SBPAX3 SGMP Example 2b in OWL

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.

       210.5   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/example2b#maximalVelocity2b"> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#MicromolePerMilligramMinute"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >120.0</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2b#maximalVelocityTerm"> maximal velocity</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2b#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/example2b#hillCoefficient2b"> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#Dimensionless"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >1.3</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2b#hillCoefficientTerm"> Hill coefficient</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2b#hillCoefficientSBORef"> <bp:comment>Hill coefficient</bp:comment> <bp:id>0000190</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/example2b#pseudoDissociationConstant2b"> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#Micromolar"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >10.0</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2b#pseudoDissociationConstantTerm"> pseudo-dissociation constant</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2b#pseudoDissociationConstantSBORef"> <bp:comment>pseudo-dissociation constant</bp:comment> <bp:id>0000194</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example2b#hillRateLawTerm"> unmodulated reversible Hill-type rate law</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example2b#hillRateLawSBORef"> <bp:comment>unmodulated reversible Hill-type rate law</bp:comment> <bp:id>0000431</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" >cGMP (cyclic GMP) -&gt; GMP</bp:displayName> <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >ACTIVATION</bp:controlType> <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:controller> <bp:Complex rdf:about="http://www.signaling-gateway.org/biopax#State_31197"> <bp:component> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_35"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >cGMP (cyclic GMP)</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >cGMP (cyclic GMP)</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_35"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_35"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >35</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:component> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_6313664"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Yamamoto T</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Manganiello VC</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Vaughan M</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" >6313664</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Purification and characterization of cyclic GMP-stimulated cyclic nucleotide phosphodiesterase from calf liver. Effects of divalent cations on activity.</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" >1983</bp:year> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_6263632"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Couchie D</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1981</bp:year> <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" >Baraniak J</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Abbad EG</bp:author> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Specificity of cyclic GMP activation of a multi-substrate cyclic nucleotide phosphodiesterase from rat liver.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Erneux C</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Dumont JE</bp:author> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Eur J Biochem</bp:source> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >6263632</bp:id> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Stec WJ</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Jastorff B</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Petridis G</bp:author> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_6276403"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Martins TJ</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mumby MC</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Beavo JA</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" >6276403</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Purification and characterization of a cyclic GMP-stimulated cyclic nucleotide phosphodiesterase from bovine tissues.</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" >1982</bp:year> </bp:PublicationXref> </bp:xref> <bp:component> <bp:Protein rdf:about="http://www.signaling-gateway.org/biopax#Protein_Afcs_A001750_GO_0005622"> <bp:entityReference> <bp:ProteinReference rdf:about="http://www.signaling-gateway.org/biopax#ProteinReference_A001750"> <bp:xref rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0003824"/> <bp:xref rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0042803"/> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0008081"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0008081</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_4000979"/> </bp:RelationshipXref> </bp:xref> <bp:organism rdf:resource="http://www.signaling-gateway.org/biopax#BioSource_Musmusculus"/> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0030553"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0030553</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_4000982"/> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0030552"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0030552</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_4000981"/> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_NP_001008548"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >NP_001008548</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:sequence rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPQPCADSLQDALLSLGAVIDIAGLRQAARDALSAVLPKVETVYTYLLDGESRLVCEDPPHELPQEGKIREAVISQKRLSCNGLGPSDLLGKPLARLVAPLAPDMQVLVIPLLDKETGSVAAVILVHCGQLSDSEEQSLQVVEKHALVALRRVQALQQRRPEAVQNTSVDASEDQKDEKGYTDHDRKILQLCGELFDLDATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTMGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFDGGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYHMKVSDDEYTKLLHDGIQPVAAIDSNFANFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELSNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNRQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEEYEVPDLDGTRAPVNGCCSLEG</bp:sequence> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0004114"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0004114</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_4000977"/> </bp:RelationshipXref> </bp:xref> <bp:xref rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0000166"/> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0016787"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0016787</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_4000980"> hydrolase 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 rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0047555"/> <bp:xref rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0046872"/> <bp:xref rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0004118"/> </bp:ProteinReference> </bp:entityReference> <bp:dataSource rdf:resource="http://www.signaling-gateway.org/biopax#Provenance_SGMP"/> <bp:cellularLocation> <bp:CellularLocationVocabulary rdf:about="http://www.signaling-gateway.org/biopax#CellularLocationVocabulary_GO_0005622"> intracellular</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_GO_0005622"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005622</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:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Phosphodiesterase 2A, cGMP stimulated</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Pde2a</bp:displayName> </bp:Protein> </bp:component> <bp:cellularLocation rdf:resource="http://www.signaling-gateway.org/biopax#CellularLocationVocabulary_GO_0005622"/> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_12271124"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Turley S</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Martinez SE</bp:author> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >12271124</bp:id> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Proc Natl Acad Sci U S A</bp:source> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Beavo JA</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Hol WG</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Wu AY</bp:author> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Glavas NA</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Tang XB</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >2002</bp:year> </bp:PublicationXref> </bp:xref> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >PDE2A-cGMP</bp:displayName> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_19828435"> <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >pubmed</bp:db> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Fennell KF</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Menniti FS</bp:author> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >19828435</bp:id> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >2009</bp:year> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Proc Natl Acad Sci U S A</bp:source> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Dillman KS</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Forman MD</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Pandit J</bp:author> </bp:PublicationXref> </bp:xref> </bp:Complex> </bp:controller> <bp:controlled> <bp:BiochemicalReaction rdf:about="http://www.signaling-gateway.org/biopax#BiochemicalReaction_4285"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >cGMP (cyclic GMP) -&gt; GMP</bp:displayName> <bp:left rdf:resource="http://www.signaling-gateway.org/biopax#SmallMolecule_35"/> <bp:right> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_81"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GMP</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GMP</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_81"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_81"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >81</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>