Author: rodche
Date: 2012-03-30 16:38:44 -0700 (Fri, 30 Mar 2012)
New Revision: 28710
Added:
core3/impl/trunk/biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
Modified:
core3/impl/trunk/biopax-impl/pom.xml
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
core3/impl/trunk/cpath2-impl/pom.xml
Log:
Embedded paxtools dependencies and added a quick (file read) test to the
biopax-impl CyActivator; so now biopax-impl fails during bundle activation with
"javax.xml.stream.FactoryConfigurationError: Provider
com.bea.xml.stream.MXParserFactory not found" mesage. Previously this error was
hidden (happens since last week). My change simply helps localize it within
biopax-impl (though cpath2-impl has the same issue) and get rid of wrapped
paxtools bundles (cytoscape-temp, which is inconvenient). We need a special
Karaf/osgi classloader hack back again. It's configuration issue. I could not
fix it by experimenting with several stax api/impl, embedding, etc.. And
original paxtools-core jar (not osgi bundle) does not depend on a particular
StAX library, it just imports javax.xml.sream API (included in Java1.6).
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2012-03-30 23:21:27 UTC (rev
28709)
+++ core3/impl/trunk/biopax-impl/pom.xml 2012-03-30 23:38:44 UTC (rev
28710)
@@ -5,14 +5,18 @@
<artifactId>impl-parent</artifactId>
<version>3.0.0-alpha8-SNAPSHOT</version>
</parent>
+
<properties>
<bundle.symbolicName>org.cytoscape.biopax-impl</bundle.symbolicName>
<bundle.namespace>org.cytoscape.biopax</bundle.namespace>
+ <paxtools.version>4.1.3-SNAPSHOT</paxtools.version>
</properties>
+
<modelVersion>4.0.0</modelVersion>
<artifactId>biopax-impl</artifactId>
<name>${bundle.symbolicName} [${bundle.namespace}]</name>
<packaging>bundle</packaging>
+
<dependencies>
<dependency>
<groupId>org.cytoscape</groupId>
@@ -50,18 +54,16 @@
<scope>provided</scope>
</dependency>
<dependency>
- <groupId>cytoscape-temp</groupId>
+ <groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.1.1</version>
- <scope>provided</scope>
+ <version>${paxtools.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.biopax.paxtools</groupId>
+ <artifactId>biopax-converter</artifactId>
+ <version>${paxtools.version}</version>
+ </dependency>
<dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>biopax-converter</artifactId>
- <version>4.1.1</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
@@ -79,9 +81,19 @@
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
-
<Export-Package>!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${project.version}"</Export-Package>
-
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
+ <Export-Package>
+
!${bundle.namespace}.internal.*,
+ !org.biopax.paxtools.*,
+
${bundle.namespace}.*;version="${project.version}"</Export-Package>
+ <Private-Package>
+
${bundle.namespace}.internal.*,
+ org.biopax.paxtools.*
+ </Private-Package>
<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>
+ <Embed-Dependency>
+
*;groupId=org.biopax.paxtools;scope=compile|runtime;type=!pom;inline=true,
+ </Embed-Dependency>
+
<Import-Package>*;resolution:=optional</Import-Package>
</instructions>
</configuration>
</plugin>
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-30 23:21:27 UTC (rev 28709)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-30 23:38:44 UTC (rev 28710)
@@ -1,5 +1,7 @@
package org.cytoscape.biopax.internal;
+import org.biopax.paxtools.io.SimpleIOHandler;
+import org.biopax.paxtools.model.Model;
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -76,6 +78,16 @@
registerService(bc,(NetworkViewAboutToBeDestroyedListener)bioPaxViewTracker,NetworkViewAboutToBeDestroyedListener.class,
new Properties());
registerService(bc,(SetCurrentNetworkViewListener)bioPaxViewTracker,SetCurrentNetworkViewListener.class,
new Properties());
+
+ //quick sanity test
+ try {
+ Model model = (new SimpleIOHandler())
+
.convertFromOWL(this.getClass().getResourceAsStream("biopax3-short-metabolic-pathway.owl"));
+ System.out.println("Started biopax-impl!");
+ } catch (Throwable t) {
+ System.out.println("Failed test biopax-impl.");
+ t.printStackTrace();
+ }
}
}
Added:
core3/impl/trunk/biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
(rev 0)
+++
core3/impl/trunk/biopax-impl/src/main/resources/org/cytoscape/biopax/internal/biopax3-short-metabolic-pathway.owl
2012-03-30 23:38:44 UTC (rev 28710)
@@ -0,0 +1,570 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns="http://www.biopax.org/examples/myExample#";
+ xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#";
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#";
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#";
+ xmlns:owl="http://www.w3.org/2002/07/owl#";
+ xmlns:p1="http://www.owl-ontologies.com/assert.owl#";
+ xml:base="http://www.biopax.org/examples/myExample#";>
+ <owl:Ontology rdf:about="">
