SBPAX3 SGMP Example 4 in OWL

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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.

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"
    xmlns:sbx3="http://vcell.org/sbpax3#"
    xmlns:uome-list="http://vcell.org/uome/list#"
    xmlns:owl="http://www.w3.org/2002/07/owl#"
    xmlns:ex="http://example.org/sgmp/example4#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:sgmp="http://www.signaling-gateway.org/biopax#"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
  <bp:Transport rdf:about="http://www.signaling-gateway.org/biopax#Transporter_transport_21385_1822">
    <bp:xref>
      <bp:PublicationXref rdf:about="http://www.signaling-gateway.org/biopax#PublicationXref_1599406">
        <bp:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Biochem J</bp:source>
        <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Clark AE</bp:author>
        <bp:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Kinetic resolution of the separate GLUT1 and GLUT4 glucose transport activities in 3T3-L1 cells.</bp:title>
        <bp:year rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
        >1992</bp:year>
        <bp:author rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Palfreyman RW</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"
        >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>
                    <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/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>
                <bp:db>SBO</bp:db>
              </bp:UnificationXref>
            </bp:xref>
          </sbx3:SBVocabulary>
        </sbx3:sbTerm>
      </sbx3:SBEntity>
    </sbx3:sbSubEntity>
    <bp:xref>
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        >Gliemann J</bp:author>
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        >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">
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        >Mikulecky DC</bp:author>
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        >pubmed</bp:db>
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        <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>
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        >J Biol Chem</bp:source>
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        >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>
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          <bp:SmallMoleculeReference rdf:about="http://www.signaling-gateway.org/biopax#SmallMoleculeReference_75">
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                >75</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: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>
        <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"
        >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>
        <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"
        >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">
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                >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>
                    <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
                    >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>
                <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
                >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>
                <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_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>
                <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_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">
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                >Gene Ontology</bp:db>
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            </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>
                <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_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>
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            <bp:xref>
              <bp:RelationshipXref rdf:about="http://www.signaling-gateway.org/biopax#RelationshipXref_GO_0022891">
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                >GO:0022891</bp:id>
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                >Gene Ontology</bp:db>
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            </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>
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                >Gene Ontology</bp:db>
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          </bp:CellularLocationVocabulary>
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            <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>
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            >pubmed</bp:db>
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            <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>