BioCyc_Reaction_Scheinput_compound00 The input for the workflow is a Biocyc compound name, for example: L-arginine or L-alanine etc 2013-09-06 13:08:11.851 UTC L-arginine 2013-09-06 13:08:23.523 UTC path_to_output_file00 This takes the input of the local directory where the user wants to store the output result of the workflow. 2013-09-06 13:08:42.977 UTC C:\Users\Arginine.txt 2013-09-06 13:08:55.99 UTC REST_Service_Reactions_Iquery0responseBody00 REST service: The function of this component is to access the BioCyc database with the user input compound and return the details of the compound in the form of an xml document 2013-09-06 13:09:58.668 UTC net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://websvc.biocyc.org/xmlquery?{query}&detail=full application/xml application/xml String false false false false true query java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Servicexml_text0nodelist11 Parse the xml document and extract reactions. 2013-09-06 13:11:06.776 UTC net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="iso-8859-1"?> <ptools-xml ptools-version="15.5" xml:base="http://BioCyc.org/xmlquery?%5bx:x%3c-human^^compounds,x^name=%22L-lysine%22%5d"> <metadata> <url>http://BioCyc.org/</url> <service_name>xmlquery</service_name> <query>[x:x&lt;-human^^compounds,x^name="L-lysine"]</query> <num_results>1</num_results> <PGDB orgid="HUMAN" version="15.5"> <species datatype="string">Homo sapiens</species> <dblink> <dblink-db>NCBI-TAXONOMY-DB</dblink-db> <dblink-oid>9606</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9606</dblink-URL> </dblink> </PGDB> </metadata> <Compound ID="HUMAN:LYS" orgid="HUMAN" frameid="LYS" detail="full"> <parent> <Compound resource="getxml?HUMAN:Amino-Acids-20" orgid="HUMAN" frameid="Amino-Acids-20" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Lysine-or-DAP" orgid="HUMAN" frameid="Lysine-or-DAP" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Positively-charged-polar-amino-acids" orgid="HUMAN" frameid="Positively-charged-polar-amino-acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Basic-Amino-Acids" orgid="HUMAN" frameid="Basic-Amino-Acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:L-Amino-Acids" orgid="HUMAN" frameid="L-Amino-Acids" class="true"/> </parent> <cml> <molecule id="LYS" title="L-lysine"> <atomArray> <atom id="LYS-atom1" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1567.0" y2="1148.0"/> <atom id="LYS-atom2" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1495.0" y2="1108.0"/> <atom id="LYS-atom3" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1635.0" y2="1104.0"/> <atom id="LYS-atom4" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1564.0" y2="1231.0" formalCharge="1"/> <atom id="LYS-atom5" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1423.0" y2="1150.0"/> <atom id="LYS-atom6" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1707.0" y2="1144.0" formalCharge="-1"/> <atom id="LYS-atom7" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1637.0" y2="1021.0"/> <atom id="LYS-atom8" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1351.0" y2="1110.0"/> <atom id="LYS-atom9" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1280.0" y2="1152.0"/> <atom id="LYS-atom10" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1208.0" y2="1112.0" formalCharge="1"/> </atomArray> <bondArray> <bond id="LYS-bond1" atomRefs="LYS-atom1 LYS-atom2" order="1"/> <bond id="LYS-bond2" atomRefs="LYS-atom1 LYS-atom3" order="1"/> <bond id="LYS-bond3" atomRefs="LYS-atom1 LYS-atom4" order="1"/> <bond id="LYS-bond4" atomRefs="LYS-atom2 LYS-atom5" order="1"/> <bond id="LYS-bond5" atomRefs="LYS-atom3 LYS-atom6" order="1"/> <bond id="LYS-bond6" atomRefs="LYS-atom3 LYS-atom7" order="2"/> <bond id="LYS-bond7" atomRefs="LYS-atom5 LYS-atom8" order="1"/> <bond id="LYS-bond8" atomRefs="LYS-atom8 LYS-atom9" order="1"/> <bond id="LYS-bond9" atomRefs="LYS-atom9 LYS-atom10" order="1"/> </bondArray> <formula concise="H 15 O 2 N 2 C 6" formalCharge="0"/> <float title="molecularWeight" units="g/mol">147.197</float> <string title="smiles">C(=O)([O-])C([N+])CCCC[N+]</string> </molecule> </cml> <common-name datatype="string">L-lysine</common-name> <dblink> <dblink-db>PUBCHEM</dblink-db> <dblink-oid>5460926</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5460926</dblink-URL> </dblink> <dblink> <dblink-db>CHEBI</dblink-db> <dblink-oid>32551</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32551</dblink-URL> </dblink> <dblink> <dblink-db>CHEBI</dblink-db> <dblink-oid>32564</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32564</dblink-URL> </dblink> <dblink> <dblink-db>PUBCHEM</dblink-db> <dblink-oid>5242389</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5242389</dblink-URL> </dblink> <dblink> <dblink-db>LIGAND-CPD</dblink-db> <dblink-oid>C00047</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.genome.ad.jp/dbget-bin/www_bget?C00047</dblink-URL> </dblink> <dblink> <dblink-db>CAS</dblink-db> <dblink-oid>56-87-1</dblink-oid> <dblink-relationship>unification</dblink-relationship> </dblink> <appears-in-right-side-of> <Reaction resource="getxml?HUMAN:1.5.1.8-RXN" orgid="HUMAN" frameid="1.5.1.8-RXN"/> </appears-in-right-side-of> <appears-in-left-side-of> <Reaction resource="getxml?HUMAN:LYSINE--TRNA-LIGASE-RXN" orgid="HUMAN" frameid="LYSINE--TRNA-LIGASE-RXN"/> <Reaction resource="getxml?HUMAN:LYSINE-RACEMASE-RXN" orgid="HUMAN" frameid="LYSINE-RACEMASE-RXN"/> </appears-in-left-side-of> <abbrev-name datatype="string">lys</abbrev-name> <molecular-weight datatype="float" units="Daltons">147.197</molecular-weight> <inchi datatype="string">InChI=1/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1/f/h9H</inchi> <pka1 datatype="float">2.2</pka1> <pka2 datatype="float">8.9</pka2> <gibbs-0 datatype="float">-85.0</gibbs-0> <pka3 datatype="float">10.28</pka3> <synonym datatype="string">K</synonym> <synonym datatype="string">lysine</synonym> <synonym datatype="string">L-lys</synonym> <synonym datatype="string">lys</synonym> <synonym datatype="string">2,6-diaminohexanoic acid</synonym> <synonym datatype="string">lysine acid</synonym> </Compound> </ptools-xml> /ptools-xml/Compound/*/Reaction/@frameid xml http://www.w3.org/XML/1998/namespace net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXML_Error_Checkin11result11 Checks for known xml errors 2013-09-06 13:10:10.195 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true result 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQuery_for_compounds_of_reactionin10out100 Build the query to return compounds that participate in a given reaction. 2013-09-06 13:13:18.89 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeREST_Service_Compounds_Iquery0responseBody00 REST Service: Functions to access the BioCyc database and extract the compounds for the given reactions and return an xml document. 2013-09-06 13:14:23.164 UTC net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://websvc.biocyc.org/xmlquery?{query} application/xml application/xml String false false false false true query java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXML_Error_Check_2in11result11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true result 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Service_2xml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="iso-8859-1"?