SBPAX3 SGMP Example 4 in OWL

This is an example of adding kinetic data to BioPAX using SBPAX3 for glucose transport kinetics (GLUT4) 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.

    Biochem J Clark AE Kinetic resolution of the separate GLUT1 and GLUT4 glucose transport activities in 3T3-L1 cells. 1992 Palfreyman RW pubmed <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1599406</bp:id> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Holman GD</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Kozka IJ</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Denton RM</bp:author> </bp:PublicationXref> </bp:xref> <bp:conversionDirection rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >LEFT-TO-RIGHT</bp:conversionDirection> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >The affinity of GLUT4 for glucose is in the sub physiological range (2-5 mM).</bp:comment> <sbx3:sbSubEntity> <sbx3:SBEntity rdf:about="http://example.org/sgmp/example4#zerothOrderRateLaw2b"> <sbx3:sbSubEntity> <sbx3:SBMeasurable rdf:about="http://example.org/sgmp/example4#zerothOrderRateConstant4"> <sbx3:hasUnit rdf:resource="http://vcell.org/uome/list#PerMinute"/> <sbx3:hasNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#double" >80000.0</sbx3:hasNumber> <sbx3:sbTerm> <sbx3:SBVocabulary rdf:about="http://example.org/sgmp/example4#zerothOrderRateConstantTerm"> <bp:term>forward zeroth order rate constant, continuous case</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example4#zerothOrderRateConstantSBORef"> <bp:comment>forward zeroth order rate constant, continuous case</bp:comment> <bp:id>0000048</bp:id> 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/example4#zerothOrderRateLawTerm"> <bp:term>mass action rate law for zeroth order irreversible reactions, continuous scheme</bp:term> <bp:xref> <bp:UnificationXref rdf:about="http://example.org/sgmp/example4#zerothOrderRateLawSBORef"> <bp:comment>mass action rate law for zeroth order irreversible reactions, continuous scheme</bp:comment> <bp:id>0000047</bp:id> SBO</bp:db> </bp:UnificationXref> </bp:xref> </sbx3:SBVocabulary> </sbx3:sbTerm> </sbx3:SBEntity> </sbx3:sbSubEntity> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_447648"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Whitesell RR</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gliemann J</bp:author> pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >447648</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Kinetic parameters of transport of 3-O-methylglucose and glucose in adipocytes.</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" >1979</bp:year> </bp:PublicationXref> </bp:xref> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_6749843"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >May JM</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mikulecky DC</bp:author> pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >6749843</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >The simple model of adipocyte hexose transport. Kinetic features, effect of insulin, and network thermodynamic computer simulations.</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:left> <bp:SmallMolecule rdf:about="http://www.signaling-gateway.org/biopax#SmallMolecule_75"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >glucose</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Glc</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_75"> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_75"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >75</bp:id> SGMP</bp:db> </bp:UnificationXref> </bp:xref> </bp:SmallMoleculeReference> </bp:entityReference> </bp:SmallMolecule> </bp:left> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_8457198"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Thomas HM</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Takeda J</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Gould GW</bp:author> pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >8457198</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Differential targeting of glucose transporter isoforms heterologously expressed in Xenopus oocytes.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Biochem J</bp:source> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1993</bp:year> </bp:PublicationXref> </bp:xref> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >CommonDirection: IN</bp:comment> <bp:xref> <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_7025902"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Taylor LP</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Holman GD</bp:author> pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >7025902</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Symmetrical kinetic parameters for 3-O-methyl-D-glucose transport in adipocytes in the presence and in the absence of insulin.