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From: <nik...@us...> - 2012-06-14 09:05:19
|
Revision: 230
http://sbfc.svn.sourceforge.net/sbfc/?rev=230&view=rev
Author: niko-rodrigue
Date: 2012-06-14 09:05:12 +0000 (Thu, 14 Jun 2012)
Log Message:
-----------
updated the sbfc jar file with the latest changes. Updated as well the jsbml jar file and made some small changes to the sbfConverter.sh to be able to pass complex options to bsub
Modified Paths:
--------------
trunk/lib/sbfc-1.1.jar
trunk/sbfConverter.sh
Added Paths:
-----------
trunk/lib/jsbml-1.0-a1-20120612-with-dependencies.jar
Removed Paths:
-------------
trunk/lib/jsbml-1.0-a1-20120417-with-dependencies.jar
Deleted: trunk/lib/jsbml-1.0-a1-20120417-with-dependencies.jar
===================================================================
(Binary files differ)
Added: trunk/lib/jsbml-1.0-a1-20120612-with-dependencies.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/jsbml-1.0-a1-20120612-with-dependencies.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/lib/sbfc-1.1.jar
===================================================================
(Binary files differ)
Modified: trunk/sbfConverter.sh
===================================================================
--- trunk/sbfConverter.sh 2012-06-14 08:44:37 UTC (rev 229)
+++ trunk/sbfConverter.sh 2012-06-14 09:05:12 UTC (rev 230)
@@ -45,7 +45,7 @@
if [ -d $SBML_DIR ]
then
- for file in $SBML_DIR/*.xml
+ for file in $SBML_DIR/*[0-9].xml
do
# Creating a log file specific to each file.
LOG_FILE_FOLDER=${SBF_CONVERTER_HOME}/log/`basename $file .xml`
@@ -57,7 +57,7 @@
fi
if [ ! "1${COMMAND}" == "1java " ] ; then
# we are on a cluster node
- COMMAND="bsub ${BSUB_OPTIONS} -o $LOG_FILE_MULTI "
+ COMMAND="bsub ${BSUB_OPTIONS} -o $LOG_FILE_MULTI java "
fi
echo "------------------------------------------------------------" >> $LOG_FILE_MULTI 2>&1
@@ -65,8 +65,8 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$file'..." >> $LOG_FILE_MULTI 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE_MULTI 2>&1
- $COMMAND org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
- sleep 0.3
+ eval $COMMAND org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
+ sleep 0.1
done
else
@@ -80,7 +80,7 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$1'..." >> $LOG_FILE 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE 2>&1
- $COMMAND org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
+ eval $COMMAND org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
fi
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|
|
From: <nik...@us...> - 2012-08-17 09:38:05
|
Revision: 245
http://sbfc.svn.sourceforge.net/sbfc/?rev=245&view=rev
Author: niko-rodrigue
Date: 2012-08-17 09:37:59 +0000 (Fri, 17 Aug 2012)
Log Message:
-----------
corrected the way we wrote annotation in the sbml2sbgnml converter
Modified Paths:
--------------
trunk/lib/sbfc-1.1.jar
trunk/src/org/sbfc/converter/sbml2dot/ConstraintFileReader.java
trunk/src/org/sbfc/converter/sbml2sbgnml/SbmlToSbgnML.java
trunk/src/org/sbfc/converter/utils/sbgn/SBGNUtils.java
Modified: trunk/lib/sbfc-1.1.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/sbml2dot/ConstraintFileReader.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2dot/ConstraintFileReader.java 2012-08-16 10:53:39 UTC (rev 244)
+++ trunk/src/org/sbfc/converter/sbml2dot/ConstraintFileReader.java 2012-08-17 09:37:59 UTC (rev 245)
@@ -10,6 +10,7 @@
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
+import org.apache.log4j.Logger;
import org.sbfc.converter.utils.sbgn.SBGNUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@@ -34,7 +35,9 @@
public static MiriamLink miriamWS;
public static HashMap<String, String> officialURIs = new HashMap<String, String>();
public static HashMap<String, String> checkedURIs = new HashMap<String, String>();
-
+
+ private static Logger logger = Logger.getLogger(ConstraintFileReader.class);
+
static {
miriamWS = new MiriamLink();
miriamWS.setAddress(MIRIAM_WS_URL);
@@ -56,7 +59,7 @@
Hashtable<String, String> speciesAnnotationMAP, Hashtable<String, String> taxonomyMap, String attributeClass)
{
String configFile = "SBML2SBGNConstraintFile.xml";
-
+
try{
// creation of a document factory
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -116,7 +119,7 @@
// Possible options for attributeClass are "classSBGN" "classBioPAX"
String classOfEntity = ((Element) physicalEntityNode).getAttribute(attributeClass);
- System.out.println("\nConstraintFileReader : parse : " + attributeClass + " = " + classOfEntity);
+ logger.debug("\nConstraintFileReader : parse : " + attributeClass + " = " + classOfEntity);
Vector<Node> physicalEntitySpecies = getChildList(physicalEntityNode, "species");
@@ -125,20 +128,20 @@
annotationMIRIAM(miriamWS, species, annotationSpecies, classOfEntity);// change here classBioPAX to classSBGN
}
- System.out.println("ConstraintFileReader : parse config file : official constraints :");
+ logger.debug("ConstraintFileReader : parse config file : official constraints :");
Vector<Node> physicalEntityConstraintList = getChildList(physicalEntityNode, "constraint");
for (Node physicalEntityConstraintNode : physicalEntityConstraintList) {
String constraint = physicalEntityConstraintNode.getTextContent();
- System.out.println(" file constraint URI = " + constraint);
+ logger.debug(" file constraint URI = " + constraint);
// Could be done by hand to speed up the application
// TODO : Function that is doing that already there ???!!!
String officialConstraintURI = miriamWS.getMiriamURI(constraint);
- System.out.println(" official constraint URI : " + officialConstraintURI + " = " + classOfEntity);
+ logger.debug(" official constraint URI : " + officialConstraintURI + " = " + classOfEntity);
if (officialConstraintURI == null) { // TODO : find a work-around for the ensembl constraint
officialConstraintURI = constraint;
@@ -158,10 +161,10 @@
}
// //print the content of the MAP
-// System.out.println("annotationSpecies:");
+// logger.debug("annotationSpecies:");
// for (Enumeration e = annotationSpecies.keys() ; e.hasMoreElements() ;) {
// String s = (String) e.nextElement();
-// System.out.println("key: "+s+" value: "+annotationSpecies.get(s));
+// logger.debug("key: "+s+" value: "+annotationSpecies.get(s));
// }
}
@@ -229,7 +232,7 @@
*/
public static void annotationMIRIAM (MiriamLink linkMiriam, String URI, Hashtable<String, String> table, String type) {
- // System.out.println("annotationMIRIAM : URI = " + URI + ", type = " + type);
+ // logger.debug("annotationMIRIAM : URI = " + URI + ", type = " + type);
if (checkedURIs.get(URI) != null) {
return;
@@ -243,12 +246,12 @@
officialURIs.put(URI, officialURN);
if (name.equals("")){
- System.out.println(URI+" URI is not contain in MIRIAM database, no answer possible");
+ logger.debug(URI+" URI is not contain in MIRIAM database, no answer possible");
} else {
String[] URIs = linkMiriam.getDataTypeURIs(name);
for (int i = 0; i < URIs.length; i++) {
table.put(URIs[i], type);
- System.out.println("key: ." + URIs[i] + ". value: " + type);
+ logger.debug("key: ." + URIs[i] + ". value: " + type);
}
}
@@ -256,7 +259,7 @@
public static void annotationMIRIAMName (MiriamLink linkMiriam, String URI, Hashtable<String, String> table, String miriamName) {
- // System.out.println("annotationMIRIAM : URI = " + URI + ", type = " + type);
+ // logger.debug("annotationMIRIAM : URI = " + URI + ", type = " + type);
String name = linkMiriam.getName(URI);
@@ -264,12 +267,12 @@
officialURIs.put(URI, officialURN);
if (name.equals("")){
- System.out.println(URI+" URI is not contain in MIRIAM database, no answer possible");
+ logger.debug(URI+" URI is not contain in MIRIAM database, no answer possible");
} else {
String[] URIs = linkMiriam.getDataTypeURIs(name);
for (int i = 0; i < URIs.length; i++) {
table.put(URIs[i], miriamName);
- // System.out.println("key: ." + URIs[i] + ". value: " + type);
+ // logger.debug("key: ." + URIs[i] + ". value: " + type);
}
}
Modified: trunk/src/org/sbfc/converter/sbml2sbgnml/SbmlToSbgnML.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2sbgnml/SbmlToSbgnML.java 2012-08-16 10:53:39 UTC (rev 244)
+++ trunk/src/org/sbfc/converter/sbml2sbgnml/SbmlToSbgnML.java 2012-08-17 09:37:59 UTC (rev 245)
@@ -65,6 +65,9 @@
*/
public class SbmlToSbgnML extends GeneralConverter {
+ private static final String SBFCANNO_PREFIX = "sbfcanno";
+ public static final String SBFC_ANNO_NAMESPACE = "http://www.sbfc.org/sbfcanno";
+
private static final int SPECIES_CARDINALITY_MAX = 4;
private static int SBGNML_MILESTONE = 2;
@@ -205,7 +208,7 @@
// if the class is in the Properties, we continue
if (pro.containsValue(SBGNclass)) {
// looping over all keys in the properties file
- for (int i = 0 ; pro.keys().hasMoreElements(); i++) {
+ for (; pro.keys().hasMoreElements(); ) {
String key = (String) pro.keys().nextElement();
logger.debug("key of properties file = " + key);
@@ -727,7 +730,7 @@
createVoidBBox(glyph);
- // TODO is it possible to retrieve informations from SBML for auxiliairy units tags???
+ // TODO is it possible to retrieve informations from SBML for auxiliary units tags???
// STATE VALUE, state tag has to be added only within a glyph, with a bbox
// adding SBML annotations for SBGNN-ML
@@ -765,7 +768,8 @@
Document document = constructeur.newDocument();
// root annotation
- Element annotation = document.createElement("annotation");
+ Element annotation = document.createElement(SBFCANNO_PREFIX + ":annotation");
+ annotation.setAttribute("xmlns:" + SBFCANNO_PREFIX, SBFC_ANNO_NAMESPACE);
// creating a child for each qualifier
for (CVTerm cvt : anno.getListOfCVTerms()) {
@@ -774,7 +778,7 @@
String cvtermName = cvt.getBiologicalQualifierType().getElementNameEquivalent();
// add the CVTerm as a child
- Element cvterm = document.createElement(cvtermName);
+ Element cvterm = document.createElement(SBFCANNO_PREFIX + ":" + cvtermName);
// append this element to the root
annotation.appendChild(cvterm);
@@ -783,10 +787,10 @@
for (String urn : cvt.getResources()) {
// create and add an element called resource
- Element resource = document.createElement("resource");
- resource.setAttribute("urn", urn);
+ Element resource = document.createElement(SBFCANNO_PREFIX + ":resource");
+ resource.setAttribute(SBFCANNO_PREFIX + ":urn", urn);
// TODO get the url of the corresponding urn if possible
- // resource.setAttribute("url", );
+ // resource.setAttribute(SBFCANNO_PREFIX + ":url", );
cvterm.appendChild(resource);
}
@@ -906,10 +910,8 @@
}
}
- SbmlToSbgnML sb = new SbmlToSbgnML();
-
// CLONE TAG TODO check that with models
- if (sb.canBeCloned(reaction)) {
+ if (canBeCloned(reaction)) {
Clone c = new Clone();
glyph.setClone(c);
}
@@ -983,6 +985,18 @@
System.out.println("output file at: " + outputFile);
System.out.println("conversion into SBGN-ML done");
+ File f2 = new File(outputFile);
+
+ try
+ {
+ SbgnUtil.readFromFile(f2);
+ }
+ catch (JAXBException e)
+ {
+ e.printStackTrace();
+ }
+
+
}
Modified: trunk/src/org/sbfc/converter/utils/sbgn/SBGNUtils.java
===================================================================
--- trunk/src/org/sbfc/converter/utils/sbgn/SBGNUtils.java 2012-08-16 10:53:39 UTC (rev 244)
+++ trunk/src/org/sbfc/converter/utils/sbgn/SBGNUtils.java 2012-08-17 09:37:59 UTC (rev 245)
@@ -129,7 +129,7 @@
}
if (biopaxPhysicalEntityType == null || biopaxPhysicalEntityType.trim().length() == 0) {
- logger.warn("Warning : cannot find a valid class for this uri");
+ logger.warn("Warning : cannot find a valid class for the uri '" + uri + "'.");
continue;
}
@@ -257,19 +257,24 @@
String sbgnClassByAnnotation = getSBGNClassThroughAnnotation(sBase.getAnnotation());
logger.debug("SBGN class by the annotation is = "+sbgnClassByAnnotation);
- if (sbgnClassBySboTerm != null) {
+ if (sbgnClassBySboTerm != null)
+ {
// warn the user that sboTerm and annotations give different SBGN classes
- if (!sbgnClassBySboTerm.equals(sbgnClassByAnnotation)) {
- logger.warn("Warning: for MetaID: "+sBase.getMetaId()+" shape for sboTerm is "+sbgnClassBySboTerm+" instead of "+sbgnClassByAnnotation+" for annotations");
+ if (sbgnClassByAnnotation != null && !sbgnClassBySboTerm.equals(sbgnClassByAnnotation))
+ {
+ logger.warn("Warning: for MetaID: '" + sBase.getMetaId() + "', the shape found with sboTerm is '" +
+ sbgnClassBySboTerm + "' instead of '" + sbgnClassByAnnotation + "' with annotations");
}
+
return sbgnClassBySboTerm;
}
- if (sbgnClassByAnnotation != null) {
+ if (sbgnClassByAnnotation != null)
+ {
return sbgnClassByAnnotation;
- } else {
- return null;
}
+
+ return null;
}
/**
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|
|
From: <nik...@us...> - 2012-08-17 13:15:39
|
Revision: 246
http://sbfc.svn.sourceforge.net/sbfc/?rev=246&view=rev
Author: niko-rodrigue
Date: 2012-08-17 13:15:33 +0000 (Fri, 17 Aug 2012)
Log Message:
-----------
change the sbo2sbgn mapping to replace 'empty set' by 'source and sink' which is the value recognized in libsbgn GlyphClazz enum
Modified Paths:
--------------
trunk/lib/sbfc-1.1.jar
trunk/src/org/sbfc/converter/utils/sbgn/sbo2sbgn.properties
Modified: trunk/lib/sbfc-1.1.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/utils/sbgn/sbo2sbgn.properties
===================================================================
--- trunk/src/org/sbfc/converter/utils/sbgn/sbo2sbgn.properties 2012-08-17 09:37:59 UTC (rev 245)
+++ trunk/src/org/sbfc/converter/utils/sbgn/sbo2sbgn.properties 2012-08-17 13:15:33 UTC (rev 246)