> <ptools-xml ptools-version="15.5" xml:base="http://BioCyc.org/xmlquery?%5bx:y:=human~1.5.1.8-RXN,x%3c-(compounds-of-reaction+y)%5d"> <metadata> <url>http://BioCyc.org/</url> <service_name>xmlquery</service_name> <query>[x:y:=human~1.5.1.8-RXN,x&lt;-(compounds-of-reaction y)]</query> <num_results>7</num_results> <PGDB orgid="HUMAN" version="15.5"> <species datatype="string">Homo sapiens</species> <dblink> <dblink-db>NCBI-TAXONOMY-DB</dblink-db> <dblink-oid>9606</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9606</dblink-URL> </dblink> </PGDB> </metadata> <Compound ID="HUMAN:SACCHAROPINE" orgid="HUMAN" frameid="SACCHAROPINE" detail="low"> <cml> <molecule id="SACCHAROPINE" title="L-saccharopine"> <atomArray> <atom id="SACCHAROPINE-atom1" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1133.0" y2="1136.0"/> <atom id="SACCHAROPINE-atom2" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1133.0" y2="1053.0"/> <atom id="SACCHAROPINE-atom3" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1062.0" y2="1177.0"/> <atom id="SACCHAROPINE-atom4" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1062.0" y2="1260.0" formalCharge="1"/> <atom id="SACCHAROPINE-atom5" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="705.0" y2="1136.0" formalCharge="1"/> <atom id="SACCHAROPINE-atom6" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="776.0" y2="1177.0"/> <atom id="SACCHAROPINE-atom7" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="990.0" y2="1136.0"/> <atom id="SACCHAROPINE-atom8" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="847.0" y2="1136.0"/> <atom id="SACCHAROPINE-atom9" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="919.0" y2="1177.0"/> <atom id="SACCHAROPINE-atom10" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1205.0" y2="1177.0" formalCharge="-1"/> <atom id="SACCHAROPINE-atom11" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="705.0" y2="1051.0"/> <atom id="SACCHAROPINE-atom12" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="776.0" y2="1010.0"/> <atom id="SACCHAROPINE-atom13" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="777.0" y2="928.0"/> <atom id="SACCHAROPINE-atom14" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="848.0" y2="1052.0" formalCharge="-1"/> <atom id="SACCHAROPINE-atom15" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="633.0" y2="1010.0"/> <atom id="SACCHAROPINE-atom16" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="562.0" y2="1051.0"/> <atom id="SACCHAROPINE-atom17" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="490.0" y2="1010.0"/> <atom id="SACCHAROPINE-atom18" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="419.0" y2="1051.0"/> <atom id="SACCHAROPINE-atom19" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="490.0" y2="928.0" formalCharge="-1"/> </atomArray> <bondArray> <bond id="SACCHAROPINE-bond1" atomRefs="SACCHAROPINE-atom1 SACCHAROPINE-atom2" order="2"/> <bond id="SACCHAROPINE-bond2" atomRefs="SACCHAROPINE-atom1 SACCHAROPINE-atom3" order="1"/> <bond id="SACCHAROPINE-bond3" atomRefs="SACCHAROPINE-atom3 SACCHAROPINE-atom4" order="1"/> <bond id="SACCHAROPINE-bond4" atomRefs="SACCHAROPINE-atom3 SACCHAROPINE-atom7" order="1"/> <bond id="SACCHAROPINE-bond5" atomRefs="SACCHAROPINE-atom5 SACCHAROPINE-atom6" order="1"/> <bond id="SACCHAROPINE-bond6" atomRefs="SACCHAROPINE-atom6 SACCHAROPINE-atom8" order="1"/> <bond id="SACCHAROPINE-bond7" atomRefs="SACCHAROPINE-atom7 SACCHAROPINE-atom9" order="1"/> <bond id="SACCHAROPINE-bond8" atomRefs="SACCHAROPINE-atom8 SACCHAROPINE-atom9" order="1"/> <bond id="SACCHAROPINE-bond9" atomRefs="SACCHAROPINE-atom10 SACCHAROPINE-atom1" order="1"/> <bond id="SACCHAROPINE-bond10" atomRefs="SACCHAROPINE-atom11 SACCHAROPINE-atom5" order="1"/> <bond id="SACCHAROPINE-bond11" atomRefs="SACCHAROPINE-atom13 SACCHAROPINE-atom12" order="2"/> <bond id="SACCHAROPINE-bond12" atomRefs="SACCHAROPINE-atom14 SACCHAROPINE-atom12" order="1"/> <bond id="SACCHAROPINE-bond13" atomRefs="SACCHAROPINE-atom11 SACCHAROPINE-atom12" order="1"/> <bond id="SACCHAROPINE-bond14" atomRefs="SACCHAROPINE-atom15 SACCHAROPINE-atom11" order="1"/> <bond id="SACCHAROPINE-bond15" atomRefs="SACCHAROPINE-atom16 SACCHAROPINE-atom15" order="1"/> <bond id="SACCHAROPINE-bond16" atomRefs="SACCHAROPINE-atom18 SACCHAROPINE-atom17" order="2"/> <bond id="SACCHAROPINE-bond17" atomRefs="SACCHAROPINE-atom19 SACCHAROPINE-atom17" order="1"/> <bond id="SACCHAROPINE-bond18" atomRefs="SACCHAROPINE-atom16 SACCHAROPINE-atom17" order="1"/> </bondArray> <formula concise="H 19 N 2 O 6 C 11" formalCharge="0"/> <float title="molecularWeight" units="g/mol">275.281</float> <string title="smiles">C([O-])(C(CCCC[N+]C(CCC([O-])=O)C([O-])=O)[N+])=O</string> </molecule> </cml> <common-name datatype="string">L-saccharopine</common-name> <synonym datatype="string">saccharopine</synonym> <synonym datatype="string">N6-(L-1,3-dicarboxypropyl)-L-lysine</synonym> <synonym datatype="string">&amp;epsilon;-N-(L-glutar-2-yl)-L-lysine</synonym> <synonym datatype="string">L-saccharopine</synonym> </Compound> <Compound ID="HUMAN:NADP" orgid="HUMAN" frameid="NADP" detail="low"> <parent> <Compound resource="getxml?HUMAN:NAD-P-OR-NOP" orgid="HUMAN" frameid="NAD-P-OR-NOP" class="true"/> </parent> <cml> <molecule id="NADP" title="NADP%2b"> <atomArray> <atom id="NADP-atom1" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="53130.0" y2="-33049.0"/> <atom id="NADP-atom2" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="72891.0" y2="-13253.0"/> <atom id="NADP-atom3" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="53105.0" y2="-16639.0" formalCharge="-1"/> <atom id="NADP-atom4" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="99778.0" y2="-47867.0"/> <atom id="NADP-atom5" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="67454.0" y2="-30291.0"/> <atom id="NADP-atom6" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="94969.0" y2="-54609.0"/> <atom id="NADP-atom7" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="79875.0" y2="-39567.0"/> <atom id="NADP-atom8" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="61335.0" y2="-24826.0"/> <atom id="NADP-atom9" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="81839.0" y2="-32502.0"/> <atom id="NADP-atom10" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="72769.0" y2="-43761.0"/> <atom id="NADP-atom11" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="79875.0" y2="-56161.0"/> <atom id="NADP-atom12" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="87072.0" y2="-52058.0"/> <atom id="NADP-atom13" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="87072.0" y2="-43761.0"/> <atom id="NADP-atom14" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="75247.0" y2="-27725.0"/> <atom id="NADP-atom15" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="77737.0" y2="-19874.0"/> <atom id="NADP-atom16" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="85987.0" y2="-19874.0"/> <atom id="NADP-atom17" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="88524.0" y2="-27725.0"/> <atom id="NADP-atom18" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="72769.0" y2="-52058.0"/> <atom id="NADP-atom19" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="94949.0" y2="-41282.0"/> <atom id="NADP-atom20" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="53121.0" y2="-24844.0"/> <atom