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Biochim Biophys Acta</bp:source> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1981</bp:year> </bp:PublicationXref> </bp:xref> <bp:right rdf:resource="http://www.signaling-gateway.org/biopax#SmallMolecule_75"/> <bp:left> <bp:Protein rdf:about="http://www.signaling-gateway.org/biopax#State_26425"> <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GLUT4</bp:standardName> <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Slc2a4 G</bp:displayName> <bp:feature> <bp:ModificationFeature rdf:about="http://www.signaling-gateway.org/biopax#ModificationFeature_G_6298"> <bp:featureLocation> <bp:SequenceSite rdf:about="http://www.signaling-gateway.org/biopax#SequenceSite_6298"> <bp:positionStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >EQUAL</bp:positionStatus> <bp:sequencePosition rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >57</bp:sequencePosition> </bp:SequenceSite> </bp:featureLocation> <bp:modificationType> <bp:SequenceModificationVocabulary rdf:about="http://www.signaling-gateway.org/biopax#SequenceModificationVocabulary_G"> <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Glycosylation</bp:term> </bp:SequenceModificationVocabulary> </bp:modificationType> </bp:ModificationFeature> </bp:feature> <bp:entityReference> <bp:ProteinReference rdf:about="http://www.signaling-gateway.org/biopax#ProteinReference_A001046"> <bp:sequence rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >MPSGFQQIGSDDGEPPRQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQKVIEQSYNATWLGRQGPGGPDSIPQGTLTTLWALSVAIFSVGGMISSFLIGIISQWLGRKRAMLANNVLAVLGGALMGLANAAASYEILILGRFLIGAYSGLTSGLVPMYVGEIAPTHLRGALGTLNQLAIVIGILVAQVLGLESMLGTATLWPLLLALTVLPALLQLILLPFCPESPRYLYIIRNLEGPARKSLKRLTGWADVSDALAELKDEKRKLERERPMSLLQLLGSRTHRQPLIIAVVLQLSQQLSGINAVFYYSTSIFESAGVGQPAYATIGAGVVNTVFTLVSVLLVERAGRRTLHLLGLAGMCGCAILMTVALLLLERVPAMSYVSIVAIFGFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGFSNWTCNFIVGMGFQYVADAMGPYVFLLFAVLLLGFFIFTFLKVPETRGRTFDQISAAFRRTPSLLEQEVKPSTELEYLGPDEND</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> Taxonomy</bp:db> </bp:UnificationXref> </bp:xref> </bp:BioSource> </bp:organism> <bp:xref> <bp:UnificationXref rdf:about="http://www.signaling-gateway.org/biopax#UnificationXref_BAB03251"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >BAB03251</bp:id> <bp:idVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >1</bp:idVersion> DDBJ</bp:db> </bp:UnificationXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0005215"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005215</bp:id> Gene Ontology</bp:db> <bp:relationshipType> <bp:RelationshipTypeVocabulary rdf:about="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_3140043"> <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >transporter 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_0005351"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005351</bp:id> Gene Ontology</bp:db> <bp:relationshipType> <bp:RelationshipTypeVocabulary rdf:about="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_3140044"> <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >sugar:hydrogen symporter 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_0005355"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005355</bp:id> Gene Ontology</bp:db> <bp:relationshipType rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_3140045"/> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0005360"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0005360</bp:id> Gene Ontology</bp:db> <bp:relationshipType> <bp:RelationshipTypeVocabulary rdf:about="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_3140046"> <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >insulin-responsive hydrogen:glucose symporter activity</bp:term> <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >go evidence code: TAS</bp:comment> </bp:RelationshipTypeVocabulary> </bp:relationshipType> </bp:RelationshipXref> </bp:xref> <bp:xref> <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0022891"> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >GO:0022891</bp:id> Gene Ontology</bp:db> <bp:relationshipType rdf:resource="http://www.signaling-gateway.org/biopax#RelationshipTypeVocabulary_3140047"/> </bp:RelationshipXref> </bp:xref> </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_0005886"> <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >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> 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_2645527"> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >James DE</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Strube M</bp:author> <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Mueckler M</bp:author> pubmed</bp:db> <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >2645527</bp:id> <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Molecular cloning and characterization of an insulin-regulatable glucose transporter.</bp:title> <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Nature</bp:source> <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int" >1989</bp:year> </bp:PublicationXref> </bp:xref> </bp:Protein> </bp:left> </bp:Transport> </rdf:RDF>