SBPAX3 SGMP Example 1 in N3

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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 :        <http://www.signaling-gateway.org/biopax#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ex:      <http://example.org/sgmp/example1#> .
@prefix bp:      <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix owl:     <http://www.w3.org/2002/07/owl#> .
@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
@prefix sgmp:    <http://www.signaling-gateway.org/biopax#> .
@prefix sbx3:    <http://vcell.org/sbpax3#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix uome-list:  <http://vcell.org/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 .