id="NADP-atom21" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="79852.0" y2="-64411.0"/> <atom id="NADP-atom22" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="44916.0" y2="-24844.0"/> <atom id="NADP-atom23" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="36666.0" y2="-33112.0"/> <atom id="NADP-atom24" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="36641.0" y2="-16612.0" formalCharge="-1"/> <atom id="NADP-atom25" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="36657.0" y2="-24862.0"/> <atom id="NADP-atom26" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="90842.0" y2="-13204.0"/> <atom id="NADP-atom27" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="99092.0" y2="-13204.0"/> <atom id="NADP-atom28" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="99092.0" y2="-21454.0"/> <atom id="NADP-atom29" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="107342.0" y2="-13204.0" formalCharge="-1"/> <atom id="NADP-atom30" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="99092.0" y2="-4954.0" formalCharge="-1"/> <atom id="NADP-atom31" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="14118.0" y2="-24811.0"/> <atom id="NADP-atom32" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="769.0" y2="-24811.0"/> <atom id="NADP-atom33" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="3318.0" y2="-16965.0"/> <atom id="NADP-atom34" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="11568.0" y2="-16965.0"/> <atom id="NADP-atom35" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="7443.0" y2="-29660.0"/> <atom id="NADP-atom36" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-1531.0" y2="-10291.0"/> <atom id="NADP-atom37" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="16418.0" y2="-10291.0"/> <atom id="NADP-atom38" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-7077.0" y2="-35610.0"/> <atom id="NADP-atom39" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-14222.0" y2="-39735.0"/> <atom id="NADP-atom40" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-21367.0" y2="-35610.0"/> <atom id="NADP-atom41" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-21367.0" y2="-27360.0"/> <atom id="NADP-atom42" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-14222.0" y2="-23235.0"/> <atom id="NADP-atom43" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-28511.0" y2="-23235.0"/> <atom id="NADP-atom44" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-28511.0" y2="-14985.0"/> <atom id="NADP-atom45" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="-35656.0" y2="-27360.0"/> <atom id="NADP-atom46" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="-7077.0" y2="-27360.0" formalCharge="1"/> <atom id="NADP-atom47" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="21248.0" y2="-28961.0"/> <atom id="NADP-atom48" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="28407.0" y2="-24862.0"/> </atomArray> <bondArray> <bond id="NADP-bond1" atomRefs="NADP-atom47 NADP-atom48" order="1"/> <bond id="NADP-bond2" atomRefs="NADP-atom31 NADP-atom47" order="1"/> <bond id="NADP-bond3" atomRefs="NADP-atom43 NADP-atom45" order="1"/> <bond id="NADP-bond4" atomRefs="NADP-atom43 NADP-atom44" order="2"/> <bond id="NADP-bond5" atomRefs="NADP-atom41 NADP-atom43" order="1"/> <bond id="NADP-bond6" atomRefs="NADP-atom42 NADP-atom41" order="1"/> <bond id="NADP-bond7" atomRefs="NADP-atom41 NADP-atom40" order="2"/> <bond id="NADP-bond8" atomRefs="NADP-atom40 NADP-atom39" order="1"/> <bond id="NADP-bond9" atomRefs="NADP-atom39 NADP-atom38" order="2"/> <bond id="NADP-bond10" atomRefs="NADP-atom38 NADP-atom46" order="1"/> <bond id="NADP-bond11" atomRefs="NADP-atom46 NADP-atom42" order="2"/> <bond id="NADP-bond12" atomRefs="NADP-atom34 NADP-atom37" order="1"/> <bond id="NADP-bond13" atomRefs="NADP-atom33 NADP-atom36" order="1"/> <bond id="NADP-bond14" atomRefs="NADP-atom32 NADP-atom46" order="1"/> <bond id="NADP-bond15" atomRefs="NADP-atom33 NADP-atom34" order="1"/> <bond id="NADP-bond16" atomRefs="NADP-atom32 NADP-atom33" order="1"/> <bond id="NADP-bond17" atomRefs="NADP-atom35 NADP-atom32" order="1"/> <bond id="NADP-bond18" atomRefs="NADP-atom35 NADP-atom31" order="1"/> <bond id="NADP-bond19" atomRefs="NADP-atom34 NADP-atom31" order="1"/> <bond id="NADP-bond20" atomRefs="NADP-atom27 NADP-atom28" order="2"/> <bond id="NADP-bond21" atomRefs="NADP-atom27 NADP-atom30" order="1"/> <bond id="NADP-bond22" atomRefs="NADP-atom27 NADP-atom29" order="1"/> <bond id="NADP-bond23" atomRefs="NADP-atom26 NADP-atom27" order="1"/> <bond id="NADP-bond24" atomRefs="NADP-atom48 NADP-atom25" order="1"/> <bond id="NADP-bond25" atomRefs="NADP-atom24 NADP-atom25" order="1"/> <bond id="NADP-bond26" atomRefs="NADP-atom23 NADP-atom25" order="2"/> <bond id="NADP-bond27" atomRefs="NADP-atom22 NADP-atom25" order="1"/> <bond id="NADP-bond28" atomRefs="NADP-atom16 NADP-atom26" order="1"/> <bond id="NADP-bond29" atomRefs="NADP-atom21 NADP-atom11" order="1"/> <bond id="NADP-bond30" atomRefs="NADP-atom1 NADP-atom20" order="2"/> <bond id="NADP-bond31" atomRefs="NADP-atom15 NADP-atom2" order="1"/> <bond id="NADP-bond32" atomRefs="NADP-atom3 NADP-atom20" order="1"/> <bond id="NADP-bond33" atomRefs="NADP-atom6 NADP-atom4" order="2"/> <bond id="NADP-bond34" atomRefs="NADP-atom4 NADP-atom19" order="1"/> <bond id="NADP-bond35" atomRefs="NADP-atom5 NADP-atom8" order="1"/> <bond id="NADP-bond36" atomRefs="NADP-atom14 NADP-atom5" order="1"/> <bond id="NADP-bond37" atomRefs="NADP-atom12 NADP-atom6" order="1"/> <bond id="NADP-bond38" atomRefs="NADP-atom10 NADP-atom7" order="2"/> <bond id="NADP-bond39" atomRefs="NADP-atom7 NADP-atom13" order="1"/> <bond id="NADP-bond40" atomRefs="NADP-atom8 NADP-atom20" order="1"/> <bond id="NADP-bond41" atomRefs="NADP-atom9 NADP-atom14" order="1"/> <bond id="NADP-bond42" atomRefs="NADP-atom9 NADP-atom17" order="1"/> <bond id="NADP-bond43" atomRefs="NADP-atom22 NADP-atom20" order="1"/> <bond id="NADP-bond44" atomRefs="NADP-atom18 NADP-atom10" order="1"/> <bond id="NADP-bond45" atomRefs="NADP-atom12 NADP-atom11" order="1"/> <bond id="NADP-bond46" atomRefs="NADP-atom11 NADP-atom18" order="2"/> <bond id="NADP-bond47" atomRefs="NADP-atom13 NADP-atom12" order="2"/> <bond id="NADP-bond48" atomRefs="NADP-atom19 NADP-atom13" order="1"/> <bond id="NADP-bond49" atomRefs="NADP-atom14 NADP-atom15" order="1"/> <bond id="NADP-bond50" atomRefs="NADP-atom15 NADP-atom16" order="1"/> <bond id="NADP-bond51" atomRefs="NADP-atom16 NADP-atom17" order="1"/> <bond id="NADP-bond52" atomRefs="NADP-atom17 NADP-atom19" order="1"/> </bondArray> <formula concise="H 25 P 3 N 7 C 21 O 17" formalCharge="0"/> <float title="molecularWeight" units="g/mol">744.418</float> <string title="smiles">C5(N(C1(C(C(C(O1)COP(OP(=O)([O-])OCC2(C(C(C(O2)[N+]3(=CC(=CC=C3)C(=O)N))O)O))([O-])=O)O)OP([O-])([O-])=O))C4(=C(C(=NC=N4)N)N=5))</string> </molecule> </cml> <common-name datatype="string">NADP&lt;sup&gt;+&lt;/sup&gt;</common-name> <synonym datatype="string">coenzyme II</synonym> <synonym datatype="string">triphosphopyridine nucleotide</synonym> <synonym datatype="string">nicotinamide adenine dinucleotide phosphate</synonym> <synonym datatype="string">NADP-oxidized</synonym> <synonym datatype="string">NADP-ox</synonym> <synonym datatype="string">NADP+</synonym> <synonym datatype="string">TPN</synonym> <synonym datatype="string">TPN+</synonym> <synonym