SBPAX3 SGMP Example 1 in N3

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. @prefix :       . @prefix rdfs:   . @prefix ex:     . @prefix bp:     . @prefix owl:    . @prefix xsd:    . @prefix sgmp:   . @prefix sbx3:   . @prefix rdf:    . @prefix uome-list: .

sgmp:PublicationXref_1899485 a      bp:PublicationXref ; bp:author "Kobayashi S"^^xsd:string, "Rollins TE"^^xsd:string , "Springer MS"^^xsd:string , "Cianciarulo DN"^^xsd:string , "Siciliano S"^^xsd:string , "Collier K"^^xsd:string , "Bonilla-Argudo V"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "1899485"^^xsd:string ; bp:source "Proc Natl Acad Sci U S A"^^xsd:string ; bp:title "Purification of the active C5a receptor from human polymorphonuclear leukocytes as a receptor-Gi complex."^^xsd:string ; bp:year "1991"^^xsd:int.

sgmp:PublicationXref_12794141 a      bp:PublicationXref ; bp:author "Zuiderweg ER"^^xsd:string, "Lu KT"^^xsd:string , "Guo RF"^^xsd:string , "Padgaonkar VA"^^xsd:string , "Weber CH"^^xsd:string , "Sarma JV"^^xsd:string , "Huber-Lang MS"^^xsd:string , "Younkin EM"^^xsd:string , "McGuire SR"^^xsd:string , "Zetoune FS"^^xsd:string , "Ward PA"^^xsd:string ; bp:db  "pubmed"^^xsd:string ; bp:id  "12794141"^^xsd:string ; bp:source "J Immunol"^^xsd:string ; bp:title "Structure-function relationships of human C5a and C5aR."^^xsd:string ; bp:year "2003"^^xsd:int.

sgmp:SmallMoleculeReference_1190 a      bp:SmallMoleculeReference ; bp:xref sgmp:UnificationXref_1190.

sgmp:Complex_24373_1190 a      bp:Complex ; bp:component sgmp:State_24373, sgmp:SmallMolecule_1190 ; bp:displayName "C5a/2(C5aR)/βγ/Gαi-GDP"^^xsd:string ; bp:xref sgmp:PublicationXref_12794141.

ex:dissocitationConstantSBORef a      bp:UnificationXref ; bp:comment "dissociation constant" ; bp:db  "SBO" ; bp:id  "0000282".

sgmp:UnificationXref_1190 a      bp:UnificationXref ; bp:db  "SGMP"^^xsd:string ; bp:id  "1190"^^xsd:string.

ex:KD1 a      sbx3:SBMeasurable ; sbx3:hasNumber "0.0010"^^xsd:double ; sbx3:hasUnit uome-list:Micromolar ; sbx3:sbTerm ex:dissocitationConstantTerm.

sgmp:State_24373 a      bp:Complex ; bp:cellularLocation sgmp:CellularLocationVocabulary_GO_0005886 ; bp:component sgmp:Complex_28276_L73_unknown_L126_unknown__GO_0005886, sgmp:Protein_Afcs_A000037_19818_M71_unknown__GO_0005886 , sgmp:Protein_Class_74_GO_0005886 , sgmp:Protein_Class_215_GO_0005886 ; bp:displayName "2(C5aR)/βγ/Gαi-GDP"^^xsd:string ; bp:xref sgmp:PublicationXref_1899485.

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

ex:dissocitationConstantTerm a      sbx3:SBVocabulary ; bp:term "dissociation constant" ; bp:xref ex:dissocitationConstantSBORef.

sgmp:CellularLocationVocabulary_GO_0005886 a      bp:CellularLocationVocabulary ; bp:term "plasma membrane"^^xsd:string ; bp:xref sgmp:UnificationXref_GO_0005886.

sgmp:SmallMolecule_1190 a      bp:SmallMolecule ; bp:dataSource sgmp:Provenance_SGMP ; bp:displayName "C5a"^^xsd:string ; bp:entityReference sgmp:SmallMoleculeReference_1190 ; bp:standardName "C5a"^^xsd:string.

sgmp:ComplexAssembly_20088 a      bp:ComplexAssembly ; sbx3:sbSubEntity ex:KD1 ; bp:comment "C5aR forms dimers and probably higher order oligomers. The functional unit remains unclear and might differ based on downstream signaling events."^^xsd:string ; bp:displayName "Complex Assembly of C5a and 2(C5aR)/βγ/Gαi-GDP"^^xsd:string ; bp:left sgmp:State_24373, sgmp:SmallMolecule_1190 ; bp:right sgmp:Complex_24373_1190.

sgmp:UnificationXref_GO_0005886 a      bp:UnificationXref ; bp:db  "Gene Ontology"^^xsd:string ; bp:id  "GO:0005886"^^xsd:string.