SBPAX3 SGMP Example 1 in OWL

This is an example of adding kinetic data to BioPAX using SBPAX3 for ligand-receptor binding (C5a receptor) 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.

     0.0010   dissociation constant   dissociation constant 0000282</bp:id> <bp:db>SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBMeasurable> </sbx3:sbSubEntity> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Complex Assembly of C5a and 2(C5aR)/βγ/Gαi-GDP</bp:displayName> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >C5aR forms dimers and probably higher order oligomers. The functional unit remains unclear and might differ based on downstream signaling events.</bp:comment> <bp:left> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_1190"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >C5a</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >C5a</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_1190"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_1190"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1190</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:left> <bp:right> <bp:Complex rdf:about="http://www.signaling-gateway.org/biopax#Complex_24373_1190"> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >C5a/2(C5aR)/βγ/Gαi-GDP</bp:displayName> <bp:component rdf:resource="http://www.signaling-gateway.org/biopax#SmallMolecule_1190"/> <bp:component> <bp:Complex rdf:about="http://www.signaling-gateway.org/biopax#State_24373"> <bp:component rdf:resource="http://www.signaling-gateway.org/biopax#Protein_Afcs_A000037_19818_M71_unknown__GO_0005886"/> <bp:component rdf:resource="http://www.signaling-gateway.org/biopax#Protein_Class_74_GO_0005886"/> <bp:component rdf:resource="http://www.signaling-gateway.org/biopax#Protein_Class_215_GO_0005886"/> <bp:component rdf:resource="http://www.signaling-gateway.org/biopax#Complex_28276_L73_unknown_L126_unknown__GO_0005886"/> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >2(C5aR)/βγ/Gαi-GDP</bp:displayName> <bp:cellularLocation> <bp:CellularLocationVocabulary rdf:about="http://www.signaling-gateway.org/biopax#CellularLocationVocabulary_GO_0005886"> plasma membrane</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_GO_0005886"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005886</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_1899485"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Bonilla-Argudo V</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Siciliano S</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Rollins TE</bp:author> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Proc Natl Acad Sci U S A</bp:source> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1899485</bp:id> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Cianciarulo DN</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Collier K</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1991</bp:year> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Kobayashi S</bp:author> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Purification of the active C5a receptor from human polymorphonuclear leukocytes as a receptor-Gi complex.</bp:title> <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" >Springer MS</bp:author> </bp:PublicationXref> </bp:xref> </bp:Complex> </bp:component> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_12794141"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Ward PA</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Zetoune FS</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >McGuire SR</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Weber CH</bp:author> <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" >Padgaonkar VA</bp:author> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >12794141</bp:id> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Guo RF</bp:author> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >2003</bp:year> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >J Immunol</bp:source> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Huber-Lang MS</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Zuiderweg ER</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Younkin EM</bp:author> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Structure-function relationships of human C5a and C5aR.</bp:title> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Sarma JV</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Lu KT</bp:author> </bp:PublicationXref> </bp:xref> </bp:Complex> </bp:right> <bp:left rdf:resource="http://www.signaling-gateway.org/biopax#State_24373"/> </bp:ComplexAssembly> </rdf:RDF>