datatype="string">TPN-ox</synonym> <synonym datatype="string">nicotinamide adenine dinucleotide-P</synonym> <synonym datatype="string">NADP(+)</synonym> <synonym datatype="string">NADP</synonym> </Compound> <Compound ID="HUMAN:WATER" orgid="HUMAN" frameid="WATER" detail="low"> <cml> <molecule id="WATER" title="H2O"> <atomArray> <atom id="WATER-atom1" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="428.0" y2="-999.0"/> <atom id="WATER-atom2" elementType="#H instance frame in HUMANBASE[F] @ #x105ad044d2&gt;" x2="429.0" y2="-1000.0"/> <atom id="WATER-atom3" elementType="#H instance frame in HUMANBASE[F] @ #x105ad044d2&gt;" x2="427.0" y2="-1000.0"/> </atomArray> <bondArray> <bond id="WATER-bond1" atomRefs="WATER-atom1 WATER-atom2" order="1"/> <bond id="WATER-bond2" atomRefs="WATER-atom1 WATER-atom3" order="1"/> </bondArray> <formula concise="H 2 O 1" formalCharge="0"/> <float title="molecularWeight" units="g/mol">18.015</float> <string title="smiles">[OH2]</string> </molecule> </cml> <common-name datatype="string">H&lt;SUB&gt;2&lt;/SUB&gt;O</common-name> <synonym datatype="string">H&lt;sub&gt;2&lt;/sub&gt;0</synonym> <synonym datatype="string">H2O</synonym> <synonym datatype="string">H20</synonym> <synonym datatype="string">hydrogen oxide</synonym> <synonym datatype="string">water</synonym> </Compound> <Compound ID="HUMAN:PROTON" orgid="HUMAN" frameid="PROTON" detail="low"> <parent> <Compound resource="getxml?HUMAN:Cations" orgid="HUMAN" frameid="Cations" class="true"/> </parent> <parent>a subatomic particle</parent> <cml> <molecule id="PROTON" title="H%2b"> <atomArray> <atom id="PROTON-atom1" elementType="#H instance frame in HUMANBASE[F] @ #x105ad044d2&gt;" x2="-1768.0" y2="-4714.0" formalCharge="1"/> </atomArray> <bondArray/> <formula concise="H 1" formalCharge="1"/> <float title="molecularWeight" units="g/mol">1.008</float> <string title="smiles">[H+]</string> </molecule> </cml> <common-name datatype="string">H&lt;SUP&gt;+&lt;/SUP&gt;</common-name> <synonym datatype="string">hydrogen ion</synonym> <synonym datatype="string">proton</synonym> <synonym datatype="string">H</synonym> </Compound> <Compound ID="HUMAN:NADPH" orgid="HUMAN" frameid="NADPH" detail="low"> <parent> <Compound resource="getxml?HUMAN:NADH-P-OR-NOP" orgid="HUMAN" frameid="NADH-P-OR-NOP" class="true"/> </parent> <cml> <molecule id="NADPH" title="NADPH"> <atomArray> <atom id="NADPH-atom1" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="53130.0" y2="-33049.0"/> <atom id="NADPH-atom2" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="72891.0" y2="-13253.0"/> <atom id="NADPH-atom3" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="53105.0" y2="-16639.0" formalCharge="-1"/> <atom id="NADPH-atom4" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="99778.0" y2="-47867.0"/> <atom id="NADPH-atom5" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="67454.0" y2="-30291.0"/> <atom id="NADPH-atom6" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="94969.0" y2="-54609.0"/> <atom id="NADPH-atom7" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="79875.0" y2="-39567.0"/> <atom id="NADPH-atom8" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="61335.0" y2="-24826.0"/> <atom id="NADPH-atom9" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="81839.0" y2="-32502.0"/> <atom id="NADPH-atom10" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="72769.0" y2="-43761.0"/> <atom id="NADPH-atom11" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="79875.0" y2="-56161.0"/> <atom id="NADPH-atom12" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="87072.0" y2="-52058.0"/> <atom id="NADPH-atom13" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="87072.0" y2="-43761.0"/> <atom id="NADPH-atom14" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="75247.0" y2="-27725.0"/> <atom id="NADPH-atom15" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="77737.0" y2="-19874.0"/> <atom id="NADPH-atom16" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="85987.0" y2="-19874.0"/> <atom id="NADPH-atom17" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="88524.0" y2="-27725.0"/> <atom id="NADPH-atom18" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="72769.0" y2="-52058.0"/> <atom id="NADPH-atom19" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="94949.0" y2="-41282.0"/> <atom id="NADPH-atom20" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="53121.0" y2="-24844.0"/> <atom id="NADPH-atom21" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="79852.0" y2="-64411.0"/> <atom id="NADPH-atom22" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="44916.0" y2="-24844.0"/> <atom id="NADPH-atom23" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="36666.0" y2="-33112.0"/> <atom id="NADPH-atom24" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="36641.0" y2="-16612.0" formalCharge="-1"/> <atom id="NADPH-atom25" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="36657.0" y2="-24862.0"/> <atom id="NADPH-atom26" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="90842.0" y2="-13204.0"/> <atom id="NADPH-atom27" elementType="#P instance frame in HUMANBASE[F] @ #x105ad04692&gt;" x2="99092.0" y2="-13204.0"/> <atom id="NADPH-atom28" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="99092.0" y2="-21454.0"/> <atom id="NADPH-atom29" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="107342.0" y2="-13204.0" formalCharge="-1"/> <atom id="NADPH-atom30" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="99092.0" y2="-4954.0" formalCharge="-1"/> <atom id="NADPH-atom31" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="14118.0" y2="-24811.0"/> <atom id="NADPH-atom32" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="769.0" y2="-24811.0"/> <atom id="NADPH-atom33" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="3318.0" y2="-16965.0"/> <atom id="NADPH-atom34" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="11568.0" y2="-16965.0"/> <atom id="NADPH-atom35" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="7443.0" y2="-29660.0"/> <atom id="NADPH-atom36" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-1531.0" y2="-10291.0"/> <atom id="NADPH-atom37" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="16418.0" y2="-10291.0"/> <atom id="NADPH-atom38" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-7077.0" y2="-35610.0"/> <atom id="NADPH-atom39" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-14222.0" y2="-39735.0"/> <atom id="NADPH-atom40" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-21367.0" y2="-35610.0"/> <atom id="NADPH-atom41" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-21367.0" y2="-27360.0"/> <atom id="NADPH-atom42" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-14222.0" y2="-23235.0"/> <atom id="NADPH-atom43" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-28511.0" y2="-23235.0"/> <atom id="NADPH-atom44" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-28511.0" y2="-14985.0"/> <atom id="NADPH-atom45" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="-35656.0" y2="-27360.0"/> <atom id="NADPH-atom46" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="-7077.0" y2="-27360.0"/> <atom id="NADPH-atom47" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="21248.0" y2="-28961.0"/> <atom id="NADPH-atom48" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="28407.0" y2="-24862.0"/> </atomArray> <bondArray> <bond