BioSource_Musmusculus"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mouse</bp:displayName> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mus musculus</bp:standardName> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_10090"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >10090</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Taxonomy</bp:db> </bp:UnificationXref> </bp:xref> </bp:BioSource> </bp:organism> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_NP_780565"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >NP_780565</bp:id> <bp:idVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1</bp:idVersion> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >RefSeq</bp:db> </bp:UnificationXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0016301"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0016301</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gene Ontology</bp:db> <bp:relationshipType> <bp:RelationshipTypeVocabulary rdf:about="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_652775"> kinase activity</bp:term> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >go evidence code: IEA</bp:comment> </bp:RelationshipTypeVocabulary> </bp:relationshipType> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0004428"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0004428</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gene Ontology</bp:db> <bp:relationshipType> <bp:RelationshipTypeVocabulary rdf:about="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_652774"> inositol or phosphatidylinositol kinase activity</bp:term> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >go evidence code: ISS</bp:comment> </bp:RelationshipTypeVocabulary> </bp:relationshipType> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0016740"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0016740</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gene Ontology</bp:db> <bp:relationshipType rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_652777"/> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0016773"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0016773</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gene Ontology</bp:db> <bp:relationshipType rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_652776"/> </bp:RelationshipXref> </bp:xref> </bp:ProteinReference> </bp:entityReference> </bp:Protein> </bp:controller> <bp:controlled> <bp:BiochemicalReaction rdf:about="http://www.signaling-gateway.org/biopax#BiochemicalReaction_3632"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ATP + phosphatidylinositol -&gt; ADP + phosphatidylinositol 4-phosphate</bp:displayName> <bp:left rdf:resource="http://www.signaling-gateway.org/biopax#SmallMolecule_26"/> <bp:left rdf:resource="http://www.signaling-gateway.org/biopax#SmallMolecule_146"/> <bp:right> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_13"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ADP</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ADP</bp:displayName> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:entityReference> <bp:SmallMoleculeReference rdf:about="http://www.signaling-gateway.org/biopax#SmallMoleculeReference_13"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_13"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >13</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >SGMP</bp:db> </bp:UnificationXref> </bp:xref> </bp:SmallMoleculeReference> </bp:entityReference> </bp:SmallMolecule> </bp:right> <bp:right> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_151"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >phosphatidylinositol 4-phosphate</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >phosphatidylinositol 4-phosphate</bp:displayName> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:entityReference> <bp:SmallMoleculeReference rdf:about="http://www.signaling-gateway.org/biopax#SmallMoleculeReference_151"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_151"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >151</bp:id> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >SGMP</bp:db> </bp:UnificationXref> </bp:xref> </bp:SmallMoleculeReference> </bp:entityReference> </bp:SmallMolecule> </bp:right> </bp:BiochemicalReaction> </bp:controlled> </bp:Catalysis> </rdf:RDF>