@@ -31,7 +31,7 @@
# source and sink
# a circle crossed by a bar linking the upper-right and lower-left corners of an invisible
# square drawn around the circle.
-SBO\:0000291=empty set
+SBO\:0000291=source and sink
# Simple chemical
SBO\:0000247=simple chemical
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From: <nik...@us...> - 2012-08-22 15:35:13
|
Revision: 247
http://sbfc.svn.sourceforge.net/sbfc/?rev=247&view=rev
Author: niko-rodrigue
Date: 2012-08-22 15:35:00 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
major update of the sbml2biopax converter to be able to use paxtools4 + use identifiers.org URL as RDF ID + using now the same base class to generate biopax L2 and L3 + some other minors improvements to remove as much as possible errors and warnings when validating the resulting biopax file
Modified Paths:
--------------
trunk/build.xml
trunk/lib/sbfc-1.1.jar
trunk/src/org/sbfc/converter/models/BioPaxModel.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l2.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAXannotationParameter_l3.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAXconfigFile_withConstraints.xml
trunk/src/org/sbfc/converter/sbml2sbgnml/SbmlToSbgnML.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/MiriamAnnotation.java
Added Paths:
-----------
trunk/lib/paxtools-4.1.1.jar
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
Removed Paths:
-------------
trunk/lib/paxtools-20100608.jar
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2012-08-17 13:15:33 UTC (rev 246)
+++ trunk/build.xml 2012-08-22 15:35:00 UTC (rev 247)
@@ -109,7 +109,7 @@
<!-- copy src files -->
<copy todir="${build.src}" overwrite="yes">
<fileset dir="${src.dir}"
- excludes="**/CVS*, **/*.class, **/*~, **/*.tgz, **/testJung/*">
+ excludes="**/CVS*, **/*.class, **/*~, **/*.tgz, **/testJung/*, **/SBML2BioPAXannotationParameter_l2.java, **/SBMLAnnotationParameter.java, **/SBMLAnnotationList.java, **/SBMLAnnotationParsing.java">
</fileset>
</copy>
<copy todir="${build.src}" overwrite="yes">
Deleted: trunk/lib/paxtools-20100608.jar
===================================================================
(Binary files differ)
Added: trunk/lib/paxtools-4.1.1.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/paxtools-4.1.1.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/lib/sbfc-1.1.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/models/BioPaxModel.java
===================================================================
--- trunk/src/org/sbfc/converter/models/BioPaxModel.java 2012-08-17 13:15:33 UTC (rev 246)
+++ trunk/src/org/sbfc/converter/models/BioPaxModel.java 2012-08-22 15:35:00 UTC (rev 247)
@@ -34,7 +34,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
-import org.biopax.paxtools.io.simpleIO.SimpleExporter;
+import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.sbfc.converter.exceptions.ReadModelError;
@@ -86,7 +86,7 @@
*/
public void modelToFile(String fileName) {
- SimpleExporter export = new SimpleExporter(getModel().getLevel());
+ SimpleIOHandler export = new SimpleIOHandler(getModel().getLevel());
try {
export.convertToOWL(model,new FileOutputStream(fileName));
@@ -117,9 +117,11 @@
}
- public String modelToString() {
+ public String modelToString()
+ {
String resModel=null;
- SimpleExporter export = new SimpleExporter(getModel().getLevel());
+ SimpleIOHandler export = new SimpleIOHandler(getModel().getLevel());
+
try {
File tempFile = File.createTempFile("BioPaxConvert", "temp");
FileOutputStream out = new FileOutputStream(tempFile);
Added: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java (rev 0)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java 2012-08-22 15:35:00 UTC (rev 247)
@@ -0,0 +1,1353 @@
+/*
+ * $Id: SBML2BioPAX_l3.java 129 2011-07-04 16:52:18Z niko-rodrigue $
+ * $URL: https://sbfc.svn.sourceforge.net/svnroot/sbfc/trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java $
+ *
+ *
+ * ==============================================================================
+ * Copyright (c) 2010-2011 the copyright is held jointly by the individual
+ * authors. See the file AUTHORS for the list of authors
+ *
+ * This file is part of The System Biology Format Converter (SBFC).
+ *
+ * SBFC is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * SBFC is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with SBFC. If not, see<http://www.gnu.org/licenses/>.
+ *
+ * ==============================================================================
+ *
+ */
+
+package org.sbfc.converter.sbml2biopax;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+import java.net.URLEncoder;
+import java.text.DateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Set;
+
+import org.biopax.paxtools.impl.level2.Level2FactoryImpl;
+import org.biopax.paxtools.impl.level3.Level3FactoryImpl;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.BioPAXFactory;
+import org.biopax.paxtools.model.Model;
+import org.biopax.paxtools.model.level3.BioSource;
+import org.biopax.paxtools.model.level3.CellularLocationVocabulary;
+import org.biopax.paxtools.model.level3.Complex;
+import org.biopax.paxtools.model.level3.Control;
+import org.biopax.paxtools.model.level3.ControlType;
+import org.biopax.paxtools.model.level3.ControlledVocabulary;
+import org.biopax.paxtools.model.level3.Controller;
+import org.biopax.paxtools.model.level3.Conversion;
+import org.biopax.paxtools.model.level3.ConversionDirectionType;
+import org.biopax.paxtools.model.level3.Level3Element;
+import org.biopax.paxtools.model.level3.Named;
+import org.biopax.paxtools.model.level3.Pathway;
+import org.biopax.paxtools.model.level3.PhysicalEntity;
+import org.biopax.paxtools.model.level3.Process;
+import org.biopax.paxtools.model.level3.Provenance;
+import org.biopax.paxtools.model.level3.Stoichiometry;
+import org.biopax.paxtools.model.level3.XReferrable;
+import org.biopax.paxtools.model.level3.Xref;
+import org.sbfc.converter.GeneralConverter;
+import org.sbfc.converter.models.BioPaxModel;
+import org.sbfc.converter.models.GeneralModel;
+import org.sbfc.converter.models.SBMLModel;
+import org.sbfc.converter.utils.sbml.sbmlannotation.MiriamAnnotation;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.CVTerm.Qualifier;
+import org.sbml.jsbml.Compartment;
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Reaction;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.SpeciesReference;
+
+import uk.ac.ebi.miriam.lib.MiriamLink;
+
+
+/**
+ * Convert an SBML file into a BioPax owl file.
+ *
+ * The package uk.ac.ebi.compneur.sbmlannotation is not used at the moment !!! Work in progress from Arnaud :-)
+ *
+ * @author Arnaud Henry
+ * @author Nicolas Rodriguez
+ * @author Camille Laibe
+ *
+ * @version 2.3
+ *
+ */
+
+// TODO : check if we could use ProteinReference and equivalent stuff as well
+
+// TODO : add a check to see if there is no Reaction and Species, then don't generate a biopax file or just with a comment about the problem
+
+// TODO : have a look at RelationXRef
+
+
+public class SBML2BioPAX extends GeneralConverter{
+
+ protected String PHYSICAL_ENTITY = "PhysicalEntity";
+ protected String CELLULAR_LOCATION_VOCABULARY = "CellularLocationVocabulary";
+ protected String PROVENANCE_CLASS_NAME = "Provenance";
+ protected String BIO_SOURCE = "BioSource";
+ protected String PATHWAY_CLASS_NAME = "Pathway";
+ protected String CONTROL = "Control";
+ protected String BIOCHEMICAL_REACTION = "BiochemicalReaction";
+ protected String COMPLEX_DIS_ASSEMBLY = "ComplexDisAssembly";
+ protected String COMPLEX_ASSEMBLY = "ComplexAssembly";
+ protected String TRANSPORT = "Transport";
+ protected String LEFT_OF_REACTION = "LEFT";
+ protected String RIGHT_OF_REACTION = "RIGHT";
+ protected String PUBLICATION_XREF_CLASS_NAME = "PublicationXref";
+ protected String UNIFICATION_XREF_CLASS_NAME = "UnificationXref";
+ protected String PHYSICAL_ENTITY_PARTICIPANT = "PhysicalEntity";
+
+ protected static final String EC_CODE_URI = "urn:miriam:ec-code";
+ protected static final String BIOMODELS_URI = "urn:miriam:biomodels.db"; // "http://identifiers.org/biomodels.db/"
+
+ public static String VERSION = "2.3";
+
+ // make this configurable in a configuration file ??
+ public static final String MIRIAM_WS_URL = "http://www.ebi.ac.uk/miriamws/main/MiriamWebServices";
+
+
+
+ // creation of the link to the web services
+ public static MiriamLink link;
+
+ public static HashMap<String, String> officialURIs = new HashMap<String, String>();
+ public static HashMap<String, String> officialNames = new HashMap<String, String>();
+
+ static {
+ link = new MiriamLink();
+ link.setAddress(MIRIAM_WS_URL);
+ }
+
+ protected int biopaxLevel = 3;
+
+
+ /**
+ * <b>Constructor SBML2BioPAX.</b><br/>
+ * Main method of the biological model export from <a href="http://sbml.org/"><b>SBML</b></a> (Systems Biology Markup Language)
+ * to <a href="http://www.biopax.org/"><b>BioPAX</b></a> (Biological PAthway eXchange format).
+ *
+ * Provide it a file when you call the program with the command
+ * <code><pre>java uk.ac.ebi.compneur.sbml2biopax.SBML2BioPAX <SBMLfile></code></pre>
+ *
+ * JSBML is used to read and check the SBML file provided.<br/>
+ *
+ * Create the SBMLDocument object and start the creation of the Ontological BioPAX model.<br/>
+ *
+ * Save the BioPAX file in the same file path and name that the input file, but replace the extension by .owl.
+ *
+ * @param theFile Path of the SBML file to export
+ */
+ public SBML2BioPAX(){
+ super();
+ }
+
+ /**
+ * Converts a SBML model into a BioPax Model.
+ * <p>
+ * Use JSBML to read the SBML model, and Paxtools to write the BioPax model in OWL.<br/>
+ * The conversion is composed of different parts:<br/> <ul>
+ * <li/>fill the Maps coming from the configuration file. They will be use to determine the specific Biopax class of the translated SBML elements.<br/>
+ * <li/>'model' translation into a BioPax pathway: source on BioModels database, taxonomy, publication references<br/>
+ * <li/>compartments treatment<br/>
+ * <li/>species treatment (following the BioPAX classes: complex, dna, rna, protein, smallMolecule).
+ * The Algorithm take care about the constraint. For example a annotation about KEGG will be typing in a smallMolecule class.
+ * But the annotation "http://www.genome.jp/kegg/compound/#C00039" describe the Deoxyribonucleotide.
+ * A second loop replace the term in dna.<br/>
+ * The Ensembl annotation is special, due to the two first terms of the identifier indicating the type dna, rna or protein of the species.
+ * ex: http://www.ensembl.org/#ENSRNOG -> dna ; ENSRNOT -> rna ; ENSRNOP -> protein
+ * <li/>reaction parsing, and creation of the physicalInteraction subclasses. If the reaction contain one or several modifier,
+ * they are translate in a control or a catalysis (if contain a EC Code). The reactants and products part are translated in biochemicalReaction as default value.
+ * If they contain several compartment and annotations for the same species, the conversion is change for a transport.
+ * If the number of species between the reactant and product is different and the annotation correspond to a complex, the conversion is change to a complexAssembly<br/></ul>
+ * @param sbmlModel SBML object create with the path provide to the constructor
+ * @return biopaxModel BioPAX ontology corresponding to the SBML exported
+ */
+ public BioPaxModel biopaxexport(SBMLModel sbmlmodel)
+ {
+ //Mapping DB URI with the BioPAX subclass of physicalEntity
+ Hashtable<String, String> annotationSpecies = new Hashtable<String, String>();
+ //Fill the MAP of publication, {key: URI_database_Publication; value:official_Name}
+ Hashtable<String, String> publicationModel = new Hashtable<String, String>();
+ //Fill the MAP of annotation database about the species in SBML, {key: URI_database_Species; value:official_Name}
+ Hashtable<String, String> speciesAnnotationMap = new Hashtable<String, String>();
+ /*Get all the URI for taxonomy*/
+ Hashtable<String, String> taxonomyMap = new Hashtable<String, String>();
+
+ // Map of the created annotations to be sure that they are unique
+ // The key is the identifiers.org URI, the value is the biopax class instance
+ Hashtable<String, BioPAXElement> annotationXMLId = new Hashtable<String, BioPAXElement>();
+
+ int nbDatasource = 0;
+ int nbBiosource = 0;
+ boolean biomodelsCommentAdded = false;
+
+ /*Fill the Maps and List for the annotation parameter*/
+ SBML2BioPAXannotationParameter_l3.parseSBML2BioPAXConfigFile(annotationSpecies, publicationModel, speciesAnnotationMap, taxonomyMap);
+
+ /*Creates the model Factory*/
+ BioPAXFactory bioPAXFactory = getBioPaxFactory();
+ BioPAXFactory elementFactory = bioPAXFactory;
+
+ /*Creates the new BioPAX Model*/
+ BioPaxModel bioPaxModelGen = new BioPaxModel(bioPAXFactory.createModel());
+
+ Model bioPaxModel = bioPaxModelGen.getModel();
+
+ org.sbml.jsbml.Model sbmlModel = sbmlmodel.getModel();
+
+ /**
+ * Model element analysis.
+ *
+ * We will create the pathway BioPax Individual.