id="NADPH-bond1" atomRefs="NADPH-atom47 NADPH-atom48" order="1"/> <bond id="NADPH-bond2" atomRefs="NADPH-atom31 NADPH-atom47" order="1"/> <bond id="NADPH-bond3" atomRefs="NADPH-atom43 NADPH-atom45" order="1"/> <bond id="NADPH-bond4" atomRefs="NADPH-atom43 NADPH-atom44" order="2"/> <bond id="NADPH-bond5" atomRefs="NADPH-atom41 NADPH-atom43" order="1"/> <bond id="NADPH-bond6" atomRefs="NADPH-atom41 NADPH-atom42" order="2"/> <bond id="NADPH-bond7" atomRefs="NADPH-atom40 NADPH-atom41" order="1"/> <bond id="NADPH-bond8" atomRefs="NADPH-atom39 NADPH-atom40" order="1"/> <bond id="NADPH-bond9" atomRefs="NADPH-atom38 NADPH-atom39" order="2"/> <bond id="NADPH-bond10" atomRefs="NADPH-atom38 NADPH-atom46" order="1"/> <bond id="NADPH-bond11" atomRefs="NADPH-atom42 NADPH-atom46" order="1"/> <bond id="NADPH-bond12" atomRefs="NADPH-atom34 NADPH-atom37" order="1"/> <bond id="NADPH-bond13" atomRefs="NADPH-atom33 NADPH-atom36" order="1"/> <bond id="NADPH-bond14" atomRefs="NADPH-atom32 NADPH-atom46" order="1"/> <bond id="NADPH-bond15" atomRefs="NADPH-atom33 NADPH-atom34" order="1"/> <bond id="NADPH-bond16" atomRefs="NADPH-atom32 NADPH-atom33" order="1"/> <bond id="NADPH-bond17" atomRefs="NADPH-atom35 NADPH-atom32" order="1"/> <bond id="NADPH-bond18" atomRefs="NADPH-atom35 NADPH-atom31" order="1"/> <bond id="NADPH-bond19" atomRefs="NADPH-atom34 NADPH-atom31" order="1"/> <bond id="NADPH-bond20" atomRefs="NADPH-atom27 NADPH-atom28" order="2"/> <bond id="NADPH-bond21" atomRefs="NADPH-atom27 NADPH-atom30" order="1"/> <bond id="NADPH-bond22" atomRefs="NADPH-atom27 NADPH-atom29" order="1"/> <bond id="NADPH-bond23" atomRefs="NADPH-atom26 NADPH-atom27" order="1"/> <bond id="NADPH-bond24" atomRefs="NADPH-atom48 NADPH-atom25" order="1"/> <bond id="NADPH-bond25" atomRefs="NADPH-atom24 NADPH-atom25" order="1"/> <bond id="NADPH-bond26" atomRefs="NADPH-atom23 NADPH-atom25" order="2"/> <bond id="NADPH-bond27" atomRefs="NADPH-atom22 NADPH-atom25" order="1"/> <bond id="NADPH-bond28" atomRefs="NADPH-atom16 NADPH-atom26" order="1"/> <bond id="NADPH-bond29" atomRefs="NADPH-atom21 NADPH-atom11" order="1"/> <bond id="NADPH-bond30" atomRefs="NADPH-atom1 NADPH-atom20" order="2"/> <bond id="NADPH-bond31" atomRefs="NADPH-atom15 NADPH-atom2" order="1"/> <bond id="NADPH-bond32" atomRefs="NADPH-atom3 NADPH-atom20" order="1"/> <bond id="NADPH-bond33" atomRefs="NADPH-atom6 NADPH-atom4" order="2"/> <bond id="NADPH-bond34" atomRefs="NADPH-atom4 NADPH-atom19" order="1"/> <bond id="NADPH-bond35" atomRefs="NADPH-atom5 NADPH-atom8" order="1"/> <bond id="NADPH-bond36" atomRefs="NADPH-atom14 NADPH-atom5" order="1"/> <bond id="NADPH-bond37" atomRefs="NADPH-atom12 NADPH-atom6" order="1"/> <bond id="NADPH-bond38" atomRefs="NADPH-atom10 NADPH-atom7" order="2"/> <bond id="NADPH-bond39" atomRefs="NADPH-atom7 NADPH-atom13" order="1"/> <bond id="NADPH-bond40" atomRefs="NADPH-atom8 NADPH-atom20" order="1"/> <bond id="NADPH-bond41" atomRefs="NADPH-atom9 NADPH-atom14" order="1"/> <bond id="NADPH-bond42" atomRefs="NADPH-atom9 NADPH-atom17" order="1"/> <bond id="NADPH-bond43" atomRefs="NADPH-atom22 NADPH-atom20" order="1"/> <bond id="NADPH-bond44" atomRefs="NADPH-atom18 NADPH-atom10" order="1"/> <bond id="NADPH-bond45" atomRefs="NADPH-atom12 NADPH-atom11" order="1"/> <bond id="NADPH-bond46" atomRefs="NADPH-atom11 NADPH-atom18" order="2"/> <bond id="NADPH-bond47" atomRefs="NADPH-atom13 NADPH-atom12" order="2"/> <bond id="NADPH-bond48" atomRefs="NADPH-atom19 NADPH-atom13" order="1"/> <bond id="NADPH-bond49" atomRefs="NADPH-atom14 NADPH-atom15" order="1"/> <bond id="NADPH-bond50" atomRefs="NADPH-atom15 NADPH-atom16" order="1"/> <bond id="NADPH-bond51" atomRefs="NADPH-atom16 NADPH-atom17" order="1"/> <bond id="NADPH-bond52" atomRefs="NADPH-atom17 NADPH-atom19" order="1"/> </bondArray> <formula concise="H 26 P 3 N 7 C 21 O 17" formalCharge="0"/> <float title="molecularWeight" units="g/mol">745.426</float> <string title="smiles">C5(N(C1(C(C(C(O1)COP(OP(=O)([O-])OCC2(C(C(C(O2)N3(C=C(CC=C3)C(=O)N))O)O))([O-])=O)O)OP([O-])([O-])=O))C4(=C(C(=NC=N4)N)N=5))</string> </molecule> </cml> <common-name datatype="string">NADPH</common-name> <synonym datatype="string">Nicotinamide adenine dinucleotide phosphate - reduced</synonym> <synonym datatype="string">NADPH+H+</synonym> <synonym datatype="string">NADPH2</synonym> <synonym datatype="string">NADPH&lt;SUB&gt;2&lt;/SUB&gt;</synonym> <synonym datatype="string">dihydrotriphosphopyridine nucleotide</synonym> <synonym datatype="string">dihydrotriphosphopyridine nucleotide reduced</synonym> <synonym datatype="string">dihydronicotinamide adenine dinucleotide phosphate</synonym> <synonym datatype="string">dihydronicotinamide adenine dinucleotide phosphate reduced</synonym> <synonym datatype="string">NADP-reduced</synonym> <synonym datatype="string">NADP-red</synonym> <synonym datatype="string">NADPH&lt;SUP&gt;+&lt;/SUP&gt;H&lt;SUP&gt;+&lt;/SUP&gt;</synonym> <synonym datatype="string">TPNH</synonym> <synonym datatype="string">dihydronicotinamide adenine dinucleotide-P</synonym> <synonym datatype="string">NADP(H)</synonym> </Compound> <Compound ID="HUMAN:2-KETOGLUTARATE" orgid="HUMAN" frameid="2-KETOGLUTARATE" detail="low"> <cml> <molecule id="2-KETOGLUTARATE" title="2-oxoglutarate"> <atomArray> <atom id="2-KETOGLUTARATE-atom1" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-71950.0" y2="-73090.0"/> <atom id="2-KETOGLUTARATE-atom2" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="211640.0" y2="-73790.0" formalCharge="-1"/> <atom id="2-KETOGLUTARATE-atom3" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="141790.0" y2="-114700.0"/> <atom id="2-KETOGLUTARATE-atom4" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="70540.0" y2="8040.0"/> <atom id="2-KETOGLUTARATE-atom5" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="141790.0" y2="-195840.0"/> <atom id="2-KETOGLUTARATE-atom6" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="70540.0" y2="-73090.0"/> <atom id="2-KETOGLUTARATE-atom7" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-212340.0" y2="-73790.0" formalCharge="-1"/> <atom id="2-KETOGLUTARATE-atom8" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-700.0" y2="-114700.0"/> <atom id="2-KETOGLUTARATE-atom9" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="-142500.0" y2="-114700.0"/> <atom id="2-KETOGLUTARATE-atom10" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="-142500.0" y2="-195840.0"/> </atomArray> <bondArray> <bond id="2-KETOGLUTARATE-bond1" atomRefs="2-KETOGLUTARATE-atom10 2-KETOGLUTARATE-atom9" order="2"/> <bond id="2-KETOGLUTARATE-bond2" atomRefs="2-KETOGLUTARATE-atom9 2-KETOGLUTARATE-atom1" order="1"/> <bond id="2-KETOGLUTARATE-bond3" atomRefs="2-KETOGLUTARATE-atom8 2-KETOGLUTARATE-atom6" order="1"/> <bond id="2-KETOGLUTARATE-bond4" atomRefs="2-KETOGLUTARATE-atom7 2-KETOGLUTARATE-atom9" order="1"/> <bond id="2-KETOGLUTARATE-bond5" atomRefs="2-KETOGLUTARATE-atom6 2-KETOGLUTARATE-atom3" order="1"/> <bond id="2-KETOGLUTARATE-bond6" atomRefs="2-KETOGLUTARATE-atom5 2-KETOGLUTARATE-atom3" order="2"/> <bond id="2-KETOGLUTARATE-bond7" atomRefs="2-KETOGLUTARATE-atom4 2-KETOGLUTARATE-atom6" order="2"/> <bond id="2-KETOGLUTARATE-bond8" atomRefs="2-KETOGLUTARATE-atom2 2-KETOGLUTARATE-atom3" order="1"/> <bond id="2-KETOGLUTARATE-bond9" atomRefs="2-KETOGLUTARATE-atom1 