+ <owl:imports
rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/>
+ </owl:Ontology>
+ <bp:Protein rdf:ID="Protein_54">
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GLK</bp:standardName>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucokinase</bp:displayName>
+ <bp:entityReference>
+ <bp:ProteinReference rdf:ID="ProteinReference_15">
+ <bp:sequence rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL</bp:sequence>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="SwissProtTrEMBL_P46880">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >P46880</bp:id>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 15608167</bp:comment>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >uniprot</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose kinase</bp:name>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucokinase</bp:displayName>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GLK</bp:standardName>
+ <bp:organism>
+ <bp:BioSource rdf:ID="Escherichia_coli">
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="taxon_562">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >562</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >taxonomy</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Escherichia coli</bp:displayName>
+ </bp:BioSource>
+ </bp:organism>
+ </bp:ProteinReference>
+ </bp:entityReference>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GLK_ECOLI</bp:name>
+ <bp:cellularLocation>
+ <bp:CellularLocationVocabulary rdf:ID="cytoplasm">
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="GO_0005737">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GO:0005737</bp:id>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 11483584 </bp:comment>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Gene Ontology</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >This example is meant to provide an illustration of how various
BioPAX slots should be filled; it is not intended to provide useful (or even
accurate) biological information </bp:comment>
+ <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >cytoplasm</bp:term>
+ </bp:CellularLocationVocabulary>
+ </bp:cellularLocation>
+ <bp:dataSource>
+ <bp:Provenance rdf:ID="SwissProtTrEMBL">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Swiss-Prot/TrEMBL</bp:displayName>
+ </bp:Provenance>
+ </bp:dataSource>
+ <bp:dataSource>
+ <bp:Provenance rdf:ID="aMAZE">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >aMAZE</bp:displayName>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:comment>
+ </bp:Provenance>
+ </bp:dataSource>
+ </bp:Protein>
+ <bp:ChemicalStructure rdf:ID="ChemicalStructure_9">
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:comment>
+ <bp:structureFormat rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >SMILES</bp:structureFormat>
+ <bp:structureData rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>[CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O)</bp:structureData>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ATP</rdfs:comment>
+ </bp:ChemicalStructure>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_52">
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity>
+ <bp:SmallMolecule rdf:ID="alpha-D-glucose_6-phosphate">
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glucose-6-phoshate</bp:name>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose-6-P</bp:name>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glucose 6-phosphate</bp:displayName>
+ <bp:entityReference>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_13">
+ <bp:molecularWeight
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >260.14</bp:molecularWeight>
+ <bp:chemicalFormula
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C6H13O9P</bp:chemicalFormula>
+ <bp:structure>
+ <bp:ChemicalStructure rdf:ID="ChemicalStructure_7">
+ <bp:structureData
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)</bp:structureData>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-glucose-6-phosphate</rdfs:comment>
+ <bp:structureFormat
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >SMILES</bp:structureFormat>
+ </bp:ChemicalStructure>
+ </bp:structure>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glucose 6-phosphate</bp:displayName>
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glu-6-p</bp:standardName>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_C00668">
+ <bp:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135</bp:comment>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C00668</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >KEGG compound</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ </bp:SmallMoleculeReference>
+ </bp:entityReference>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >D-glucose-6-P</bp:name>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ <bp:dataSource>