+ *
+ * */
+ String idmodel = new String();
+
+ if (sbmlModel.isSetId()) {
+ idmodel = sbmlModel.getId();
+ } else if (sbmlModel.isSetName()) {
+ idmodel = sbmlModel.getName();
+ } else {
+ idmodel = "BioModel";
+ }
+
+ //Creating the Pathway
+ BioPAXElement pathway = elementFactory.create(PATHWAY_CLASS_NAME, idmodel);
+
+ // Comment BioPAX date creation (today)
+ addComment(pathway, "This BioPAX Level" + biopaxLevel + " file was automatically generated on " + DateFormat.getDateInstance().format(new Date()) +
+ " by SBML2BioPAX-" + VERSION + ", BioModels.net, EMBL-EBI.");
+
+ //Adding the pathway to the model
+ bioPaxModel.add(pathway);
+
+ //Pathway annotation
+
+ //External references
+ for (CVTerm cvterm : sbmlModel.getAnnotation().getListOfCVTerms())
+ {
+ for (String annotationURI : cvterm.getResources()) // The qualifier is ignored at the moment in the biopax export
+ {
+ MiriamAnnotation miriamAnnotation = parseMiriamAnnotation(annotationURI);
+
+ if (miriamAnnotation != null) // it is a recognized URI
+ {
+ String annotationDB = miriamAnnotation.getUri(); // ex: http://identifiers.org/pubmed
+ String annotationIdentifier = miriamAnnotation.getId();// ex: 10659856
+
+ String rdfId = miriamAnnotation.getIdentifiers_orgURI();
+
+ if (rdfId == null)
+ {
+ debug("Could not create a proper miriamAnnotation for " + annotationURI);
+ continue;
+ }
+
+ if (publicationModel.containsKey(annotationDB)) // This is a publication annotation
+ {
+ // TODO : specific thing about the publication
+
+ String annotationDBname = publicationModel.get(annotationDB);
+
+ // check that the annotationDBnameplusIdentifier is unique and don't add it several times
+ BioPAXElement xref = annotationXMLId.get(rdfId);
+
+ if (xref == null)
+ {
+ //Creating the publication xref
+ xref = elementFactory.create(PUBLICATION_XREF_CLASS_NAME, rdfId);
+ setXrefDb(xref, annotationDBname);
+ setXrefId(xref, annotationIdentifier);
+
+ annotationXMLId.put(rdfId, xref); // filling the Map
+ }
+
+ //Adding the xref to the pathway
+ addXref(pathway, xref);
+ //Adding the xref to the model
+ bioPaxModel.add(xref);
+ }
+ else if (taxonomyMap.containsKey(annotationDB)) // Taxonomy annotation
+ {
+ BioPAXElement xref = annotationXMLId.get(rdfId);
+
+ if (xref == null)
+ {
+ //Creating the unification xref
+ xref = elementFactory.create(UNIFICATION_XREF_CLASS_NAME, rdfId);
+ setXrefId(xref, annotationIdentifier);
+ setXrefDb(xref, taxonomyMap.get(annotationDB));
+
+ annotationXMLId.put(rdfId, xref); // filling the Map
+
+ //Adding the xref to the model
+ bioPaxModel.add(xref);
+ }
+
+
+ //Creating the bioSource element
+ nbBiosource++;
+ BioPAXElement biosource = elementFactory.create(BIO_SOURCE, "biosource_" + nbBiosource);
+ // biosource.setDisplayName("bioSource");
+
+ addXref(biosource, xref);
+
+ //Adding the bioSource to the pathway
+ setOrganismToPathway(pathway, biosource);
+
+ //Adding the biosource to the model
+ bioPaxModel.add(biosource);
+ }
+ else // Any other annotation, not publication and not taxonomy, we create a UnificationXref
+ {
+ //all the other externals references BioModels, GO, KEGGpathway
+ // if (speciesAnnotationMap.containsKey(annotationDB)){ // Don't think this test if necessary anymore
+
+ BioPAXElement xref = annotationXMLId.get(rdfId);
+
+ if (xref == null)
+ {
+ //Creating the UnificationXref xref
+ xref = elementFactory.create(UNIFICATION_XREF_CLASS_NAME, rdfId);
+ setXrefId(xref, annotationIdentifier);
+
+ String db = speciesAnnotationMap.get(annotationDB);
+
+ if (db == null)
+ {
+ debug("The database " + annotationDB + " is not in the speciesAnnotation Map");
+
+ db = getDatatypeName(annotationDB);
+ }
+
+ setXrefDb(xref, db);
+
+ annotationXMLId.put(rdfId, xref); // filling the Map
+ }
+
+ //Adding the xref to the pathway
+ addXref(pathway, xref);
+ //adding xref to the model
+ bioPaxModel.add(xref);
+
+ // dataSource: the direct link to the original model
+ if (annotationDB.equals(BIOMODELS_URI) && cvterm.isModelQualifier()
+ && cvterm.getModelQualifierType().equals(CVTerm.Qualifier.BQM_IS))
+ {
+ // TODO : add Biomodels Publication ??
+ // TODO : For the other biomodels isDerivedFrom we should have a look at the relationXref
+
+ // TODO : this relationXref might more appropriate for the qualifier other than is
+
+ if (!biomodelsCommentAdded)
+ {
+ addComment(pathway, "The original model, '" + sbmlModel.getId() + "', was published in BioModels Database (http://www.ebi.ac.uk/biomodels/).");
+ biomodelsCommentAdded = true;
+ }
+
+ //Creating the dataSource element
+ nbDatasource++;
+
+ BioPAXElement datasource = elementFactory.create(PROVENANCE_CLASS_NAME, "datasource_" + nbDatasource);
+ addName(datasource, "BioModels Database");
+ setDisplayName(datasource, "BioModels Database");
+
+ addXref(datasource, xref);
+
+ //Adding the datasource to the model and to the pathway
+ bioPaxModel.add(datasource);
+ addDataSource(pathway, datasource);
+ }
+ }
+ }
+ else
+ {
+ debug("Could not create a proper miriamAnnotation for " + annotationURI);
+ continue;
+ }
+ }
+ }
+
+ // TODO : put the VCard in the BioPax file ??
+
+ //VCARD annotation
+// if (annotation.contains("<vCard:")){
+// String annotationVCARD = annotation.substring(annotation.indexOf("<vCard:"));
+// String lastpart = annotationVCARD.substring(annotationVCARD.lastIndexOf("</vCard:"));
+// int lastmarkup = annotationVCARD.lastIndexOf("</vCard:")+lastpart.indexOf('>')+1;
+// annotationVCARD = annotationVCARD.substring(0, lastmarkup);
+// Resource vcard = null;
+// String personURI = new String();
+// if (annotationVCARD.contains("vCard:Family")){
+// String family = annotationVCARD.substring(annotationVCARD.indexOf("vCard:Family")+13);
+// family = family.substring(0,family.indexOf("</vCard:Family"));
+// personURI = family;
+
+// vcard = biopaxModel.createResource(personURI);
+// vcard.addProperty(VCARD.Family, family);
+// }
+// if (annotationVCARD.contains("vCard:Given")){
+// String given = annotationVCARD.substring(annotationVCARD.indexOf("vCard:Given")+12);
+// given = given.substring(0, given.indexOf("</vCard:Given"));
+// vcard.addProperty(VCARD.Given, given);
+// }
+// if (annotationVCARD.contains("vCard:EMAIL")){
+// String email = annotationVCARD.substring(annotationVCARD.indexOf("vCard:EMAIL")+12);
+// email = email.substring(0, email.indexOf("</vCard:EMAIL"));
+// vcard.addProperty(VCARD.EMAIL, email);
+// }
+// if (annotationVCARD.contains("vCard:Orgname")){
+// String orgname = annotationVCARD.substring(annotationVCARD.indexOf("vCard:Orgname")+14);
+// orgname = orgname.substring(0, orgname.indexOf("</vCard:Orgname"));
+// vcard.addProperty(VCARD.Orgname, orgname);
+// }
+
+ //// BioPAXtool.addBiopaxLinkedProperty("COMMENT", personURI, sbmlModel.getId(), biopaxModel);
+// Individual pathwayind = biopaxModel.getIndividual(namespaceString+sbmlModel.getId());
+// Property vcardprop = biopaxModel.getProperty(biopaxString+"COMMENT");
+// Resource res = biopaxModel.getResource(namespaceString+personURI);
+// pathwayind.addProperty(vcardprop,res);
+// pathwayind.addProperty(vcardprop,"Model creator");
+// }
+
+
+
+ /**
+ * Compartments
+ *
+ *
+ *
+ * */
+ for (Compartment compartment : sbmlModel.getListOfCompartments())
+ {
+ //Creating the openControlledVocabulary
+ BioPAXElement vocab = elementFactory.create(CELLULAR_LOCATION_VOCABULARY, compartment.getId());
+
+ //Adding the openControlledVocabulary to the model
+ bioPaxModel.add(vocab);
+
+ if (compartment.isSetName())
+ {
+ //Adding the compartment name to the openControlledVocabulary
+ addTerm(vocab, compartment.getName());
+ }
+ else
+ {
+ //Adding the compartment id to the openControlledVocabulary
+ addTerm(vocab, compartment.getId());
+ }
+
+ //Compartment annotation
+ for (CVTerm cvterm : compartment.getAnnotation().getListOfCVTerms())
+ {
+ for (String annotation : cvterm.getResources())
+ {
+ MiriamAnnotation miriamAnnotation = parseMiriamAnnotation(annotation);
+
+ if (miriamAnnotation == null)
+ {
+ debug("Could not create a proper miriamAnnotation for " + annotation);
+ continue;
+ }
+
+ String annotationDB = miriamAnnotation.getUri();
+ String annotationIdentifier = miriamAnnotation.getId();
+ String rdfId = miriamAnnotation.getIdentifiers_orgURI();
+
+ if (speciesAnnotationMap.containsKey(annotationDB))
+ {
+ annotationDB = speciesAnnotationMap.get(annotationDB);
+ }
+ else
+ {
+ debug("The database " + annotationDB + " is not in the speciesAnnotation Map");
+ annotationDB = getDatatypeName(annotationDB);
+ }
+
+ BioPAXElement xref = annotationXMLId.get(rdfId);
+
+ if (xref == null)
+ {
+ // Creating the xref
+ xref = elementFactory.create(UNIFICATION_XREF_CLASS_NAME, rdfId);
+ setXrefId(xref, annotationIdentifier);
+ setXrefDb(xref, annotationDB);
+
+ annotationXMLId.put(rdfId, xref);
+ }
+
+ //Adding the xref to the openControlledVocabulary
+ addXref(vocab, xref);
+
+ //adding xref to the model
+ if(bioPaxModel.getByID(rdfId) == null)
+ {
+ debug("Adding an xref to the model !!! Compartment : " + rdfId);
+
+ bioPaxModel.add(xref);
+ }
+
+ }
+ }
+ }
+
+
+ /**
+ * Species
+ *
+ */
+ // System.out.println("SBML2BioPAX : URI Map : \n" + officialURIs);
+ // System.out.println("\n\nSBML2BioPAX : annotationSpeciesMap : \n" + annotationSpecies);
+
+ for (Species species : sbmlModel.getListOfSpecies())
+ {
+ String physicalEntityType = PHYSICAL_ENTITY; // default value, will change depending of the annotations
+ boolean isAComplex = false; // true if the annotation contain bqbiol:hasPart or reference to BIND database
+
+ ArrayList<MiriamAnnotation> speciesAnnotationList = new ArrayList<MiriamAnnotation>();
+
+ // WARNING : if two annotations are contradictory (the last is taken)
+
+ for (CVTerm cvterm : species.getAnnotation().getListOfCVTerms())
+ {
+ Qualifier cvTermQualifier = Qualifier.BQB_UNKNOWN;
+
+ if (cvterm.isBiologicalQualifier())
+ {
+ cvTermQualifier = cvterm.getBiologicalQualifierType();
+ }
+
+ if (cvTermQualifier.equals(Qualifier.BQB_HAS_PART))
+ {
+ isAComplex = true;
+ }
+
+ for (String annotation : cvterm.getResources())
+ {
+ MiriamAnnotation miriamAnnotation = parseMiriamAnnotation(annotation);
+
+ if (miriamAnnotation == null)
+ {
+ debug("Could not create a proper miriamAnnotation for " + annotation);
+ continue;
+ }
+
+ String annotationDB = miriamAnnotation.getUri();
+ String annotationIdentifier = miriamAnnotation.getId();
+ String annotationTestEnsembl = "";
+ speciesAnnotationList.add(miriamAnnotation);
+
+ // System.out.println("SBML2BioPax : miriamAnnotation = " + annotationDB + ", " + annotationIdentifier);
+
+ // constraint on a database which have yet an other entry
+ // ex:Chebi (small molecule DB) contain DNA and RNA and Ensembl
+ String officialAnnotation = null;
+
+ try
+ {
+ // TODO : here we have to be sure to normalize to the URIs used in the constraint file
+ officialAnnotation = annotationDB + ":" + URLEncoder.encode(annotationIdentifier, "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ officialAnnotation = annotation;
+ e.printStackTrace();
+ }
+
+ if ((annotationDB.length() + 8) < officialAnnotation.length()){
+ annotationTestEnsembl = officialAnnotation.substring(0, officialAnnotation.lastIndexOf(":") + 8);
+ }
+
+ // System.out.println("SBML2BioPax : species annotationDB = " + annotationDB);
+
+ if (annotationSpecies.containsKey(annotationDB)){
+
+ if ((annotationSpecies.get(annotationDB)).equals("complex")){
+ isAComplex = true;
+ }
+
+ physicalEntityType = annotationSpecies.get(annotationDB);
+
+ // System.out.println("SBML2BioPax : species physicalEntityType = " + physicalEntityType);
+
+ if (annotationSpecies.containsKey(officialAnnotation)){
+ physicalEntityType = annotationSpecies.get(annotation);
+ }
+ }
+ else
+ {
+ //Test for Ensembl annotation, check the 7 first characters of the identifier
+ if (annotationSpecies.containsKey(annotationTestEnsembl)){
+
+ if (speciesAnnotationList.size() == 0){
+ physicalEntityType = annotationSpecies.get(annotationTestEnsembl);
+ }
+
+ // System.out.println("SBML2BioPax : Ensembl : annotation = " + officialAnnotation);
+ // System.out.println("SBML2BioPax : Ensembl : physicalEntityType = " + physicalEntityType + "\n");
+ }
+ else {
+ //constraint on a database which have not already an other entry
+ if (annotationSpecies.containsKey(annotation)){
+ physicalEntityType = annotationSpecies.get(annotation);
+ }
+ }
+ }
+ }
+ if (isAComplex){
+ physicalEntityType = "Complex";
+ }
+ }
+
+ if (biopaxLevel == 2)
+ {
+ // Putting the first letter to lower case for BioPax Level 2 class name
+ physicalEntityType = physicalEntityType.substring(0, 1).toLowerCase() + physicalEntityType.substring(1);
+ }
+
+ //Creating the bioPaxElement corresponding to the physicalEntityType
+ BioPAXElement physicalEntity = elementFactory.create(physicalEntityType, species.getId());
+
+ if (species.isSetName())
+ {
+ //Setting the name
+ setDisplayName(physicalEntity, species.getName());
+ addName(physicalEntity, species.getName());
+ }
+ else
+ {
+ //Setting the id as name
+ setDisplayName(physicalEntity, species.getId());
+ }
+
+ for (int l = 0; l < speciesAnnotationList.size(); l++)
+ {
+ MiriamAnnotation miriamAnno = speciesAnnotationList.get(l);
+ String rdfId = miriamAnno.getIdentifiers_orgURI();
+
+ if (rdfId == null)
+ {
+ debug("Could not create a proper miriamAnnotation for '" + speciesAnnotationList.get(l).getUri()
+ + "' : '" + speciesAnnotationList.get(l).getId());
+ continue;
+ }
+
+ BioPAXElement xref = annotationXMLId.get(rdfId);
+
+ if (xref == null)
+ {
+ //Creating the unification xref
+ xref = elementFactory.create(UNIFICATION_XREF_CLASS_NAME, rdfId);
+ setXrefId(xref, miriamAnno.getId());
+
+ setXrefDb(xref, officialNames.get(miriamAnno.getUri()));
+
+ annotationXMLId.put(rdfId, xref);
+ }
+
+ //Adding the xref to the physicalEntity
+ addXref(physicalEntity, xref);
+
+ if(bioPaxModel.getByID(rdfId) == null)
+ {
+ debug("Adding an xref to the model !!! Species : " + rdfId);
+
+ bioPaxModel.add(xref);
+ }
+
+ }
+
+ //Adding the physicalEntity to the model
+ bioPaxModel.add(physicalEntity);
+ }
+
+
+
+ /**
+ * Reactions
+ *
+ * */
+ //Comment: -An EC-code can be added for the biochemicalReactions
+ for (Reaction reaction : sbmlModel.getListOfReactions())
+ {
+ String conversionI...