2-KETOGLUTARATE-atom8" order="1"/> </bondArray> <formula concise="H 4 O 5 C 5" formalCharge="0"/> <float title="molecularWeight" units="g/mol">144.084</float> <string title="smiles">C(CC(=O)C([O-])=O)C([O-])=O</string> </molecule> </cml> <common-name datatype="string">2-oxoglutarate</common-name> <synonym datatype="string">2-oxoglutarate</synonym> <synonym datatype="string">ketoglutarate</synonym> <synonym datatype="string">&amp;alpha;-ketoglutarate</synonym> <synonym datatype="string">2-oxoglutaric acid</synonym> <synonym datatype="string">&amp;alpha;-ketoglutaric acid</synonym> <synonym datatype="string">&amp;alpha;-oxoglutarate</synonym> <synonym datatype="string">2-ketoglutaric acid</synonym> <synonym datatype="string">2-ketoglutarate</synonym> <synonym datatype="string">2-oxopentanedionic acid</synonym> <synonym datatype="string">2-oxopentanedionate</synonym> </Compound> <Compound ID="HUMAN:LYS" orgid="HUMAN" frameid="LYS" detail="low"> <parent> <Compound resource="getxml?HUMAN:Amino-Acids-20" orgid="HUMAN" frameid="Amino-Acids-20" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Lysine-or-DAP" orgid="HUMAN" frameid="Lysine-or-DAP" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Positively-charged-polar-amino-acids" orgid="HUMAN" frameid="Positively-charged-polar-amino-acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Basic-Amino-Acids" orgid="HUMAN" frameid="Basic-Amino-Acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:L-Amino-Acids" orgid="HUMAN" frameid="L-Amino-Acids" class="true"/> </parent> <cml> <molecule id="LYS" title="L-lysine"> <atomArray> <atom id="LYS-atom1" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1567.0" y2="1148.0"/> <atom id="LYS-atom2" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1495.0" y2="1108.0"/> <atom id="LYS-atom3" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1635.0" y2="1104.0"/> <atom id="LYS-atom4" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1564.0" y2="1231.0" formalCharge="1"/> <atom id="LYS-atom5" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1423.0" y2="1150.0"/> <atom id="LYS-atom6" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1707.0" y2="1144.0" formalCharge="-1"/> <atom id="LYS-atom7" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1637.0" y2="1021.0"/> <atom id="LYS-atom8" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1351.0" y2="1110.0"/> <atom id="LYS-atom9" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1280.0" y2="1152.0"/> <atom id="LYS-atom10" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1208.0" y2="1112.0" formalCharge="1"/> </atomArray> <bondArray> <bond id="LYS-bond1" atomRefs="LYS-atom1 LYS-atom2" order="1"/> <bond id="LYS-bond2" atomRefs="LYS-atom1 LYS-atom3" order="1"/> <bond id="LYS-bond3" atomRefs="LYS-atom1 LYS-atom4" order="1"/> <bond id="LYS-bond4" atomRefs="LYS-atom2 LYS-atom5" order="1"/> <bond id="LYS-bond5" atomRefs="LYS-atom3 LYS-atom6" order="1"/> <bond id="LYS-bond6" atomRefs="LYS-atom3 LYS-atom7" order="2"/> <bond id="LYS-bond7" atomRefs="LYS-atom5 LYS-atom8" order="1"/> <bond id="LYS-bond8" atomRefs="LYS-atom8 LYS-atom9" order="1"/> <bond id="LYS-bond9" atomRefs="LYS-atom9 LYS-atom10" order="1"/> </bondArray> <formula concise="H 15 O 2 N 2 C 6" formalCharge="0"/> <float title="molecularWeight" units="g/mol">147.197</float> <string title="smiles">C(=O)([O-])C([N+])CCCC[N+]</string> </molecule> </cml> <common-name datatype="string">L-lysine</common-name> <synonym datatype="string">K</synonym> <synonym datatype="string">lysine</synonym> <synonym datatype="string">L-lys</synonym> <synonym datatype="string">lys</synonym> <synonym datatype="string">2,6-diaminohexanoic acid</synonym> <synonym datatype="string">lysine acid</synonym> </Compound> </ptools-xml> /ptools-xml/Compound/common-name xml http://www.w3.org/XML/1998/namespace net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_String_Duplicatesstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_compoundsin11result11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true result 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQuery_for_reactions_of_compoundin10out100net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeREST_Service_Reactions_IIquery0responseBody00 REST Service: Functions to access the BioCyc database and extract the reactions for the given compounds and return an xml document. 2013-09-06 13:14:52.610 UTC net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://websvc.biocyc.org/xmlquery?{query}&detail=full application/xml application/xml String false false false false true query java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXML_Error_Check_3in11result11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true result 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Service_3xml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="iso-8859-1"?> <ptools-xml ptools-version="15.5" xml:base="http://BioCyc.org/xmlquery?%5bx:x%3c-human^^compounds,x^name=%22L-lysine%22%5d"> <metadata> <url>http://BioCyc.org/</url> <service_name>xmlquery</service_name> <query>[x:x&lt;-human^^compounds,x^name="L-lysine"]</query> <num_results>1</num_results> <PGDB orgid="HUMAN" version="15.5"> <species datatype="string">Homo sapiens</species> <dblink> <dblink-db>NCBI-TAXONOMY-DB</dblink-db> <dblink-oid>9606</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9606</dblink-URL> </dblink> </PGDB> </metadata> <Compound ID="HUMAN:LYS" orgid="HUMAN" frameid="LYS" detail="full"> <parent> <Compound resource="getxml?HUMAN:Amino-Acids-20" orgid="HUMAN" frameid="Amino-Acids-20" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Lysine-or-DAP" orgid="HUMAN" frameid="Lysine-or-DAP" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Positively-charged-polar-amino-acids" orgid="HUMAN" frameid="Positively-charged-polar-amino-acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:Basic-Amino-Acids" orgid="HUMAN" frameid="Basic-Amino-Acids" class="true"/> </parent> <parent> <Compound resource="getxml?HUMAN:L-Amino-Acids" orgid="HUMAN" frameid="L-Amino-Acids" class="true"/> </parent> <cml> <molecule id="LYS" title="L-lysine"> <atomArray> <atom id="LYS-atom1" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1567.0" y2="1148.0"/> <atom id="LYS-atom2" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1495.0" y2="1108.0"/> <atom id="LYS-atom3" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1635.0" y2="1104.0"/> <atom id="LYS-atom4" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1564.0" y2="1231.0" formalCharge="1"/> <atom id="LYS-atom5" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1423.0" y2="1150.0"/> <atom id="LYS-atom6" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1707.0" y2="1144.0" formalCharge="-1"/> <atom id="LYS-atom7" elementType="#O instance frame in HUMANBASE[F] @ #x105ad04672&gt;" x2="1637.0" y2="1021.0"/> <atom id="LYS-atom8" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1351.0" y2="1110.0"/> <atom id="LYS-atom9" elementType="#C instance frame in HUMANBASE[F] @ #x105ad043b2&gt;" x2="1280.0" y2="1152.0"/> <atom id="LYS-atom10" elementType="#N instance frame in HUMANBASE[F] @ #x105ad045f2&gt;" x2="1208.0" y2="1112.0" formalCharge="1"/> </atomArray> <bondArray> <bond id="LYS-bond1" atomRefs="LYS-atom1 LYS-atom2" order="1"/> <bond id="LYS-bond2" atomRefs="LYS-atom1 