+ <bp:Provenance rdf:ID="KEGG">
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Kyoto Encyclopedia of Genes and Genomes</bp:standardName>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >KEGG</bp:displayName>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:comment>
+ </bp:Provenance>
+ </bp:dataSource>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >a-D-glu-6-p</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beeta-D-glucose-6-p</bp:name>
+ </bp:SmallMolecule>
+ </bp:physicalEntity>
+ </bp:Stoichiometry>
+ <bp:BiochemicalReaction rdf:ID="phosphoglucoisomerase">
+ <bp:eCNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >5.3.1.9 </bp:eCNumber>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_57">
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity>
+ <bp:SmallMolecule rdf:ID="beta-D-fructose_6-phosphate">
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ><FONT FACE="Symbol">b</FONT>-D-fructose-6-phosphate
</bp:name>
+ <bp:entityReference>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_14">
+ <bp:structure>
+ <bp:ChemicalStructure rdf:ID="ChemicalStructure_8">
+ <bp:structureData
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO)</bp:structureData>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-fructose-6-phosphate</rdfs:comment>
+ <bp:structureFormat
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >SMILES</bp:structureFormat>
+ </bp:ChemicalStructure>
+ </bp:structure>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-fructose 6-phosphate</bp:displayName>
+ <bp:molecularWeight
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >260.14</bp:molecularWeight>
+ <bp:chemicalFormula
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C6H13O9P</bp:chemicalFormula>
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-fru-6-p</bp:standardName>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_C05345">
+ <bp:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ <bp:id
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C05345</bp:id>
+ <bp:db
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg compound</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ </bp:SmallMoleculeReference>
+ </bp:entityReference>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:xref rdf:resource="#KEGG_C05345"/>
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-fru-6-p</bp:standardName>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-fructose 6-phosphate</bp:displayName>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ </bp:SmallMolecule>
+ </bp:physicalEntity>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:conversionDirection
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >REVERSIBLE</bp:conversionDirection>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glu-6-p <=> beta-D-fru-6-p</bp:displayName>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:left rdf:resource="#alpha-D-glucose_6-phosphate"/>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_R02740">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg reaction</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >R02740</bp:id>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-Glucose 6-phosphate => beta-D-Fructose 6-phosphate</bp:name>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glu-6-p <=> b-D-fru-6-p</bp:standardName>
+ <bp:right rdf:resource="#beta-D-fructose_6-phosphate"/>
+ <bp:deltaG>
+ <bp:DeltaG rdf:ID="DeltaG_12">
+ <bp:deltaGPrime0 rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >0.4</bp:deltaGPrime0>
+ </bp:DeltaG>
+ </bp:deltaG>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-Glucose 6-phosphate ketol-isomerase</bp:name>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_58">
+ <bp:physicalEntity rdf:resource="#alpha-D-glucose_6-phosphate"/>
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ </bp:BiochemicalReaction>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_10">
+ <bp:structure>
+ <bp:ChemicalStructure rdf:ID="ChemicalStructure_6">
+ <bp:structureFormat
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >SMILES</bp:structureFormat>
+ <bp:structureData
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O))</bp:structureData>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ADP</rdfs:comment>
+ </bp:ChemicalStructure>
+ </bp:structure>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_C00008">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C00008</bp:id>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg compound</bp:db>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >adenosine diphosphate</bp:name>
+ <bp:chemicalFormula rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C10H15N5O10P2</bp:chemicalFormula>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ADP</bp:standardName>