[truncated message content] |
|
From: <nik...@us...> - 2013-03-21 16:47:24
|
Revision: 252
http://sbfc.svn.sourceforge.net/sbfc/?rev=252&view=rev
Author: niko-rodrigue
Date: 2013-03-21 16:47:17 +0000 (Thu, 21 Mar 2013)
Log Message:
-----------
changed sbfConverter.sh to be able to find miriam.xml everywhere + added a script to be able to update the miriam registry export easily + changed minor version numbers
Modified Paths:
--------------
trunk/build.xml
trunk/sbfConverter.sh
Added Paths:
-----------
trunk/updateMiriamRegistry.sh
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2013-03-14 16:49:43 UTC (rev 251)
+++ trunk/build.xml 2013-03-21 16:47:17 UTC (rev 252)
@@ -12,11 +12,11 @@
</tstamp>
<property name="Name" value="System Biology Format Converter"/>
<property name="name" value="sbfc"/>
- <property name="version" value="1.2"/>
+ <property name="version" value="1.3.1"/>
<property name="sbml2xpp.version" value="1.2"/>
<property name="sbml2octave.version" value="1.0"/>
- <property name="sbml2biopax.version" value="3.0"/>
+ <property name="sbml2biopax.version" value="3.1.1"/>
<property name="year" value="${YEAR}"/>
@@ -346,7 +346,7 @@
<!-- Including only the necessary jar files -->
<copy todir="${dist.dir}/lib">
- <fileset dir="${jars.dir}/" includes="jsbml*.jar ${name}-${version}.jar Miriam* paxtool*">
+ <fileset dir="${jars.dir}/" includes="jsbml*.jar ${name}-${version}.jar miriam* paxtool*">
</fileset>
</copy>
Modified: trunk/sbfConverter.sh
===================================================================
--- trunk/sbfConverter.sh 2013-03-14 16:49:43 UTC (rev 251)
+++ trunk/sbfConverter.sh 2013-03-21 16:47:17 UTC (rev 252)
@@ -1,6 +1,7 @@
#!/bin/bash
-SBF_CONVERTER_HOME=`dirname $0`
+RESOLVE_LINK=`readlink -f $0`
+SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
LIB_PATH=${SBF_CONVERTER_HOME}/lib
if [ $# -lt 3 ]
@@ -65,7 +66,7 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$file'..." >> $LOG_FILE_MULTI 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE_MULTI 2>&1
- eval $COMMAND -Dmiriam.xml.export=/scratch/rodrigue/src/sbfConverter/sbfc/trunk/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
+ eval $COMMAND -Dmiriam.xml.export=${RESOLVE_LINK}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
sleep 0.1
done
else
@@ -80,7 +81,7 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$1'..." >> $LOG_FILE 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE 2>&1
- eval $COMMAND -Dmiriam.xml.export=/scratch/rodrigue/src/sbfConverter/sbfc/trunk/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
+ eval $COMMAND -Dmiriam.xml.export=${RESOLVE_LINK}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
fi
Added: trunk/updateMiriamRegistry.sh
===================================================================
--- trunk/updateMiriamRegistry.sh (rev 0)
+++ trunk/updateMiriamRegistry.sh 2013-03-21 16:47:17 UTC (rev 252)
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+wget --content-disposition http://www.ebi.ac.uk/miriam/main/export/xml/
+
+TODAY=`date +%F`
+
+mv Resources_all.xml miriam-${TODAY}.xml
+
+cp miriam-${TODAY}.xml miriam.xml
\ No newline at end of file
Property changes on: trunk/updateMiriamRegistry.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:eol-style
+ native
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2013-03-21 17:25:48
|
Revision: 254
http://sbfc.svn.sourceforge.net/sbfc/?rev=254&view=rev
Author: niko-rodrigue
Date: 2013-03-21 17:25:39 +0000 (Thu, 21 Mar 2013)
Log Message:
-----------
fixed sbfConverter.sh miriam.xml location + corrected the and dist target to include all the new files in the sitribution
Modified Paths:
--------------
trunk/build.xml
trunk/sbfConverter.sh
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2013-03-21 16:48:55 UTC (rev 253)
+++ trunk/build.xml 2013-03-21 17:25:39 UTC (rev 254)
@@ -193,7 +193,7 @@
<copy todir="${dist.dir}">
- <fileset dir="${basedir}/" includes="LICENSE.txt NEWS.txt README *.sh src/**/*.properties src/**/*.xml log4j.properties build.xml">
+ <fileset dir="${basedir}/" includes="LICENSE.txt NEWS.txt README *.sh src/**/*.properties src/**/*.xml log4j.properties build.x miriam.xml">
</fileset>
</copy>
<chmod dir="${dist.dir}" perm="ugo+rx" includes="*.sh"/>
@@ -252,7 +252,7 @@
<!-- Including only the necessary scripts -->
<copy todir="${dist.dir}">
- <fileset dir="${basedir}/" includes="sbfConverter.sh ${cname}*.sh"/>
+ <fileset dir="${basedir}/" includes="sbfConverter.sh ${cname}*.sh updateMiriamRegistry.sh"/>
</copy>
<chmod dir="${dist.dir}" perm="ugo+rx" includes="*.sh"/>
Modified: trunk/sbfConverter.sh
===================================================================
--- trunk/sbfConverter.sh 2013-03-21 16:48:55 UTC (rev 253)
+++ trunk/sbfConverter.sh 2013-03-21 17:25:39 UTC (rev 254)
@@ -66,7 +66,7 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$file'..." >> $LOG_FILE_MULTI 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE_MULTI 2>&1
- eval $COMMAND -Dmiriam.xml.export=${RESOLVE_LINK}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
+ eval $COMMAND -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $file >> $LOG_FILE_MULTI 2>&1
sleep 0.1
done
else
@@ -81,7 +81,7 @@
echo "`basename $0`: Convertion, using $CONVERTER_NAME, for '$1'..." >> $LOG_FILE 2>&1
echo "------------------------------------------------------------" >> $LOG_FILE 2>&1
- eval $COMMAND -Dmiriam.xml.export=${RESOLVE_LINK}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
+ eval $COMMAND -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml org.sbfc.converter.Converter $MODEL_NAME $CONVERTER_NAME $SBML_DIR >> $LOG_FILE 2>&1
fi
Modified: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java 2013-03-21 16:48:55 UTC (rev 253)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java 2013-03-21 17:25:39 UTC (rev 254)
@@ -623,7 +623,7 @@
physicalEntityType = physicalEntityType.substring(0, 1).toLowerCase() + physicalEntityType.substring(1);
}
- System.out.println("PhysicalEntity type : " + physicalEntityType);
+ // System.out.println("PhysicalEntity type : " + physicalEntityType);
//Creating the bioPaxElement corresponding to the physicalEntityType
BioPAXElement physicalEntity = elementFactory.create(physicalEntityType, species.getId());
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2013-03-27 16:37:30
|
Revision: 256
http://sbfc.svn.sourceforge.net/sbfc/?rev=256&view=rev
Author: niko-rodrigue
Date: 2013-03-27 16:37:22 +0000 (Wed, 27 Mar 2013)
Log Message:
-----------
corrections to the identifierUtil scripts and code to work fine with the new miriam local + uodated the sbfc jar file + updated miriam.xml
Modified Paths:
--------------
trunk/identifiersUtil.sh
trunk/miriam.xml
trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java
trunk/url2urn.sh
Added Paths:
-----------
trunk/lib/sbfc-1.3.1.jar
Removed Paths:
-------------
trunk/lib/sbfc-1.2.jar
Modified: trunk/identifiersUtil.sh
===================================================================
--- trunk/identifiersUtil.sh 2013-03-27 13:29:46 UTC (rev 255)
+++ trunk/identifiersUtil.sh 2013-03-27 16:37:22 UTC (rev 256)
@@ -1,6 +1,8 @@
#!/bin/bash
-SBF_CONVERTER_HOME=`dirname $0`
+RESOLVE_LINK=`readlink -f $0`
+
+SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
LIB_PATH=${SBF_CONVERTER_HOME}/lib
if [ $# -lt 2 ]
@@ -31,10 +33,10 @@
LOG_FILE_FOLDER=${SBF_CONVERTER_HOME}/log/`basename $SBML_DIR .xml`
LOG_FILE=${LOG_FILE_FOLDER}/`basename $SBML_DIR .xml`-$CONVERTER_NAME-export-`date +%F`.log
-COMMAND="bsub -o $LOG_FILE java "
+COMMAND="bsub -o $LOG_FILE java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml "
if [ "`which bsub 2> /dev/null`" == "" ] ; then
- COMMAND="java "
+ COMMAND="java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml "
fi
export CLASSPATH=
@@ -57,7 +59,7 @@
mkdir -p $LOG_FILE_FOLDER
fi
if [ "$COMMAND" != "java " ] ; then
- COMMAND="bsub -o $LOG_FILE_MULTI java "
+ COMMAND="bsub -o $LOG_FILE_MULTI java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml "
fi
echo "------------------------------------------------------------" >> $LOG_FILE_MULTI 2>&1
Deleted: trunk/lib/sbfc-1.2.jar
===================================================================
(Binary files differ)
Added: trunk/lib/sbfc-1.3.1.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/sbfc-1.3.1.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/miriam.xml
===================================================================
--- trunk/miriam.xml 2013-03-27 13:29:46 UTC (rev 255)
+++ trunk/miriam.xml 2013-03-27 16:37:22 UTC (rev 256)
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Export of MIRIAM Resources (full) -->
-<!-- Generated: Thu Mar 21 16:42:42 GMT 2013 -->
+<!-- Generated: Wed Mar 27 13:18:21 GMT 2013 -->
<!-- http://www.ebi.ac.uk/miriam/ -->
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2013-03-21T16:42:42+00:00" data-version="2013-03-21T11:02:00+00:00">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2013-03-27T13:18:21+00:00" data-version="2013-03-21T17:27:14+00:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
<comment>BIND doesn't exist any more and its successor (BOND) is not open-access.</comment>
<name>BIND</name>
@@ -58,6 +58,7 @@
<uri type="URL">http://identifiers.org/chebi/</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/chebi/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.chebi</uri>
+ <uri type="URL" deprecated="true">http://identifiers.org/obo.chebi/</uri>
</uris>
<namespace>chebi</namespace>
<documentations>
@@ -536,7 +537,7 @@
<documentation type="PMID">urn:miriam:pubmed:15608177</documentation>
</documentations>
<resources>
- <resource id="MIR:00100018" state="down" reliability="97">
+ <resource id="MIR:00100018" state="down" reliability="96">
<dataResource>http://www.ebi.ac.uk/interpro/</dataResource>
<dataEntityExample>IPR000100</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id</dataEntry>
@@ -691,7 +692,7 @@
<dataInstitution>National Center for Biotechnology Information</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100028" state="up" reliability="99">
+ <resource id="MIR:00100028" state="down" reliability="99">
<dataResource>http://www.ebi.ac.uk/Databases/MEDLINE/medline.html</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id]</dataEntry>
@@ -699,7 +700,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100032" state="down" reliability="99">
+ <resource id="MIR:00100032" state="down" reliability="98">
<dataResource>http://www.ebi.ac.uk/citexplore/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id</dataEntry>
@@ -2295,7 +2296,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100078" state="up" reliability="70">
+ <resource id="MIR:00100078" state="up" reliability="71">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>AT1G01030</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?type=locus&name=$id</dataEntry>
@@ -2697,7 +2698,7 @@
<documentation type="PMID">urn:miriam:pubmed:10592232</documentation>
</documentations>
<resources>
- <resource id="MIR:00100089" state="up" reliability="99">
+ <resource id="MIR:00100089" state="down" reliability="98">
<dataResource>http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/</dataResource>
<dataEntityExample>PR00001</dataEntityExample>
<dataEntry>http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false&regexpr=off</dataEntry>
@@ -2881,7 +2882,7 @@
<documentation type="URL">http://www.jsbi.org/journal/GIW04/GIW04P058.pdf</documentation>
</documentations>
<resources>
- <resource id="MIR:00100095" state="up" reliability="92">
+ <resource id="MIR:00100095" state="down" reliability="92">
<dataResource>http://www.3dmet.dna.affrc.go.jp/</dataResource>
<dataEntityExample>B00162</dataEntityExample>
<dataEntry>http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id</dataEntry>
@@ -3217,7 +3218,7 @@
<documentation type="URL">http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100105" state="up" reliability="98">
+ <resource id="MIR:00100105" state="down" reliability="98">
<dataResource>http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp</dataResource>
<dataEntityExample>37</dataEntityExample>
<dataEntry>http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id</dataEntry>
@@ -5230,7 +5231,7 @@
<dataInstitution>Department of Biochemistry, Stellenbosch University</dataInstitution>
<dataLocation>South Africa</dataLocation>
</resource>
- <resource id="MIR:00100169" state="down" reliability="92">
+ <resource id="MIR:00100169" state="up" reliability="92">
<dataResource>http://jjj.bio.vu.nl/database/index.html</dataResource>
<dataEntityExample>curien</dataEntityExample>
<dataEntry>http://jjj.bio.vu.nl/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$id</dataEntry>
@@ -7380,7 +7381,7 @@
<documentation type="PMID">urn:miriam:pubmed:17904107</documentation>
</documentations>
<resources>
- <resource id="MIR:00100248" state="down" reliability="50">
+ <resource id="MIR:00100248" state="down" reliability="49">
<dataResource>http://2dbase.techfak.uni-bielefeld.de/</dataResource>
<dataEntityExample>P39172</dataEntityExample>
<dataEntry>http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$id</dataEntry>
@@ -7797,7 +7798,7 @@
<documentation type="PMID">urn:miriam:pubmed:19884133</documentation>
</documentations>
<resources>
- <resource id="MIR:00100261" state="down" reliability="84">
+ <resource id="MIR:00100261" state="down" reliability="83">
<dataResource>http://bacteria.ensembl.org/</dataResource>
<dataEntityExample>EBESCT00000015660</dataEntityExample>
<dataEntry>http://bacteria.ensembl.org/id/$id</dataEntry>
@@ -8863,7 +8864,7 @@
<documentation type="PMID">urn:miriam:pubmed:18931379</documentation>
</documentations>
<resources>
- <resource id="MIR:00100290" state="up" reliability="96">
+ <resource id="MIR:00100290" state="up" reliability="95">
<dataResource>http://swissmodel.expasy.org/</dataResource>
<dataEntityExample>P23298</dataEntityExample>
<dataEntry>http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id</dataEntry>
@@ -8903,7 +8904,7 @@
<documentation type="PMID">urn:miriam:pubmed:19028744</documentation>
</documentations>
<resources>
- <resource id="MIR:00100291" state="down" reliability="89">
+ <resource id="MIR:00100291" state="down" reliability="88">
<dataResource>http://www.vectorbase.org/</dataResource>
<dataEntityExample>ISCW007415</dataEntityExample>
<dataEntry>https://www.vectorbase.org/search/site/$id?&site="Genome"</dataEntry>
@@ -9002,7 +9003,7 @@
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100295" state="down" reliability="78">
+ <resource id="MIR:00100295" state="down" reliability="77">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>CCO:P0000023</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1507?p=terms&conceptid=$id</dataEntry>
@@ -9476,7 +9477,7 @@
<documentation type="PMID">urn:miriam:pubmed:22135287</documentation>
</documentations>
<resources>
- <resource id="MIR:00100317" state="up" reliability="98">
+ <resource id="MIR:00100317" state="up" reliability="97">
<dataResource>http://lemur.amu.edu.pl/share/php/mirnest/</dataResource>
<dataEntityExample>MNEST029358</dataEntityExample>
<dataEntry>http://lemur.amu.edu.pl/share/php/mirnest/search.php?search_term=$id</dataEntry>
@@ -10019,7 +10020,7 @@
<dataInstitution>BCCM, Brussels</dataInstitution>
<dataLocation>Belgium</dataLocation>
</resource>
- <resource id="MIR:00100336" state="up" reliability="88">
+ <resource id="MIR:00100336" state="up" reliability="89">
<dataResource>http://www.fr.cabri.org/</dataResource>
<dataEntityExample>dsmz_mutz-id:ACC 291</dataEntityExample>
<dataEntry>http://www.fr.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]</dataEntry>
@@ -14093,7 +14094,7 @@
<documentation type="PMID">urn:miriam:pubmed:22121216</documentation>
</documentations>
<resources>
- <resource id="MIR:00100467" state="up" reliability="100">
+ <resource id="MIR:00100467" state="up" reliability="99">
<dataResource>http://pombe.oridb.org/index.php</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://pombe.oridb.org/details.php?id=$id</dataEntry>
@@ -14127,7 +14128,7 @@
<documentation type="PMID">urn:miriam:pubmed:22121216</documentation>