LYS-atom3" order="1"/> <bond id="LYS-bond3" atomRefs="LYS-atom1 LYS-atom4" order="1"/> <bond id="LYS-bond4" atomRefs="LYS-atom2 LYS-atom5" order="1"/> <bond id="LYS-bond5" atomRefs="LYS-atom3 LYS-atom6" order="1"/> <bond id="LYS-bond6" atomRefs="LYS-atom3 LYS-atom7" order="2"/> <bond id="LYS-bond7" atomRefs="LYS-atom5 LYS-atom8" order="1"/> <bond id="LYS-bond8" atomRefs="LYS-atom8 LYS-atom9" order="1"/> <bond id="LYS-bond9" atomRefs="LYS-atom9 LYS-atom10" order="1"/> </bondArray> <formula concise="H 15 O 2 N 2 C 6" formalCharge="0"/> <float title="molecularWeight" units="g/mol">147.197</float> <string title="smiles">C(=O)([O-])C([N+])CCCC[N+]</string> </molecule> </cml> <common-name datatype="string">L-lysine</common-name> <dblink> <dblink-db>PUBCHEM</dblink-db> <dblink-oid>5460926</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5460926</dblink-URL> </dblink> <dblink> <dblink-db>CHEBI</dblink-db> <dblink-oid>32551</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32551</dblink-URL> </dblink> <dblink> <dblink-db>CHEBI</dblink-db> <dblink-oid>32564</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32564</dblink-URL> </dblink> <dblink> <dblink-db>PUBCHEM</dblink-db> <dblink-oid>5242389</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5242389</dblink-URL> </dblink> <dblink> <dblink-db>LIGAND-CPD</dblink-db> <dblink-oid>C00047</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.genome.ad.jp/dbget-bin/www_bget?C00047</dblink-URL> </dblink> <dblink> <dblink-db>CAS</dblink-db> <dblink-oid>56-87-1</dblink-oid> <dblink-relationship>unification</dblink-relationship> </dblink> <appears-in-right-side-of> <Reaction resource="getxml?HUMAN:1.5.1.8-RXN" orgid="HUMAN" frameid="1.5.1.8-RXN"/> </appears-in-right-side-of> <appears-in-left-side-of> <Reaction resource="getxml?HUMAN:LYSINE--TRNA-LIGASE-RXN" orgid="HUMAN" frameid="LYSINE--TRNA-LIGASE-RXN"/> <Reaction resource="getxml?HUMAN:LYSINE-RACEMASE-RXN" orgid="HUMAN" frameid="LYSINE-RACEMASE-RXN"/> </appears-in-left-side-of> <abbrev-name datatype="string">lys</abbrev-name> <molecular-weight datatype="float" units="Daltons">147.197</molecular-weight> <inchi datatype="string">InChI=1/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1/f/h9H</inchi> <pka1 datatype="float">2.2</pka1> <pka2 datatype="float">8.9</pka2> <gibbs-0 datatype="float">-85.0</gibbs-0> <pka3 datatype="float">10.28</pka3> <synonym datatype="string">K</synonym> <synonym datatype="string">lysine</synonym> <synonym datatype="string">L-lys</synonym> <synonym datatype="string">lys</synonym> <synonym datatype="string">2,6-diaminohexanoic acid</synonym> <synonym datatype="string">lysine acid</synonym> </Compound> </ptools-xml> /ptools-xml/Compound/*/Reaction/@frameid xml http://www.w3.org/XML/1998/namespace net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_3inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeREST_Service_Genesquery0responseBody00 REST Service: Functions to access the BioCyc database and extract the genes/enzymes that catalyze the set of input reactions and return an xml document. 2013-09-06 13:15:47.932 UTC net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://websvc.biocyc.org/xmlquery?{query}&detail=full application/xml application/xml String false false false false true query java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXML_Error_Check_5in11result11net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true result 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Service_5xml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="iso-8859-1"?> <ptools-xml ptools-version="15.5" xml:base="http://BioCyc.org/xmlquery?%5bx:y:=human~%22RXN-3741%22,x%3c-(reaction-to-genes+y)%5d"> <metadata> <url>http://BioCyc.org/</url> <service_name>xmlquery</service_name> <query>[x:y:=human~"RXN-3741",x&lt;-(reaction-to-genes y)]</query> <num_results>1</num_results> <PGDB orgid="HUMAN" version="15.5"> <species datatype="string">Homo sapiens</species> <dblink> <dblink-db>NCBI-TAXONOMY-DB</dblink-db> <dblink-oid>9606</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9606</dblink-URL> </dblink> </PGDB> </metadata> <Gene ID="HUMAN:HS06361" orgid="HUMAN" frameid="HS06361" detail="full"> <parent> <Gene resource="getxml?HUMAN:Genes" orgid="HUMAN" frameid="Genes" class="true"/> </parent> <common-name datatype="string">GGH</common-name> <centisome-position datatype="float" units="CENTISOMES">43.653454</centisome-position> <component-of> <Genetic-Element resource="getxml?HUMAN:CHR-8" orgid="HUMAN" frameid="CHR-8"/> </component-of> <dblink> <dblink-db>NCBI-GENE</dblink-db> <dblink-oid>8836</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/gene?term=8836</dblink-URL> </dblink> <dblink> <dblink-db>UCSC</dblink-db> <dblink-oid>NM_003878</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&amp;position=NM_003878</dblink-URL> </dblink> <dblink> <dblink-db>MIM</dblink-db> <dblink-oid>601509</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/omim/601509</dblink-URL> </dblink> <dblink> <dblink-db>ENTREZ</dblink-db> <dblink-oid>U55206</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&amp;id=U55206</dblink-URL> </dblink> <dblink> <dblink-db>ENTREZ</dblink-db> <dblink-oid>BC025025</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&amp;id=BC025025</dblink-URL> </dblink> <dblink> <dblink-db>ENTREZ</dblink-db> <dblink-oid>AF147082</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&amp;id=AF147082</dblink-URL> </dblink> <dblink> <dblink-db>UNIGENE</dblink-db> <dblink-oid>78619</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&amp;CID=78619</dblink-URL> </dblink> <dblink> <dblink-db>REFSEQ</dblink-db> <dblink-oid>NP_003869</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_003869</dblink-URL> </dblink> <dblink> <dblink-db>REFSEQ</dblink-db> <dblink-oid>NM_003878</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_003878</dblink-URL> </dblink> <dblink> <dblink-db>ENSEMBL</dblink-db> <dblink-oid>ENSG00000137563</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000137563</dblink-URL> </dblink> <dblink> <dblink-db>GENECARDS</dblink-db> <dblink-oid>GGH</dblink-oid> <dblink-relationship>unification</dblink-relationship> <dblink-URL>http://www.genecards.org/cgi-bin/carddisp.pl?gene=GGH</dblink-URL> </dblink> <left-end-position datatype="integer">63867238</left-end-position> <right-end-position datatype="integer">63891018</right-end-position> <synonym datatype="string">GH</synonym> <transcription-direction datatype="string">-</transcription-direction> <product> <Protein resource="getxml?HUMAN:HS06361-MONOMER" orgid="HUMAN" frameid="HS06361-MONOMER"/> </product> </Gene> </ptools-xml> /ptools-xml/Gene/common-name xml http://www.w3.org/XML/1998/namespace net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokehgnchgnc.gd_app_sym_filter0hgnc.gd_pub_eg_id10 Biomart service to convert HGNC symbols to entrez ids. 2013-09-06 13:13:38.525 UTC net.sf.taverna.t2.activitiesbiomart-activity1.4net.sf.taverna.t2.activities.biomart.BiomartActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 10 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 3 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_and_populate_temporary_file_2content0filepath00net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity content 0 'text/plain' java.lang.String true filepath 0 'text/plain' 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_Files_2filelist1outputfile0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity filelist 1 l('text/plain') java.lang.String true outputfile 0 'text/plain' java.lang.String true displayresults 0 'text/plain' java.lang.String true results 0 'text/plain' 0 workflow net.sourceforge.taverna.scuflworkers.io.ConcatenateFileListWorker net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQuery_for_reaction_to_genesin10out100net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 10 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_String_Duplicates_3stringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_6inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_String_Duplicates_4stringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_7inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokequery_for_REST_servicein10out100 This builds the query with the input compound for the REST interface. 