+ <bp:molecularWeight rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >427.2</bp:molecularWeight>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Adenosine 5'-diphosphate</bp:displayName>
+ </bp:SmallMoleculeReference>
+ <bp:PublicationXref rdf:ID="PublicationXref49">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >2549346</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PubMed</bp:db>
+ </bp:PublicationXref>
+ <bp:UnificationXref rdf:ID="Swiss-ProtTrEMBL_Q9KH85">
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ > PMID: 15608167</bp:comment>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Q9KH85</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >UniProt</bp:db>
+ </bp:UnificationXref>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_11">
+ <bp:structure rdf:resource="#ChemicalStructure_9"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >adenosine triphosphate</bp:name>
+ <bp:molecularWeight rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >507.18</bp:molecularWeight>
+ <bp:chemicalFormula rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C10H16N5O13P3</bp:chemicalFormula>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ATP</bp:standardName>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_C00002">
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C00002</bp:id>
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg compound</bp:db>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Adenosine 5'-triphosphate</bp:displayName>
+ </bp:SmallMoleculeReference>
+ <bp:SmallMolecule rdf:ID="ADP">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Adenosine 5'-diphosphate</bp:displayName>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ADP</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >adenosine diphosphate</bp:name>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:entityReference rdf:resource="#SmallMoleculeReference_10"/>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:xref rdf:resource="#KEGG_C00008"/>
+ <bp:availability rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:availability>
+ </bp:SmallMolecule>
+ <bp:BiochemicalPathwayStep rdf:ID="BiochemicalPathwayStep_3">
+ <bp:stepDirection rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >LEFT-TO-RIGHT</bp:stepDirection>
+ <bp:stepConversion rdf:resource="#phosphoglucoisomerase"/>
+ <bp:stepProcess>
+ <bp:Catalysis
rdf:ID="phosphoglucose_isomerase_converts_alpha-D-gluc-6-p_to_beta-D-fruc-6-p">
+ <bp:controller>
+ <bp:Protein rdf:ID="phosphoglucose_isomerase">
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose-6-phosphate isomerase</bp:name>
+ <bp:entityReference>
+ <bp:ProteinReference rdf:ID="ProteinReference_16">
+ <bp:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >This example is meant to provide an illustration of how
various BioPAX slots should be filled; it is not intended to provide useful (or
even accurate) biological information </bp:comment>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PHI</bp:name>
+ <bp:sequence
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+
>KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT</bp:sequence>
+ <bp:xref rdf:resource="#Swiss-ProtTrEMBL_Q9KH85"/>
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PGI</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >phosphohexose isomerase</bp:name>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >phosphoglucose isomerase</bp:displayName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose-6-phosphate isomerase</bp:name>
+ <bp:organism rdf:resource="#Escherichia_coli"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GPI</bp:name>
+ </bp:ProteinReference>
+ </bp:entityReference>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PHI</bp:name>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >phosphoglucose isomerase</bp:displayName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >phosphohexose isomerase</bp:name>
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PGI</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GPI</bp:name>
+ </bp:Protein>
+ </bp:controller>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >catalysis of (beta-D-glu-6-p <=>
beta-D-fruc-6-p)</bp:displayName>
+ <bp:catalysisDirection
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >LEFT-TO-RIGHT</bp:catalysisDirection>
+ <bp:controlled rdf:resource="#phosphoglucoisomerase"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PGI -> (b-d-glu-6-p <=> b-D-fru-6p)</bp:standardName>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >The source of this data did not store catalyses of reactions as
separate objects, so there are no unification x-refs pointing to the source of
these BioPAX instances. </bp:comment>
+ <bp:availability rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:availability>