</documentations>
<resources>
- <resource id="MIR:00100468" state="up" reliability="100">
+ <resource id="MIR:00100468" state="up" reliability="99">
<dataResource>http://cerevisiae.oridb.org/index.php</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://cerevisiae.oridb.org/details.php?id=$id</dataEntry>
@@ -14390,7 +14391,7 @@
<documentation type="PMID">urn:miriam:pubmed:20398331</documentation>
</documentations>
<resources>
- <resource id="MIR:00100478" state="up" reliability="99">
+ <resource id="MIR:00100478" state="up" reliability="98">
<dataResource>http://www.lrg-sequence.org/</dataResource>
<dataEntityExample>LRG_1</dataEntityExample>
<dataEntry>ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$id.xml</dataEntry>
@@ -14771,7 +14772,7 @@
<documentation type="PMID">urn:miriam:pubmed:18689816</documentation>
</documentations>
<resources>
- <resource id="MIR:00100499" state="up" reliability="94">
+ <resource id="MIR:00100499" state="up" reliability="95">
<dataResource>http://kinase.bioinformatics.tw/</dataResource>
<dataEntityExample>AURKA</dataEntityExample>
<dataEntry>http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$id&drawing=0&sorting=0&kinome=1</dataEntry>
@@ -14806,7 +14807,7 @@
<documentation type="PMID">urn:miriam:pubmed:18689816</documentation>
</documentations>
<resources>
- <resource id="MIR:00100500" state="up" reliability="94">
+ <resource id="MIR:00100500" state="up" reliability="95">
<dataResource>http://kinase.bioinformatics.tw/</dataResource>
<dataEntityExample>AURKA</dataEntityExample>
<dataEntry>http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$id&drawing=0&sorting=0&kinome=0</dataEntry>
@@ -15040,7 +15041,7 @@
<dataInstitution>European Bioinformatics Institute, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100510" state="up" reliability="97">
+ <resource id="MIR:00100510" state="up" reliability="98">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>0004859</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1136?p=terms&conceptid=efo:EFO_$id</dataEntry>
@@ -15569,7 +15570,7 @@
<documentation type="URL">http://tolweb.org</documentation>
</documentations>
<resources>
- <resource id="MIR:00100525" state="up" reliability="92">
+ <resource id="MIR:00100525" state="up" reliability="93">
<dataResource>http://tolweb.org/tree/</dataResource>
<dataEntityExample>98034</dataEntityExample>
<dataEntry>http://tolweb.org/$id</dataEntry>
@@ -15605,7 +15606,7 @@
<documentation type="URL">http://variationontology.org/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100526" state="up" reliability="92">
+ <resource id="MIR:00100526" state="up" reliability="93">
<dataResource>http://www.variationontology.org/</dataResource>
<dataEntityExample>VariO:0294</dataEntityExample>
<dataEntry>http://www.variationontology.org/cgi-bin/amivario/term-details.cgi?term=$id</dataEntry>
@@ -16130,7 +16131,7 @@
<documentation type="URL">http://www.biocarta.com/about/index.asp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100544" state="unknown" reliability="0">
+ <resource id="MIR:00100544" state="up" reliability="100">
<dataResource>http://www.biocarta.com/</dataResource>
<dataEntityExample>h_aktPathway</dataEntityExample>
<dataEntry>http://www.biocarta.com/pathfiles/$id.asp</dataEntry>
@@ -16166,7 +16167,7 @@
<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
</documentations>
<resources>
- <resource id="MIR:00100545" state="unknown" reliability="0">
+ <resource id="MIR:00100545" state="up" reliability="100">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>P00266</dataEntityExample>
<dataEntry>http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$id</dataEntry>
Modified: trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java 2013-03-27 13:29:46 UTC (rev 255)
+++ trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java 2013-03-27 16:37:22 UTC (rev 256)
@@ -53,9 +53,9 @@
if (annotationPrefix == null) {
update = true;
} else if (annotationPrefix.equals(urlPrefix)) {
- url2urn = true;
- } else if (annotationPrefix.equals(urnPrefix)) {
urn2url = true;
+ } else if (annotationPrefix.equals(urnPrefix)) {
+ url2urn = true;
}
for (CVTerm cvTerm : sbase.getCVTerms()) {
@@ -83,6 +83,8 @@
newURI = link.getMiriamURI(annotationString);
}
+ // System.out.println(annotationPrefix + " @" + annotationString + "@ ==> " + newURI);
+
if (newURI == null) {
System.out.println("Error : the uri '" + annotationString + "' is not recognized by miriamws !!");
newURI = annotationString;
@@ -188,8 +190,7 @@
String jsbmlWriteFileName = fileName.replaceFirst(".xml", fileNameSuffix + ".xml");
- System.out.printf("Reading %s and writing %s\n",
- fileName, jsbmlWriteFileName);
+ System.out.printf("Reading %s and writing %s\n", fileName, jsbmlWriteFileName);
SBMLDocument testDocument;
long afterRead = 0;
@@ -234,10 +235,8 @@
*
* @return
*/
- public static String anyStringAnnotationsUpdate(String anyString) {
-
- // TODO : matches the annotations to change
-
- return anyString;
+ public static String anyStringAnnotationsUpdate(String anyURI)
+ {
+ return link.getMiriamURI(anyURI);
}
}
Modified: trunk/url2urn.sh
===================================================================
--- trunk/url2urn.sh 2013-03-27 13:29:46 UTC (rev 255)
+++ trunk/url2urn.sh 2013-03-27 16:37:22 UTC (rev 256)
@@ -11,10 +11,7 @@
#
##${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel URL2URN $1
-#${SBF_CONVERTER_HOME}/identifiersUtil.sh -m $@
+${SBF_CONVERTER_HOME}/identifiersUtil.sh -m $@
-echo The converter url to urn is not yet implemented, waiting for the update of the miriam web services.
-exit 2
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2013-09-26 10:03:26
|
Revision: 259
http://sourceforge.net/p/sbfc/code/259
Author: niko-rodrigue
Date: 2013-09-26 10:03:23 +0000 (Thu, 26 Sep 2013)
Log Message:
-----------
updated the paxtools jar + when creating a biopax L2 model, we also use the LevelUpgrader paxtools class to create automatically a Biopax L3 model that contain more or less the correct L3 entities that are missing in our own L3 converter. We need to check if we are happy with this L3 version or if we want ot make some modifications
Modified Paths:
--------------
trunk/src/org/sbfc/converter/models/BioPaxModel.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
Added Paths:
-----------
trunk/lib/paxtools-4.2.0-no-jena.jar
Removed Paths:
-------------
trunk/lib/paxtools-4.1.1.jar
Deleted: trunk/lib/paxtools-4.1.1.jar
===================================================================
(Binary files differ)
Added: trunk/lib/paxtools-4.2.0-no-jena.jar
===================================================================
(Binary files differ)
Index: trunk/lib/paxtools-4.2.0-no-jena.jar
===================================================================
--- trunk/lib/paxtools-4.2.0-no-jena.jar 2013-05-01 15:46:45 UTC (rev 258)
+++ trunk/lib/paxtools-4.2.0-no-jena.jar 2013-09-26 10:03:23 UTC (rev 259)
Property changes on: trunk/lib/paxtools-4.2.0-no-jena.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/zip
\ No newline at end of property
Modified: trunk/src/org/sbfc/converter/models/BioPaxModel.java
===================================================================
--- trunk/src/org/sbfc/converter/models/BioPaxModel.java 2013-05-01 15:46:45 UTC (rev 258)
+++ trunk/src/org/sbfc/converter/models/BioPaxModel.java 2013-09-26 10:03:23 UTC (rev 259)
@@ -34,7 +34,9 @@
import java.io.FileOutputStream;
import java.io.IOException;
+import org.biopax.paxtools.converter.LevelUpgrader;
import org.biopax.paxtools.io.SimpleIOHandler;
+import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.sbfc.converter.exceptions.ReadModelError;
@@ -97,6 +99,25 @@
} catch (RuntimeException e) {
e.printStackTrace();
}
+
+ if (model.getLevel().equals(BioPAXLevel.L2))
+ {
+ LevelUpgrader levelUpgrader = new LevelUpgrader();
+
+ Model level3Model = levelUpgrader.filter(model);
+
+ export = new SimpleIOHandler(level3Model.getLevel());
+
+ try {
+ export.convertToOWL(level3Model,new FileOutputStream(fileName + "L3upgrade.owl"));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (RuntimeException e) {
+ e.printStackTrace();
+ }
+ }
}
Modified: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java 2013-05-01 15:46:45 UTC (rev 258)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX.java 2013-09-26 10:03:23 UTC (rev 259)
@@ -35,10 +35,9 @@
import java.util.Hashtable;
import java.util.Set;
-import org.biopax.paxtools.impl.level2.Level2FactoryImpl;
-import org.biopax.paxtools.impl.level3.Level3FactoryImpl;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.BioPAXFactory;
+import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.BioSource;
import org.biopax.paxtools.model.level3.CellularLocationVocabulary;
@@ -1037,11 +1036,11 @@
{
if (biopaxLevel == 3)
{
- return new Level3FactoryImpl();
+ return BioPAXLevel.L3.getDefaultFactory();
}
else if (biopaxLevel == 2)
{
- return new Level2FactoryImpl();
+ return BioPAXLevel.L2.getDefaultFactory();
}
return null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2013-09-26 10:05:32
|
Revision: 260
http://sourceforge.net/p/sbfc/code/260
Author: niko-rodrigue
Date: 2013-09-26 10:05:27 +0000 (Thu, 26 Sep 2013)
Log Message:
-----------
updated the identifiersUtil converter to be able to correct incomplete ec-code annotations by adding '.-' for the missing part. It will also remove ec-code annotation where the identifiers is empty
Modified Paths:
--------------
trunk/build.xml
trunk/miriam.xml
trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java
trunk/src/org/sbfc/converter/sbml2sbml/SBML2SBML.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotation.java
Added Paths:
-----------
trunk/lib/sbfc-1.3.2.jar
Removed Paths:
-------------
trunk/lib/sbfc-1.3.1.jar
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2013-09-26 10:03:23 UTC (rev 259)
+++ trunk/build.xml 2013-09-26 10:05:27 UTC (rev 260)
@@ -12,7 +12,7 @@
</tstamp>
<property name="Name" value="System Biology Format Converter"/>
<property name="name" value="sbfc"/>
- <property name="version" value="1.3.1"/>
+ <property name="version" value="1.3.2"/>
<property name="sbml2xpp.version" value="1.2"/>
<property name="sbml2octave.version" value="1.0"/>
Deleted: trunk/lib/sbfc-1.3.1.jar
===================================================================
(Binary files differ)
Added: trunk/lib/sbfc-1.3.2.jar
===================================================================
(Binary files differ)
Index: trunk/lib/sbfc-1.3.2.jar
===================================================================
--- trunk/lib/sbfc-1.3.2.jar 2013-09-26 10:03:23 UTC (rev 259)
+++ trunk/lib/sbfc-1.3.2.jar 2013-09-26 10:05:27 UTC (rev 260)
Property changes on: trunk/lib/sbfc-1.3.2.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/zip
\ No newline at end of property
Modified: trunk/miriam.xml
===================================================================
--- trunk/miriam.xml 2013-09-26 10:03:23 UTC (rev 259)
+++ trunk/miriam.xml 2013-09-26 10:05:27 UTC (rev 260)
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- Export of MIRIAM Resources (full) -->
-<!-- Generated: Wed Mar 27 13:18:21 GMT 2013 -->
-<!-- http://www.ebi.ac.uk/miriam/ -->
+<!-- Export of Identifiers.org's Registry (full) -->
+<!-- Generated: Thu Sep 26 10:25:10 BST 2013 -->
+<!-- http://identifiers.org/registry/ -->
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2013-03-27T13:18:21+00:00" data-version="2013-03-21T17:27:14+00:00">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2013-09-26T10:25:10+01:00" data-version="2013-09-24T14:04:20+01:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
- <comment>BIND doesn't exist any more and its successor (BOND) is not open-access.</comment>
+ <comment>BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
<name>BIND</name>
<synonyms>
<synonym>Biomolecular Interaction Network Database</synonym>
@@ -81,6 +81,14 @@
<dataInstitution>European Bioinformatics Institute, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
+ <resource id="MIR:00100565" state="down" reliability="98">
+ <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataEntityExample>CHEBI:36927</dataEntityExample>
+ <dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
+ <dataInfo>ChEBI through BioPortal</dataInfo>
+ <dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
</resources>
<tags>
<tag>chemical</tag>
@@ -97,9 +105,9 @@
</annotation>
</datatype>
- <datatype id="MIR:00000003" pattern="^ENS[A-Z]*[FPTG]\d{11}(\.\d+)?$">
+ <datatype id="MIR:00000003" pattern="^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z]))$" restricted="true">
<name>Ensembl</name>
- <definition>Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.</definition>
+ <definition>Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.</definition>
<uris>
<uri type="URN">urn:miriam:ensembl</uri>
<uri type="URL">http://identifiers.org/ensembl/</uri>
@@ -110,15 +118,45 @@
<documentation type="PMID">urn:miriam:pubmed:16381931</documentation>
</documentations>
<resources>
- <resource id="MIR:00100011" state="up" reliability="98">
+ <resource id="MIR:00100011" state="up" reliability="98" primary="true">
<dataResource>http://www.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://www.ensembl.org/id/$id</dataEntry>
- <dataInfo>Ensembl</dataInfo>
- <dataInstitution>Sanger Institute and European Bioinformatics Institute</dataInstitution>
+ <dataInfo>Ensembl at Sanger/EMBL-EBI</dataInfo>
+ <dataInstitution>Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
+ <resource id="MIR:00100561" state="up" reliability="97">
+ <dataResource>http://uswest.ensembl.org/</dataResource>
+ <dataEntityExample>ENSG00000139618</dataEntityExample>
+ <dataEntry>http://uswest.ensembl.org/id/$id</dataEntry>
+ <dataInfo>Ensembl US West mirror</dataInfo>
+ <dataInstitution></dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
+ <resource id="MIR:00100562" state="up" reliability="97">
+ <dataResource>http://useast.ensembl.org/</dataResource>
+ <dataEntityExample>ENSG00000139618</dataEntityExample>
+ <dataEntry>http://useast.ensembl.org/id/$id</dataEntry>
+ <dataInfo>Ensembl US East mirror</dataInfo>
+ <dataInstitution></dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
+ <resource id="MIR:00100563" state="up" reliability="97">
+ <dataResource>http://asia.ensembl.org/</dataResource>
+ <dataEntityExample>ENSG00000139618</dataEntityExample>
+ <dataEntry>http://asia.ensembl.org/id/$id</dataEntry>
+ <dataInfo>Ensembl Asia mirror</dataInfo>
+ <dataInstitution></dataInstitution>
+ <dataLocation>Singapore</dataLocation>
+ </resource>
</resources>
+ <restrictions>
+ <restriction type="2" desc="Data aggregation">
+ <statement>While Ensembl data is nominally restricted to vertebrate species, it also includes out groups (Dorsophila, Saccharomyces and C. elegans) used in comparative analysis. These species can also be referenced through Ensembl Genomes datasets.</statement>
+ <link desc="Ensembl overlap">http://www.ensemblgenomes.org/info/data_access</link>
+ </restriction>
+ </restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
@@ -172,7 +210,7 @@
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100003" state="up" reliability="98">
+ <resource id="MIR:00100003" state="up" reliability="99">
<dataResource>http://enzyme.expasy.org/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://enzyme.expasy.org/EC/$id</dataEntry>
@@ -234,6 +272,7 @@
<namespace>uniprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381842</documentation>
+ <documentation type="PMID">urn:miriam:pubmed:23161681</documentation>
</documentations>
<resources>
<resource id="MIR:00100134" state="up" reliability="100">
@@ -244,7 +283,7 @@
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
- <resource id="MIR:00100164" state="up" reliability="99">
+ <resource id="MIR:00100164" state="up" reliability="99" primary="true">
<dataResource>http://purl.uniprot.org/</dataResource>
<dataEntityExample>P62158</dataEntityExample>
<dataEntry>http://purl.uniprot.org/uniprot/$id</dataEntry>
@@ -323,7 +362,7 @@
<documentation type="URL">http://www.ncbi.nlm.nih.gov/books/NBK53758/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100007" state="up" reliability="99">