2013-09-06 12:07:22.90 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeREST_Service_Reactions_Iqueryquery_for_REST_serviceout1XPath_Servicexml_textXML_Error_CheckresultXML_Error_Checkin1REST_Service_Reactions_IresponseBodyFlatten_ListinputlistXPath_ServicenodelistQuery_for_compounds_of_reactionin1Flatten_ListoutputlistREST_Service_Compounds_IqueryQuery_for_compounds_of_reactionout1XML_Error_Check_2in1REST_Service_Compounds_IresponseBodyXPath_Service_2xml_textXML_Error_Check_2resultFlatten_List_2inputlistXPath_Service_2nodelistRemove_String_DuplicatesstringlistFlatten_List_2outputlistFilter_compoundsin1Remove_String_DuplicatesstrippedlistQuery_for_reactions_of_compoundin1Filter_compoundsresultREST_Service_Reactions_IIqueryQuery_for_reactions_of_compoundout1XML_Error_Check_3in1REST_Service_Reactions_IIresponseBodyXPath_Service_3xml_textXML_Error_Check_3resultFlatten_List_3inputlistXPath_Service_3nodelistREST_Service_GenesqueryQuery_for_reaction_to_genesout1XML_Error_Check_5in1REST_Service_GenesresponseBodyXPath_Service_5xml_textXML_Error_Check_5resulthgnchgnc.gd_app_sym_filterRemove_String_Duplicates_4strippedlistCreate_and_populate_temporary_file_2contentFlatten_List_7outputlistConcatenate_Files_2filelistCreate_and_populate_temporary_file_2filepathConcatenate_Files_2outputfilepath_to_output_fileQuery_for_reaction_to_genesin1Remove_String_Duplicates_3strippedlistRemove_String_Duplicates_3stringlistFlatten_List_3outputlistFlatten_List_6inputlistXPath_Service_5nodelistRemove_String_Duplicates_4stringlistFlatten_List_6outputlistFlatten_List_7inputlisthgnchgnc.gd_pub_eg_idquery_for_REST_servicein1input_compound 8ccd5505-58bc-4fc1-96bd-d24c56197e9b 2012-03-13 11:04:49.175 UTC 3ebdae68-492b-4e2e-a0e0-47bb5b101b9d 2011-11-09 02:05:17.683 UTC 61c781e8-e625-4cc4-bcb2-de230a502229 2012-03-10 21:43:02.74 UTC 276fce76-9314-4405-9c12-d71aebddd38b 2012-03-12 15:27:01.437 UTC 1d73ed19-c93a-4068-8ca0-c72b488cb123 2011-11-04 12:36:21.807 UTC 18cf8075-a1a3-428b-8592-d25637c374e9 2011-11-04 13:19:34.856 UTC 1695c44d-1b5e-4c5d-8d1b-a01420eed720 2011-11-05 11:34:41.208 UTC 07a08a0d-cdba-4e65-8a65-7083fd67ab1a 2011-11-28 04:31:47.386 UTC f1ecfa11-ad61-460f-9ebe-c23675901115 2011-11-05 10:55:44.643 UTC 204cb8ff-802a-4bc7-9322-1c1388893b2c 2011-11-27 17:59:24.964 UTC BioCyc:Reaction Scheme 2013-09-06 13:00:08.747 UTC bf3cec14-c535-4762-b6d2-ea3195b11861 2012-03-10 20:59:50.124 UTC e120ca7c-1817-4e64-acca-802587982b01 2012-03-12 14:51:39.78 UTC 31b0415f-259c-4f51-850c-6f735f3add41 2012-03-12 14:54:57.156 UTC 8bb9a003-18c5-4d7f-947e-fff0e9306e58 2011-11-09 22:28:08.188 UTC 25c6f061-00b0-48e6-92e2-2407635bf837 2011-11-09 15:02:30.915 UTC 3ee9c111-7f1f-48fd-b823-db329d174594 2011-11-10 15:43:18.233 UTC edec1a28-161f-46ab-b1cb-09eb7ee39f04 2011-11-05 10:02:24.913 UTC a4868bad-146f-46b6-9832-f9bfc272dad0 2011-11-09 23:51:30.489 UTC 69a2d7a2-f5c5-4851-bf03-0a0d6ff74c55 2011-11-04 13:14:46.225 UTC 0ddeef70-e565-4342-a50f-3c208f06935c 2012-03-10 22:08:22.805 UTC ad386c9c-4b53-4911-8ddc-f4a1e99127bd 2011-11-05 11:27:11.852 UTC b16d7f44-3165-4fd0-bc79-e56cccbee242 2012-03-10 22:11:47.288 UTC d32b1306-185d-4d36-ab18-2dd6e76302e1 2012-02-28 04:58:59.33 UTC 1bf8b758-9b8e-4667-9afe-d6b240341131 2011-11-27 16:27:56.958 UTC e5daf8bb-fb10-4f1d-99b3-aebcda37bccf 2011-11-10 15:00:17.893 UTC 34914f78-7777-4f87-a223-73bed9b5c42b 2011-11-29 11:42:23.85 UTC 16651860-950f-4ba9-86ce-d215d49a0202 2011-11-27 11:52:48.44 UTC 2912cbd5-7c00-49af-989e-d901fbd28d79 2012-03-10 22:41:00.406 UTC 3126f012-3794-4036-9661-e80ca0cd9818 2011-11-09 05:54:07.639 UTC cc7c2a5e-cbc4-461b-8cba-b6b4363afe9d 2011-11-05 10:17:45.808 UTC b7fb74ee-3f5a-4ffe-beb6-878ddc91fd6a 2013-09-06 13:15:48.166 UTC 13fb4e59-4e39-4ea3-ab62-2ab9cc5c55bb 2011-11-05 10:58:19.942 UTC 2c9060e2-fdd2-40c1-b0e7-7fc26215b049 2011-11-08 18:37:14.940 UTC 802f93cd-de23-479f-b89d-4c9c091b0017 2012-03-10 21:34:17.148 UTC 9913a4dd-ebc6-431c-ae7a-b4df480487e4 2011-11-05 11:20:21.742 UTC Harish Dharuri 2013-09-06 12:59:55.886 UTC 37b662ff-8049-4793-a04f-8e3e6e5f2228 2012-03-10 22:12:35.641 UTC fe7913fd-a3b3-427d-9cee-0e2cf83a0364 2013-09-06 13:08:55.333 UTC 21beef7f-ebec-4cda-9ce8-e3f1c7758212 2011-11-05 10:06:44.645 UTC 14fcb989-a0b6-4ad4-9a1d-ddc6f57f4b75 2011-11-09 23:51:16.284 UTC 396715b6-8518-4a68-bfd5-f6c66233c30b 2011-11-27 18:09:47.375 UTC 786e885f-fa53-470a-babf-bd981c3ce35d 2011-11-28 04:13:47.234 UTC The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps: 1. determine all the reactions that the given metabolite participates in 2. determine all the compounds that participate in these reactions 3. filter certain compounds like H2O, ATP etc to avoid non-specific connections 4. determine all the reactions that the compounds passing through step 3 participate in 5. determine the enzymes that drive the reactions from step 4 6. determine genes corresponding to the enzymes in step 5 7. store the entrez gene ids as a text file 2013-09-06 13:01:14.288 UTC 54a38bbb-b585-46b4-9430-d3a118b94ec5 2011-11-05 11:15:07.541 UTC 99c17385-cf50-47b4-b47c-bea409de8d17 2011-11-05 11:53:47.179 UTC d91b8d75-fe81-4f27-835b-d6ec89e09557 2011-11-08 18:12:02.509 UTC 4579e0f4-07db-408b-8ddf-52f7bbdd3e4f 2011-11-05 11:01:01.685 UTC d300ff63-7ddc-4e37-8e69-d26544c3c6b5 2011-11-05 12:07:17.871 UTC 4a7e2160-211c-4a8d-b700-8d9c456064ab 2011-11-10 16:51:40.423 UTC bbda6045-02f9-4482-8634-8f480ac3303b 2011-11-04 13:11:15.937 UTC 821f13ea-243c-44b6-90e4-31baf4ca65bf 2011-11-05 10:49:59.755 UTC 21fceaaf-9120-44ff-8a6a-44ebeed84f30 2012-03-10 22:25:19.516 UTC 5b3922d1-511c-476e-aa3a-9a1eb8c6bb19 2011-11-09 14:46:05.165 UTC 68662d31-5122-4948-9c8c-3d76099d6cec 2011-11-04 12:17:53.140 UTC 0aa6990f-866c-41b0-8370-fe0ad023678c 2011-11-05 15:05:29.257 UTC 90a0a770-12bb-410c-8228-871d4759f771 2011-11-27 18:17:04.504 UTC 328385c1-85a3-4f64-8569-440072f97608 2011-11-27 11:47:51.405 UTC ddea633c-90ea-4585-b2e6-3d837c1820d8 2011-11-08 18:52:26.309 UTC c1a08713-bce8-41be-b1d4-7d56fa3b7fb9 2012-03-10 21:25:03.388 UTC a8954ce1-964b-454b-b7d5-0eb6de2f6688 2012-03-12 15:23:42.531 UTC 7514afb2-2d4f-4d82-a52e-9f499758f30f 2012-02-28 04:51:00.549 UTC 52077999-9a07-4111-914f-e82fc1d5651b 2011-11-09 23:12:07.561 UTC edaa83f2-ec2c-477e-9364-9c71b3a7c2d1 2011-11-04 12:13:24.668 UTC d7d2f029-b551-4cb0-8fc4-12069083faef 2012-03-12 15:07:16.0 UTC 315ed1fd-44af-4822-9f0c-96940f4254bc 2011-11-05 10:26:52.622 UTC