+ <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ACTIVATION</bp:controlType>
+ </bp:Catalysis>
+ </bp:stepProcess>
+ </bp:BiochemicalPathwayStep>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_37">
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity>
+ <bp:SmallMolecule rdf:ID="alpha-D-glucose">
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glucose</bp:displayName>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glu</bp:standardName>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ><FONT FACE="Symbol">a</FONT>-D-glucose </bp:name>
+ <bp:entityReference>
+ <bp:SmallMoleculeReference rdf:ID="SmallMoleculeReference_12">
+ <bp:standardName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glu</bp:standardName>
+ <bp:structure>
+ <bp:ChemicalStructure rdf:ID="ChemicalStructure_5">
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >alpha-D-glucose</rdfs:comment>
+ <bp:structureData
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C1(C(O)C(O)C(O)C(O1)CO)(O)</bp:structureData>
+ <bp:structureFormat
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >SMILES</bp:structureFormat>
+ </bp:ChemicalStructure>
+ </bp:structure>
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_C00267">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg compound</bp:db>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C00267</bp:id>
+ <bp:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:displayName
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glucose</bp:displayName>
+ <bp:chemicalFormula
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >C6H12O6</bp:chemicalFormula>
+ <bp:molecularWeight
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >180.16</bp:molecularWeight>
+ </bp:SmallMoleculeReference>
+ </bp:entityReference>
+ </bp:SmallMolecule>
+ </bp:physicalEntity>
+ </bp:Stoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_43">
+ <bp:physicalEntity>
+ <bp:SmallMolecule rdf:ID="ATP">
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ATP</bp:standardName>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Adenosine 5'-triphosphate</bp:displayName>
+ <bp:entityReference rdf:resource="#SmallMoleculeReference_11"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >adenosine triphosphate</bp:name>
+ <bp:cellularLocation rdf:resource="#cytoplasm"/>
+ </bp:SmallMolecule>
+ </bp:physicalEntity>
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ </bp:Stoichiometry>
+ <bp:BiochemicalReaction rdf:ID="glucokinase">
+ <bp:xref>
+ <bp:UnificationXref rdf:ID="KEGG_R01786">
+ <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >kegg reaction</bp:db>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >PMID: 9847135 </bp:comment>
+ <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >R01786</bp:id>
+ </bp:UnificationXref>
+ </bp:xref>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose ATP phosphotransferase </bp:name>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >beta-D-glu + ATP => beta-D-glu-6-p + ADP</bp:displayName>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:conversionDirection
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >REVERSIBLE</bp:conversionDirection>
+ <bp:participantStoichiometry rdf:resource="#Stoichiometry_43"/>
+ <bp:participantStoichiometry rdf:resource="#Stoichiometry_37"/>
+ <bp:left rdf:resource="#ATP"/>
+ <bp:participantStoichiometry rdf:resource="#Stoichiometry_52"/>
+ <bp:right rdf:resource="#ADP"/>
+ <bp:eCNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >2.7.1.1 </bp:eCNumber>
+ <bp:left rdf:resource="#alpha-D-glucose"/>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:spontaneous rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean";
+ >true</bp:spontaneous>
+ <bp:right rdf:resource="#alpha-D-glucose_6-phosphate"/>
+ <bp:eCNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >2.7.1.2 </bp:eCNumber>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ATP:D-glucose 6-phosphotransferase </bp:name>
+ <bp:participantStoichiometry>
+ <bp:Stoichiometry rdf:ID="Stoichiometry_49">
+ <bp:stoichiometricCoefficient
rdf:datatype="http://www.w3.org/2001/XMLSchema#float";
+ >1.0</bp:stoichiometricCoefficient>
+ <bp:physicalEntity rdf:resource="#ADP"/>
+ </bp:Stoichiometry>
+ </bp:participantStoichiometry>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >b-D-glu => b-D-glu-6-p</bp:standardName>
+ </bp:BiochemicalReaction>
+ <bp:Pathway rdf:ID="Pathway50">
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glucose degradation</bp:name>
+ <bp:pathwayOrder rdf:resource="#BiochemicalPathwayStep_3"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >glycolysis</bp:standardName>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >This example is meant to provide an illustration of how various BioPAX
slots should be filled; it is not intended to provide useful (or even accurate)