+ <resource id="MIR:00100007" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/Taxonomy/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id</dataEntry>
@@ -339,7 +378,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100299" state="probably up" reliability="97">
+ <resource id="MIR:00100299" state="probably up" reliability="98">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/Taxon:$id</dataEntry>
@@ -347,10 +386,10 @@
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100507" state="up" reliability="100">
+ <resource id="MIR:00100507" state="down" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>9606</dataEntityExample>
- <dataEntry>http://bioportal.bioontology.org/ontologies/1132?p=terms&conceptid=obo:NCBITaxon_$id</dataEntry>
+ <dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_$id</dataEntry>
<dataInfo>Taxonomy through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
@@ -387,7 +426,7 @@
<documentation type="PMID">urn:miriam:pubmed:20587024</documentation>
</documentations>
<resources>
- <resource id="MIR:00100006" state="up" reliability="99">
+ <resource id="MIR:00100006" state="up" reliability="99" primary="true">
<dataResource>http://www.ebi.ac.uk/biomodels/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/biomodels-main/$id</dataEntry>
@@ -395,7 +434,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100107" state="up" reliability="98">
+ <resource id="MIR:00100107" state="up" reliability="94">
<dataResource>http://biomodels.caltech.edu/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://biomodels.caltech.edu/$id</dataEntry>
@@ -500,12 +539,12 @@
<documentation type="PMID">urn:miriam:pubmed:17145710</documentation>
</documentations>
<resources>
- <resource id="MIR:00100017" state="up" reliability="95">
+ <resource id="MIR:00100017" state="up" reliability="96">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>EBI-2307691</dataEntityExample>
- <dataEntry>http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id</dataEntry>
- <dataInfo>IntAct</dataInfo>
- <dataInstitution>European Bioinformatics Institute</dataInstitution>
+ <dataEntry>http://www.ebi.ac.uk/intact/interaction/$id</dataEntry>
+ <dataInfo>IntAct at EBI</dataInfo>
+ <dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
</resources>
@@ -537,10 +576,10 @@
<documentation type="PMID">urn:miriam:pubmed:15608177</documentation>
</documentations>
<resources>
- <resource id="MIR:00100018" state="down" reliability="96">
+ <resource id="MIR:00100018" state="up" reliability="96">
<dataResource>http://www.ebi.ac.uk/interpro/</dataResource>
<dataEntityExample>IPR000100</dataEntityExample>
- <dataEntry>http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id</dataEntry>
+ <dataEntry>http://www.ebi.ac.uk/interpro/entry/$id</dataEntry>
<dataInfo>InterPro</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
@@ -684,7 +723,7 @@
<documentation type="PMID">urn:miriam:pubmed:16381840</documentation>
</documentations>
<resources>
- <resource id="MIR:00100023" state="up" reliability="99">
+ <resource id="MIR:00100023" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/PubMed/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/pubmed/$id</dataEntry>
@@ -692,22 +731,6 @@
<dataInstitution>National Center for Biotechnology Information</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100028" state="down" reliability="99">
- <dataResource>http://www.ebi.ac.uk/Databases/MEDLINE/medline.html</dataResource>
- <dataEntityExample>16333295</dataEntityExample>
- <dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id]</dataEntry>
- <dataInfo>PubMed through SRS@EBI</dataInfo>
- <dataInstitution>European Bioinformatics Institute</dataInstitution>
- <dataLocation>United Kingdom</dataLocation>
- </resource>
- <resource id="MIR:00100032" state="down" reliability="98">
- <dataResource>http://www.ebi.ac.uk/citexplore/</dataResource>
- <dataEntityExample>16333295</dataEntityExample>
- <dataEntry>http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id</dataEntry>
- <dataInfo>CiteXplore</dataInfo>
- <dataInstitution>European Bioinformatics Institute</dataInstitution>
- <dataLocation>United Kingdom</dataLocation>
- </resource>
<resource id="MIR:00100064" state="up" reliability="96">
<dataResource>http://www.hubmed.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
@@ -724,6 +747,22 @@
<dataInstitution>Europe PubMed Central partners</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
+ <resource id="MIR:00100028" obsolete="true">
+ <dataResource>http://www.ebi.ac.uk/Databases/MEDLINE/medline.html</dataResource>
+ <dataEntityExample>16333295</dataEntityExample>
+ <dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id]</dataEntry>
+ <dataInfo>PubMed through SRS@EBI</dataInfo>
+ <dataInstitution>European Bioinformatics Institute</dataInstitution>
+ <dataLocation>United Kingdom</dataLocation>
+ </resource>
+ <resource id="MIR:00100032" obsolete="true">
+ <dataResource>http://www.ebi.ac.uk/citexplore/</dataResource>
+ <dataEntityExample>16333295</dataEntityExample>
+ <dataEntry>http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id</dataEntry>
+ <dataInfo>CiteXplore</dataInfo>
+ <dataInstitution>European Bioinformatics Institute</dataInstitution>
+ <dataLocation>United Kingdom</dataLocation>
+ </resource>
<resource id="MIR:00100462" obsolete="true">
<dataResource>http://ukpmc.ac.uk/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
@@ -766,7 +805,7 @@
<documentation type="PMID">urn:miriam:pubmed:15608251</documentation>
</documentations>
<resources>
- <resource id="MIR:00100024" state="up" reliability="99">
+ <resource id="MIR:00100024" state="up" reliability="99" primary="true">
<dataResource>http://omim.org/</dataResource>
<dataEntityExample>603903</dataEntityExample>
<dataEntry>http://omim.org/entry/$id</dataEntry>
@@ -902,7 +941,7 @@
</uris>
<namespace>doi</namespace>
<resources>
- <resource id="MIR:00100010" state="up" reliability="99">
+ <resource id="MIR:00100010" state="up" reliability="99" primary="true">
<dataResource>http://www.doi.org/</dataResource>
<dataEntityExample>10.1038/nbt1156</dataEntityExample>
<dataEntry>http://dx.doi.org/$id</dataEntry>
@@ -1049,11 +1088,13 @@
</synonyms>
<definition>The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.</definition>
<uris>
- <uri type="URN">urn:miriam:obo.go</uri>
- <uri type="URL">http://identifiers.org/obo.go/</uri>
+ <uri type="URN">urn:miriam:go</uri>
+ <uri type="URL">http://identifiers.org/go/</uri>
<uri type="URL" deprecated="true">http://www.geneontology.org/</uri>
+ <uri type="URN" deprecated="true">urn:miriam:obo.go</uri>
+ <uri type="URL" deprecated="true">http://identifiers.org/obo.go/</uri>
</uris>
- <namespace>obo.go</namespace>
+ <namespace>go</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681407</documentation>
<documentation type="PMID">urn:miriam:pubmed:10802651</documentation>
@@ -1067,7 +1108,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100013" state="up" reliability="98">
+ <resource id="MIR:00100013" state="up" reliability="98" primary="true">
<dataResource>http://amigo.geneontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=$id</dataEntry>
@@ -1083,14 +1124,22 @@
<dataInstitution>The Jackson Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100237" state="up" reliability="98">
+ <resource id="MIR:00100237" state="down" reliability="98">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
- <dataEntry>http://bioportal.bioontology.org/ontologies/1070?p=terms&conceptid=$id</dataEntry>
+ <dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
<dataInfo>GO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
+ <resource id="MIR:00100585" state="up" reliability="100">
+ <dataResource>http://www.pantherdb.org/</dataResource>
+ <dataEntityExample>GO:0000003</dataEntityExample>
+ <dataEntry>http://www.pantherdb.org/panther/category.do?categoryAcc=$id</dataEntry>
+ <dataInfo>GO through PANTHER</dataInfo>
+ <dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
<resource id="MIR:00100014" obsolete="true">
<dataResource>http://ep.ebi.ac.uk/EP/GO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
@@ -1176,7 +1225,7 @@
<documentation type="PMID">urn:miriam:pubmed:17118155</documentation>
</documentations>
<resources>
- <resource id="MIR:00100034" state="up" reliability="99">
+ <resource id="MIR:00100034" state="up" reliability="99" primary="true">
<dataResource>http://www.ebi.ac.uk/sbo/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/sbo/main/$id</dataEntry>
@@ -1184,7 +1233,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100176" state="up" reliability="99">
+ <resource id="MIR:00100176" state="up" reliability="98">
<dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
@@ -1192,10 +1241,10 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100242" state="up" reliability="100">
+ <resource id="MIR:00100242" state="down" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
- <dataEntry>http://bioportal.bioontology.org/ontologies/1046?p=terms&conceptid=$id</dataEntry>
+ <dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
<dataInfo>SBO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
@@ -1292,7 +1341,7 @@
<datatype id="MIR:00000027" pattern="^WBGene\d{8}$">
<name>WormBase</name>
- <definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results.</definition>
+ <definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:wormbase</uri>
<uri type="URL">http://identifiers.org/wormbase/</uri>
@@ -1397,7 +1446,7 @@
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100044" state="up" reliability="87">
+ <resource id="MIR:00100044" state="up" reliability="88">
<dataResource>http://pfam.sbc.su.se/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sbc.su.se/family/$id</dataEntry>
@@ -1465,14 +1514,6 @@
<documentation type="URL">http://insdc.org/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100048" state="up" reliability="99">
- <dataResource>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBL</dataResource>
- <dataEntityExample>X58356</dataEntityExample>
- <dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$id]+-view+EmblEntry</dataEntry>
- <dataInfo>INSDC through SRS at EMBL-EBI</dataInfo>
- <dataInstitution>European Molecular Biology Laboratory (EBI)</dataInstitution>
- <dataLocation>United Kingdom</dataLocation>
- </resource>
<resource id="MIR:00100049" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/Genbank/</dataResource>
<dataEntityExample>X58356</dataEntityExample>
@@ -1489,7 +1530,7 @@
<dataInstitution>DNA Data Bank of Japan</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100487" state="probably up" reliability="92">
+ <resource id="MIR:00100487" state="probably up" reliability="96">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>X58356</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
@@ -1505,6 +1546,14 @@
<dataInstitution>National Center for Biotechnology Information, Bethesda, Maryland</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
+ <resource id="MIR:00100048" obsolete="true">
+ <dataResource>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBL</dataResource>
+ <dataEntityExample>X58356</dataEntityExample>
+ <dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$id]+-view+EmblEntry</dataEntry>
+ <dataInfo>INSDC through SRS at EMBL-EBI</dataInfo>
+ <dataInstitution>European Molecular Biology Laboratory (EBI)</dataInstitution>
+ <dataLocation>United Kingdom</dataLocation>
+ </resource>
</resources>
<tags>
<tag>nucleotide</tag>
@@ -1568,7 +1617,7 @@
<documentation type="URL">http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep_format.shtml</documentation>
</documentations>
<resources>
- <resource id="MIR:00100051" state="up" reliability="96">
+ <resource id="MIR:00100051" state="up" reliability="96" primary="true">
<dataResource>http://www.wormbase.org/db/seq/protein</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
<dataEntry>http://www.wormbase.org/db/seq/protein?name=$id</dataEntry>
@@ -1576,7 +1625,7 @@
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100052" state="up" reliability="90">
+ <resource id="MIR:00100052" state="up" reliability="91">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
<dataEntry>http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id</dataEntry>
@@ -1635,7 +1684,7 @@
<documentation type="PMID">urn:miriam:pubmed:16381852</documentation>
</documentations>
<resources>
- <resource id="MIR:00100056" state="up" reliability="98">
+ <resource id="MIR:00100056" state="up" reliability="99">
<dataResource>http://www.expasy.org/prosite/</dataResource>
<dataEntityExample>PS00001</dataEntityExample>
<dataEntry>http://prosite.expasy.org/$id</dataEntry>
@@ -1678,7 +1727,7 @@
<documentation type="PMID">urn:miriam:pubmed:17170002</documentation>
</documentations>
<resources>
- <resource id="MIR:00100058" state="up" reliability="94">
+ <resource id="MIR:00100058" state="up" reliability="95">
<dataResource>http://pubchem.ncbi.nlm.nih.gov/</dataResource>
<dataEntityExample>100101</dataEntityExample>
<dataEntry>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$id</dataEntry>
@@ -1856,7 +1905,7 @@
<documentation type="URL">http://www.springerlink.com/content/kw1kv13614272400/?p=9b9a98e3b7c04ec189cd2927fcc83808&pi=8</documentation>
</documentations>
<resources>
- <resource id="MIR:00100063" state="probably up" reliability="95">
+ <resource id="MIR:00100063" state="probably up" reliability="96">
<dataResource>http://sabiork.h-its.org/</dataResource>
<dataEntityExample>75</dataEntityExample>
<dataEntry>http://sabiork.h-its.org/newSearch?q=sabioreactionid:$id</dataEntry>
@@ -1879,7 +1928,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000039" pattern="^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+(\.\d+)?$">
+ <datatype id="MIR:00000039" pattern="^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$">
<name>RefSeq</name>
<definition>The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.</definition>
<uris>
@@ -1965,7 +2014,7 @@
<documentation type="PMID">urn:miriam:pubmed:14681372</documentation>
</documentations>
<resources>
- <resource id="MIR:00100069" state="up" reliability="95">
+ <resource id="MIR:00100069" state="up" reliability="96">
<dataResource>http://www.ebi.ac.uk/uniparc/</dataResource>
<dataEntityExample>UPI000000000A</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$id</dataEntry>
@@ -2021,7 +2070,8 @@
</tags>
</datatype>
- <datatype id="MIR:00000043" pattern="^IPI\d{8}$">
+ <datatype id="MIR:00000043" pattern="^IPI\d{8}$" obsolete="true" replacement="MIR:00000005">
+ <comment>As of April 2013, this collection is no longer maintained. An ftp archive is available at ftp://ftp.ebi.ac.uk/pub/databases/IPI.</comment>
<name>IPI</name>
<synonyms>
<synonym>International Protein Index</synonym>
@@ -2036,7 +2086,7 @@
<documentation type="PMID">urn:miriam:pubmed:15221759</documentation>
</documentations>
<resources>
- <resource id="MIR:00100071" state="up" reliability="99">
+ <resource id="MIR:00100071" state="down" reliability="91">
<dataResource>http://www.ebi.ac.uk/IPI</dataResource>
<dataEntityExample>IPI00000001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ipi&id=$id&format=default&style=html</dataEntry>
@@ -2171,7 +2221,7 @@
<synonyms>
<synonym>RGD</synonym>
</synonyms>
- <definition>Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community.</definition>
+ <definition>Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.</definition>
<uris>
<uri type="URN">urn:miriam:rgd</uri>
<uri type="URL">http://identifiers.org/rgd/</uri>
@@ -2259,7 +2309,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100077" state="up" reliability="98">
+ <resource id="MIR:00100077" state="up" reliability="99">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>Gene:2200934</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?accession=$id</dataEntry>
@@ -2296,7 +2346,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100078" state="up" reliability="71">
+ <resource id="MIR:00100078" state="up" reliability="74">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEnti...
[truncated message content] |
|
From: <nik...@us...> - 2014-01-17 11:29:21
|
Revision: 262
http://sourceforge.net/p/sbfc/code/262
Author: niko-rodrigue
Date: 2014-01-17 11:29:18 +0000 (Fri, 17 Jan 2014)
Log Message:
-----------
did a bit of cleaning to remove unused classes and libraries
Modified Paths:
--------------
trunk/build.xml
trunk/lib/sbfc-1.3.2.jar
Removed Paths:
-------------
trunk/lib/jung-io-2.0.2-SNAPSHOT-sources.jar
trunk/lib/jung-io-2.0.2-SNAPSHOT.jar
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotation.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationConfigFile.xml
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationList.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationParameter.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationParsing.java
trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLVCard.java
trunk/src/org/sbfc/testJung/
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2013-09-30 13:25:06 UTC (rev 261)
+++ trunk/build.xml 2014-01-17 11:29:18 UTC (rev 262)
@@ -109,7 +109,7 @@
<!-- copy src files -->
<copy todir="${build.src}" overwrite="yes">
<fileset dir="${src.dir}"
- excludes="**/CVS*, **/*.class, **/*~, **/*.tgz, **/testJung/*, **/SBML2BioPAXannotationParameter_l2.java, **/SBMLAnnotationParameter.java, **/SBMLAnnotationList.java, **/SBMLAnnotationParsing.java">
+ excludes="**/CVS*, **/*.class, **/*~, **/*.tgz">
</fileset>
</copy>
<copy todir="${build.src}" overwrite="yes">
Deleted: trunk/lib/jung-io-2.0.2-SNAPSHOT-sources.jar
===================================================================
(Binary files differ)
Deleted: trunk/lib/jung-io-2.0.2-SNAPSHOT.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/sbfc-1.3.2.jar
===================================================================
(Binary files differ)
Deleted: trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotation.java
===================================================================
--- trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotation.java 2013-09-30 13:25:06 UTC (rev 261)
+++ trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotation.java 2014-01-17 11:29:18 UTC (rev 262)
@@ -1,179 +0,0 @@
-/*
- * $Id$
- * $URL$
- *
- *
- * ==============================================================================
- * Copyright (c) 2010 the copyright is held jointly by the individual
- * authors. See the file AUTHORS for the list of authors
- *
- * This file is part of The System Biology Format Converter (SBFC).
- *
- * SBFC is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * SBFC is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with SBFC. If not, see<http://www.gnu.org/licenses/>.
- *
- * ==============================================================================
- *
- */
-
-package org.sbfc.converter.utils.sbml.sbmlannotation;
-
-// import com.hp.hpl.jena.ontology.Individual;
-
-/**
- * Stores one annotation.
- *
- * @author Arnaud Henry, Nicolas Rodriguez
- *
- */
-public class SBMLAnnotation {
-
- // private Individual xref;
- private String annotationType; //dc, rdf, dcterms, vcard, bqbio
- private String relationType;
- private String db;
- private String uri;
-
- //dc:
- // isVersionOf
- // relation
- // hasPart
-
- //bqmodel:
- // is -> BioModels
- // isDescribedBy -> pubMed
-
- //bqbiol:
- // is -> unificationXref
- // hasPart -> complex
- // isPart -> molecule of a complex
- // isVersionOf -> relationshipXref
- // hasVersion -> relationshipXref ?what the difference with isVersionOf? SBMLressource <-version-> Reference
- // isHomologTo -> relationshipXref
-
- //Constructors
-
- /**
- * Creates a new <code>SBMLAnnotation</code>.
- *
- * @param a the annotation type.
- * @param r the relation type.
- * @param u the uri.
- */
- public SBMLAnnotation(String a, String r, String u){
- annotationType = a;
- relationType = r;
- uri = u;
- }
-
- /**
- * Creates a new <code>SBMLAnnotation</code>.
- *
- * @param a the annotation type.
- * @param r the relation type.
- * @param u the uri.
- * @param d the database name.
- */
- public SBMLAnnotation(String a, String r, String u, String d){
- annotationType = a;
- relationType = r;
- uri = u;
- db = d;
- }
-
- //Individual
-
- /**
- * Sets the individual.
- *
- * @param ind the individual.
- */
-// public void setIndividual(Individual ind){
-// xref = ind;
-// }
-//
-// /**
-// * Returns the individual.
-// *
-// * @return the individual.
-// */
-// public Individual getIndividual(){
-// return xref;
-// }
-
- //Annotation type
- /**
- * Sets the annotation type.
- *
- * @param atype
- */
- public void setAnnotationType(String atype) {
- annotationType = new String(atype);
- }
-
- /**
- * Returns the annotation type.
- *
- * @return the annotation type.
- */
- public String getAnnotationType() {
- return annotationType;
- }
-
- /**
- * Returns the relation type.
- *
- * @return the relation type.
- */
- public String getRelationType() {
- return relationType;
- }
-
- /**
- * @return
- */
- public String getURI() {
- return uri;
- }
- /**
- * Returns the database name.
- *
- * @return the db the database name.
- */
- public String getDb() {
- return db;
- }
-
- public String toString() {
-
- StringBuffer buffer = new StringBuffer();
-
- buffer.append("\nType: " + annotationType + " " + relationType).append("\n");
-
- if (uri != null) {
- buffer.append("URI: " + uri).append("\n");
- }
- if (db != null) {
- buffer.append("database: " + db).append("\n");
- }
-
-// if (xref != null) {
-// buffer.append(xref).append("\n");
-// }
-
- return buffer.toString();
- }
-
-}
-
-
Deleted: trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationConfigFile.xml
===================================================================
--- trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationConfigFile.xml 2013-09-30 13:25:06 UTC (rev 261)
+++ trunk/src/org/sbfc/converter/utils/sbml/sbmlannotation/SBMLAnnotationConfigFile.xml 2014-01-17 11:29:18 UTC (rev 262)
@@ -1,407 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?xml-stylesheet type="text/xsl" href="SBML2BioPAXconfigFile.xsl"?>
-<!-- SBML2BioPAX configuration file
- *
- * ==============================================================================
- * Copyright (c) 2010 the copyright is held jointly by the individual
- * authors. See the file AUTHORS for the list of authors
- *
- * This file is part of The System Biology Format Converter (SBFC).
- *
- * SBFC is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * SBFC is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with SBFC. If not, see<http://www.gnu.org/licenses/>.
- *
- * ==============================================================================
- *
- */
- -->
-<sbml2biopax>
- <!-- Part to indicate the different SBML annotation URI -->
- <sbml2biopaxAnnotationParameter>
-
- <publicationModel>
- <publication>http://www.doi.org/</publication>
- <publication>http://www.pubmed.gov/</publication>
- </publicationModel>
-
- <speciesAnnotationMap>
- <species>http://www.bind.ca/</species>
- <species>http://www.ebi.ac.uk/chebi/</species>
- <species>http://www.ensembl.org/</species>
- <species>http://www.uniprot.org/</species>
- <species>http://www.ebi.ac.uk/interpro/</species>
- <species>http://www.genome.jp/kegg/compound/</species>
- <species>http://pir.georgetown.edu/pirsf/</species>
- <species>http://www.geneontology.org/</species><!--for the GO component (compartment)-->
- <species>http://www.ec-code.org/</species>
- <species>http://www.ebi.ac.uk/biomodels/</species>
- </speciesAnnotationMap>
-
- <taxonomyMap>
- <taxonomy>http://www.taxonomy.org/</taxonomy>
- </taxonomyMap>
-
- <!-- Annotation part to modify for change the mapping SBML->BioPAX -->
- <!-- <physicalEntity value="BioPAXclass"> <species>SBMLannotationURI</species> </physicalEntity> -->
- <annotationSpecies>
- <physicalEntity classBioPAX="complex">
- <species>http://www.bind.ca/</species>
- </physicalEntity>
-
- <physicalEntity classBioPAX="protein">
- <constraint>http://www.ensembl.org/#ENSRNOP</constraint>
- <species>http://www.uniprot.org/</species>
- <species>http://www.ebi.ac.uk/interpro/</species>
- <species>http://pir.georgetown.edu/pirsf/</species>
-<!--KEGG entries for protein-->
- <constraint>http://www.genome.jp/kegg/compound/#C00017</constraint><!-- Protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C00173</constraint><!-- Acyl-[acyl-carrier protein]; Long-chain-acyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C00229</constraint><!-- Acyl-carrier protein; ACP; [Acyl-carrier protein]; Holo-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C00326</constraint><!-- Glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C00562</constraint><!-- Phosphoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C00585</constraint><!-- Protein tyrosine; [protein]-L-tyrosine -->
- <constraint>http://www.genome.jp/kegg/compound/#C00613</constraint><!-- Peptidyl-L-arginine; Protein L-arginine; L-Arginyl-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C00614</constraint><!-- Protein glutamate; Protein L-glutamate -->
- <constraint>http://www.genome.jp/kegg/compound/#C00615</constraint><!-- Protein histidine; Protein L-histidine -->
- <constraint>http://www.genome.jp/kegg/compound/#C00685</constraint><!-- 3-Oxoacyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C00693</constraint><!-- trans-2,3-Dehydroacyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C01140</constraint><!-- alpha-D-Glucosyl-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C01167</constraint><!-- Protein tyrosine phosphate; [protein]-L-tyrosine phosphate -->
- <constraint>http://www.genome.jp/kegg/compound/#C01203</constraint><!-- Oleoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C01209</constraint><!-- Malonyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C01237</constraint><!-- Enoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C01242</constraint><!-- S-Aminomethyldihydrolipoylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C01271</constraint><!-- (3R)-3-Hydroxyacyl-[acyl-carrier protein]; (R)-3-Hydroxyacyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C01560</constraint><!-- C-Protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C01834</constraint><!-- Lipoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C01867</constraint><!-- tau-Protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02051</constraint><!-- Lipoylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02065</constraint><!-- Protein alanine -->
- <constraint>http://www.genome.jp/kegg/compound/#C02188</constraint><!-- Protein lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C02189</constraint><!-- Protein serine -->
- <constraint>http://www.genome.jp/kegg/compound/#C02315</constraint><!-- Protein dithiol -->
- <constraint>http://www.genome.jp/kegg/compound/#C02399</constraint><!-- D-Xylosylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02429</constraint><!-- L-Leucyl-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02461</constraint><!-- Protein Cys-Cys -->
- <constraint>http://www.genome.jp/kegg/compound/#C02582</constraint><!-- Protein disulfide -->
- <constraint>http://www.genome.jp/kegg/compound/#C02583</constraint><!-- Protein glutamine; Protein L-glutamine -->
- <constraint>http://www.genome.jp/kegg/compound/#C02705</constraint><!-- Mucus glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02743</constraint><!-- Protein L-cysteine -->
- <constraint>http://www.genome.jp/kegg/compound/#C02815</constraint><!-- C4b-binding protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02863</constraint><!-- O-D-Mannosylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C02972</constraint><!-- Dihydrolipoylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03021</constraint><!-- Protein asparagine; Protein L-asparagine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03022</constraint><!-- Protein L-citrulline -->
- <constraint>http://www.genome.jp/kegg/compound/#C03023</constraint><!-- Protein L-methionine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03024</constraint><!-- Reduced flavoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03121</constraint><!-- Glycoprotein inositol -->
- <constraint>http://www.genome.jp/kegg/compound/#C03157</constraint><!-- O-Phospho-tau-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03161</constraint><!-- Oxidized flavoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03268</constraint><!-- D-Mannosylglycoprotein; Glycoprotein D-mannose -->
- <constraint>http://www.genome.jp/kegg/compound/#C03304</constraint><!-- Poliovirus polyprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03306</constraint><!-- Protein L-isoaspartate -->
- <constraint>http://www.genome.jp/kegg/compound/#C03371</constraint><!-- Acyl-protein thiolester -->
- <constraint>http://www.genome.jp/kegg/compound/#C03412</constraint><!-- N-Palmitoylglycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03422</constraint><!-- O-Palmitoylglycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03424</constraint><!-- O-beta-D-Xylosylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03429</constraint><!-- Protein 5-hydroxylysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03533</constraint><!-- Picornavirus polyprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03635</constraint><!-- Protein N-ubiquityllysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03636</constraint><!-- Protein N5-alkylglutamine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03637</constraint><!-- Protein serine D-xyloside -->
- <constraint>http://www.genome.jp/kegg/compound/#C03688</constraint><!-- Apo-[acyl-carrier protein]; Apoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03721</constraint><!-- Protein tyrosine-O-sulfate -->
- <constraint>http://www.genome.jp/kegg/compound/#C03788</constraint><!-- Microsomal-membrane protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C03800</constraint><!-- Protein S-methyl-L-cysteine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03803</constraint><!-- Ribosomal-protein L-alanine -->
- <constraint>http://www.genome.jp/kegg/compound/#C03895</constraint><!-- Protein L-methionine S-oxide -->
- <constraint>http://www.genome.jp/kegg/compound/#C03896</constraint><!-- Protein(N-Glu, Asp, Cystine) -->
- <constraint>http://www.genome.jp/kegg/compound/#C03939</constraint><!-- Acetyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04010</constraint><!-- Glycoprotein phospho-D-mannose -->