biological information </bp:comment>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Glycolysis Pathway</bp:displayName>
+ <bp:availability rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >see http://www.amaze.ulb.ac.be/</bp:availability>
+ <bp:organism rdf:resource="#Escherichia_coli"/>
+ <bp:availability rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >All data within the pathway has the same availability</bp:availability>
+ <bp:pathwayComponent
rdf:resource="#phosphoglucose_isomerase_converts_alpha-D-gluc-6-p_to_beta-D-fruc-6-p"/>
+ <bp:pathwayComponent>
+ <bp:Catalysis
rdf:ID="glucokinase_converts_alpha-D-glu_to_alpha-D-glu-6-p">
+ <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >ACTIVATION</bp:controlType>
+ <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >catalysis of (alpha-D-glu <=> alpha-D-glu-6-p)</bp:displayName>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:controlled rdf:resource="#glucokinase"/>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >The source of this data did not store catalyses of reactions as
separate objects, so there are no unification x-refs pointing to the source of
these BioPAX instances. </bp:comment>
+ <bp:controller rdf:resource="#Protein_54"/>
+ <bp:standardName rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >GLK -> (a-D-glu <=> a-D-glu-6-p)</bp:standardName>
+ <bp:catalysisDirection
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >LEFT-TO-RIGHT</bp:catalysisDirection>
+ </bp:Catalysis>
+ </bp:pathwayComponent>
+ <bp:pathwayComponent rdf:resource="#phosphoglucoisomerase"/>
+ <bp:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ ></bp:comment>
+ <bp:pathwayComponent rdf:resource="#glucokinase"/>
+ <bp:name rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >Embden-Meyerhof pathway</bp:name>
+ <bp:xref rdf:resource="#PublicationXref49"/>
+ <bp:dataSource rdf:resource="#KEGG"/>
+ <bp:dataSource rdf:resource="#aMAZE"/>
+ <bp:pathwayOrder>
+ <bp:BiochemicalPathwayStep rdf:ID="BiochemicalPathwayStep_2">
+ <bp:stepConversion rdf:resource="#glucokinase"/>
+ <bp:nextStep rdf:resource="#BiochemicalPathwayStep_3"/>
+ <bp:stepDirection
rdf:datatype="http://www.w3.org/2001/XMLSchema#string";
+ >LEFT-TO-RIGHT</bp:stepDirection>
+ <bp:stepProcess
rdf:resource="#glucokinase_converts_alpha-D-glu_to_alpha-D-glu-6-p"/>
+ </bp:BiochemicalPathwayStep>
+ </bp:pathwayOrder>
+ </bp:Pathway>
+</rdf:RDF>
Modified: core3/impl/trunk/cpath2-impl/pom.xml
===================================================================
--- core3/impl/trunk/cpath2-impl/pom.xml 2012-03-30 23:21:27 UTC (rev
28709)
+++ core3/impl/trunk/cpath2-impl/pom.xml 2012-03-30 23:38:44 UTC (rev
28710)
@@ -5,14 +5,18 @@
<artifactId>impl-parent</artifactId>
<version>3.0.0-alpha8-SNAPSHOT</version>
</parent>
+
<properties>
<bundle.symbolicName>org.cytoscape.cpath2-impl</bundle.symbolicName>
<bundle.namespace>org.cytoscape.cpath2</bundle.namespace>
+ <paxtools.version>4.1.3-SNAPSHOT</paxtools.version>
</properties>
+
<modelVersion>4.0.0</modelVersion>
<artifactId>cpath2-impl</artifactId>
<name>${bundle.symbolicName} [${bundle.namespace}]</name>
<packaging>bundle</packaging>
+
<dependencies>
<dependency>
<groupId>org.cytoscape</groupId>
@@ -55,18 +59,6 @@
<artifactId>swing-application-api</artifactId>
<scope>provided</scope>
</dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>paxtools-core</artifactId>
- <version>4.1.1</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>biopax-converter</artifactId>
- <version>4.1.1</version>
- <scope>provided</scope>
- </dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>vizmap-api</artifactId>
@@ -94,6 +86,16 @@
<artifactId>mockito-all</artifactId>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.biopax.paxtools</groupId>
+ <artifactId>paxtools-core</artifactId>
+ <version>${paxtools.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.biopax.paxtools</groupId>
+ <artifactId>biopax-converter</artifactId>
+ <version>${paxtools.version}</version>
+ </dependency>
</dependencies>
<build>
@@ -146,9 +148,19 @@
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
-
<Export-Package>!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${project.version}"</Export-Package>
-
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
+ <Export-Package>
+
!${bundle.namespace}.internal.*,
+ !org.biopax.paxtools.*,
+
${bundle.namespace}.*;version="${project.version}"</Export-Package>
+ <Private-Package>
+
${bundle.namespace}.internal.*,
+ org.biopax.paxtools.*
+ </Private-Package>
<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>
+ <Embed-Dependency>
+
*;groupId=org.biopax.paxtools;scope=compile|runtime;type=!pom;inline=true,
+ </Embed-Dependency>
+
<Import-Package>*;resolution:=optional</Import-Package>
</instructions>
</configuration>
</plugin>
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