- <constraint>http://www.genome.jp/kegg/compound/#C04087</constraint><!-- Protein Ntau-methyl-L-histidine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04088</constraint><!-- Stearoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04128</constraint><!-- Low-density lipoprotein L-serine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04142</constraint><!-- Protein glutamate methyl ester; Protein L-glutamate methyl ester -->
- <constraint>http://www.genome.jp/kegg/compound/#C04143</constraint><!-- Protein N(omega)-Methyl-L-arginine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04174</constraint><!-- 2-Decenoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04180</constraint><!-- 3-Decenoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04195</constraint><!-- Glycoprotein phosphatidylinositol -->
- <constraint>http://www.genome.jp/kegg/compound/#C04246</constraint><!-- But-2-enoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04253</constraint><!-- Electron-transferring flavoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04261</constraint><!-- Protein N(pi)-phospho-L-histidine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04262</constraint><!-- Protein N(tau)-phospho-L-histidine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04263</constraint><!-- Protein N6-(4-Aminobutyl)-L-lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04310</constraint><!-- Protein L-glutamate O5-methyl ester -->
- <constraint>http://www.genome.jp/kegg/compound/#C04311</constraint><!-- Protein L-isoaspartate methyl ester; Protein L-isoaspartate alpha-methyl ester -->
- <constraint>http://www.genome.jp/kegg/compound/#C04341</constraint><!-- Ribosomal-protein N-acetyl-L-alanine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04342</constraint><!-- Soluble variant-surface-glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04364</constraint><!-- 2-Hexadecenoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04375</constraint><!-- 4-N-(N-Acetyl-D-glucosaminyl)-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04386</constraint><!-- Myelin proteolipid O-palmitoylprotein; O-Palmitoyl-[myelin proteolipid] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04391</constraint><!-- O-Phospho-microsomal-membrane protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04419</constraint><!-- Carboxybiotin-carboxyl-carrier protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04506</constraint><!-- Protein C-terminal S-farnesyl-L-cysteine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04542</constraint><!-- Protein beta-D-galactosyl-L-hydroxylysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04565</constraint><!-- Low-density lipoprotein O-phospho-L-serine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04570</constraint><!-- Reduced electron-transferring flavoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04571</constraint><!-- Retinol-(cellular-retinol-binding-protein) -->
- <constraint>http://www.genome.jp/kegg/compound/#C04618</constraint><!-- (3R)-3-Hydroxybutanoyl-[acyl-carrier protein]; (R)-3-Hydroxybutanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04619</constraint><!-- (3R)-3-Hydroxydecanoyl-[acyl-carrier protein]; (R)-3-Hydroxydecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04620</constraint><!-- (3R)-3-Hydroxyoctanoyl-[acyl-carrier protein]; (R)-3-Hydroxyoctanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04633</constraint><!-- (3R)-3-Hydroxypalmitoyl-[acyl-carrier protein]; (R)-3-Hydroxypalmitoyl-[acyl-carrier protein]; (3R)-3-Hydroxyhexadecanoyl-[acyl-carrier protein]; (R)-3-Hydroxyhexadecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C04645</constraint><!-- 6-(D-Glucose-1-phospho)-D-mannosylglycoprotein; Glycoprotein 6-(D-glucose-1-phospho)-D-mannose -->
- <constraint>http://www.genome.jp/kegg/compound/#C04648</constraint><!-- Glycoprotein alpha-L-fucosyl-(1,2)-D-galactose; alpha-L-Fucosyl-(1->2)-D-galactosyl-R -->
- <constraint>http://www.genome.jp/kegg/compound/#C04679</constraint><!-- Protein N6-[(R)-4-amino-2-hydroxybutyl]-L-lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04680</constraint><!-- Retinyl-ester-(cellular-retinol-binding-protein) -->
- <constraint>http://www.genome.jp/kegg/compound/#C04688</constraint><!-- (3R)-3-Hydroxytetradecanoyl-[acyl-carrier protein]; (R)-3-Hydroxytetradecanoyl-[acyl-carrier protein]; beta-Hydroxymyristyl-[acyl-carrier protein]; HMA -->
- <constraint>http://www.genome.jp/kegg/compound/#C04748</constraint><!-- Protein C-terminal S-farnesyl-L-cysteine methyl ester -->
- <constraint>http://www.genome.jp/kegg/compound/#C04750</constraint><!-- beta-D-Galactosyl-1,3-N-acetyl-alpha-D-galactosaminyl-R; beta-D-Galactosyl-1,3-N-acetyl-D-galactosaminyl-R; Glycoprotein D-galactosyl-1,3-N-acetyl-D-galactosamine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04755</constraint><!-- Glycoprotein N-acetyl-D-glucosaminyl-phospho-D-mannose -->
- <constraint>http://www.genome.jp/kegg/compound/#C04781</constraint><!-- Glycoprotein(non-reducing N- or O-acylneuraminyl residue) -->
- <constraint>http://www.genome.jp/kegg/compound/#C04786</constraint><!-- 3-beta-D-Galactosyl-4-D-galactosyl-O-beta-D-xylosylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04788</constraint><!-- Glycano-1,3-(N-acetyl-alpha-D-galactosaminyl)-glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04791</constraint><!-- beta-D-Galactosyl-1,4-N-acetyl-D-glucosaminyl-glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04817</constraint><!-- Protein alpha-D-glucosyl-1,2-beta-D-galactosyl-L-hydroxylysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C04825</constraint><!-- 3-beta-D-Galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C04848</constraint><!-- Variant-surface-glycoprotein 1,2-didecanoyl-sn-phosphatidylinositol; 1,2-Didecanoyl-sn-phosphatidylinositol; 1,2-Didecanoyl-sn-glycero-3-phosphoinositol -->
- <constraint>http://www.genome.jp/kegg/compound/#C04866</constraint><!-- Glycoprotein alpha-D-galactosyl-(1,3)-[alpha-L-fucosyl-(1,2)]-D-galactose; alpha-D-Galactosyl-(1->3)-[alpha-L-fucosyl(1->2)]-D-galactosyl-R -->
- <constraint>http://www.genome.jp/kegg/compound/#C04903</constraint><!-- 3-beta-D-Glucuronosyl-3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein; beta-D-Glucuronyl-1,3-D-galactosylproteoglycan -->
- <constraint>http://www.genome.jp/kegg/compound/#C04907</constraint><!-- alpha-N-Acetylneuraminyl-2,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosaminyl-glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C05046</constraint><!-- Protein(Arg,Arg-Pro) -->
- <constraint>http://www.genome.jp/kegg/compound/#C05047</constraint><!-- Protein(Arg-,Lys-,Phe-) -->
- <constraint>http://www.genome.jp/kegg/compound/#C05048</constraint><!-- Protein(Gly-,Ala-,Val-,Leu-,Ile-) -->
- <constraint>http://www.genome.jp/kegg/compound/#C05049</constraint><!-- Protein(Phe-,Leu) -->
- <constraint>http://www.genome.jp/kegg/compound/#C05169</constraint><!-- Protein aspartate -->
- <constraint>http://www.genome.jp/kegg/compound/#C05207</constraint><!-- [Myeline basic protein] L-arginine; [Myelin basic protein]-arginine -->
- <constraint>http://www.genome.jp/kegg/compound/#C05223</constraint><!-- Dodecanoyl-[acyl-carrier protein]; --> Dodecanoyl-[acp]; Lauroyl-[acyl-carrier protein]
- <constraint>http://www.genome.jp/kegg/compound/#C05250</constraint><!-- [Protein-PII] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05321</constraint><!-- [Myeline basic protein] N(omega)-methyl-L-arginine; [Myelin basic protein]-N(omega)-methylarginine -->
- <constraint>http://www.genome.jp/kegg/compound/#C05326</constraint><!-- Uridylyl-[protein-PII] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05517</constraint><!-- 5-Aminomethyldihydrolipoylprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C05544</constraint><!-- Protein N6-methyl-L-lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C05545</constraint><!-- Protein N6,N6-dimethyl-L-lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C05546</constraint><!-- Protein N6,N6,N6-trimethyl-L-lysine -->
- <constraint>http://www.genome.jp/kegg/compound/#C05744</constraint><!-- Acetoacetyl-[acp]; Acetoacetyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05745</constraint><!-- Butyryl-[acp]; Butyryl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05746</constraint><!-- 3-Oxohexanoyl-[acp]; 3-Oxohexanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05747</constraint><!-- (R)-3-Hydroxyhexanoyl-[acp]; (R)-3-Hydroxyhexanoyl-[acyl-carrier protein]; D-3-Hydroxyhexanoyl-[acp]; D-3-Hydroxyhexanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05748</constraint><!-- trans-Hex-2-enoyl-[acp]; trans-Hex-2-enoyl-[acyl-carrier protein]; (2E)-Hexenoyl-[acp]-->
- <constraint>http://www.genome.jp/kegg/compound/#C05749</constraint><!-- Hexanoyl-[acp]; Hexanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05750</constraint><!-- 3-Oxooctanoyl-[acp]; 3-Oxooctanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05751</constraint><!-- trans-Oct-2-enoyl-[acp]; trans-Oct-2-enoyl-[acyl-carrier protein]; 2-Octenoyl-[acyl-carrier protein]; (2E)-Octenoyl-[acp] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05752</constraint><!-- Octanoyl-[acp]; Octanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05753</constraint><!-- 3-Oxodecanoyl-[acp]; 3-Oxodecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05754</constraint><!-- trans-Dec-2-enoyl-[acp]; trans-Dec-2-enoyl-[acyl-carrier protein]; (2E)-Decenoyl-[acp] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05755</constraint><!-- Decanoyl-[acp]; Decanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05756</constraint><!-- 3-Oxododecanoyl-[acp]; 3-Oxododecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05757</constraint><!-- (R)-3-Hydroxydodecanoyl-[acp]; (R)-3-Hydroxydodecanoyl-[acyl-carrier protein]; D-3-Hydroxydodecanoyl-[acp]; D-3-Hydroxydodecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05758</constraint><!-- trans-Dodec-2-enoyl-[acp]; trans-Dodec-2-enoyl-[acyl-carrier protein]; (2E)-Dodecenoyl-[acp] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05759</constraint><!-- 3-Oxotetradecanoyl-[acp]; 3-Oxotetradecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05760</constraint><!-- trans-Tetradec-2-enoyl-[acp]; trans-Tetradec-2-enoyl-[acyl-carrier protein]; (2E)-Tetradecenoyl-[acp] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05761</constraint><!-- Tetradecanoyl-[acp]; Tetradecanoyl-[acyl-carrier protein]; Myristoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05762</constraint><!-- 3-Oxohexadecanoyl-[acp]; 3-Oxohexadecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05763</constraint><!-- trans-Hexadec-2-enoyl-[acp]; trans-Hexadec-2-enoyl-[acyl-carrier protein]; (2E)-Hexadecenoyl-[acp] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05764</constraint><!-- Hexadecanoyl-[acp]; Hexadecanoyl-[acyl-carrier protein] -->
- <constraint>http://www.genome.jp/kegg/compound/#C05883</constraint><!-- Protein N-(N-acetyl-D-glucosaminyl-(alpha-D-mannosyl)3-beta-D-mannosyl-diacetylchitobiosyl)-L-asparagine -->
- <constraint>http://www.genome.jp/kegg/compound/#C06246</constraint><!-- Gla protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C06247</constraint><!-- Gla protein precursor -->
- <constraint>http://www.genome.jp/kegg/compound/#C06250</constraint><!-- Holo-[carboxylase]; Biotin-carboxyl-carrier protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C06395</constraint><!-- [Protein]-L-serine -->
- <constraint>http://www.genome.jp/kegg/compound/#C06396</constraint><!-- [Protein]-D-serine -->
- <constraint>http://www.genome.jp/kegg/compound/#C06411</constraint><!-- Flavoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C06412</constraint><!-- Palmitoyl-protein -->
- <constraint>http://www.genome.jp/kegg/compound/#C06483</constraint><!-- Glycoprotein-N-Acetyl-alpha-D-galactosaminyl-(1,3)-[alpha-L-fucosyl-(1,2)]-D-galactose -->
- <constraint>http://www.genome.jp/kegg/compound/#C11377</constraint><!-- alpha-N-Acetylneuraminyl-2,6-beta-D-galactosyl-1,4-N-acetyl-D-glucosaminyl-glycoprotein -->
- <constraint>http://www.genome.jp/kegg/compound/#C11572</constraint><!-- Glycoprotein with the oligosaccharide chain attached by N-glycosyl linkage to protein L-asparagine -->
- </physicalEntity>
-
- <physicalEntity classBioPAX="rna">
- <constraint>http://www.ensembl.org/#ENSRNOT</constraint>
- <constraint>http://www.ebi.ac.uk/chebi/#CHEBI:18111</constraint><!-- ribosomal RNA -->
- <constraint>http://www.ebi.ac.uk/chebi/#CHEBI:33699</constraint><!-- messenger RNA -->
- <constraint>http://www.ebi.ac.uk/chebi/#CHEBI:17843</constraint><!-- transfer RNA -->
- ...
[truncated message content] |
|
From: <nik...@us...> - 2014-03-14 16:25:12
|
Revision: 263
http://sourceforge.net/p/sbfc/code/263
Author: niko-rodrigue
Date: 2014-03-14 16:25:09 +0000 (Fri, 14 Mar 2014)
Log Message:
-----------
updated the jsbml jar file and sbfc compiled jar + changed the minimal java supported to 1.6
Modified Paths:
--------------
trunk/build.xml
trunk/src/org/sbfc/converter/sbml2graphml/Sbml2Graphml.java
Added Paths:
-----------
trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
trunk/lib/sbfc-1.3.3.jar
Removed Paths:
-------------
trunk/lib/jsbml-1.0-bmdb-20130930-with-dependencies.jar
trunk/lib/sbfc-1.3.2.jar
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2014-01-17 11:29:18 UTC (rev 262)
+++ trunk/build.xml 2014-03-14 16:25:09 UTC (rev 263)
@@ -12,7 +12,7 @@
</tstamp>
<property name="Name" value="System Biology Format Converter"/>
<property name="name" value="sbfc"/>
- <property name="version" value="1.3.2"/>
+ <property name="version" value="1.3.3"/>
<property name="sbml2xpp.version" value="1.2"/>
<property name="sbml2octave.version" value="1.0"/>
@@ -128,8 +128,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.5"
- target="1.5"
+ source="1.6"
+ target="1.6"
classpathref="sbfc.classpath">
</javac>
</target>
Added: trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
===================================================================
(Binary files differ)
Index: trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
===================================================================
--- trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar 2014-01-17 11:29:18 UTC (rev 262)
+++ trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar 2014-03-14 16:25:09 UTC (rev 263)
Property changes on: trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/zip
\ No newline at end of property
Deleted: trunk/lib/jsbml-1.0-bmdb-20130930-with-dependencies.jar
===================================================================
(Binary files differ)
Deleted: trunk/lib/sbfc-1.3.2.jar
===================================================================
(Binary files differ)
Added: trunk/lib/sbfc-1.3.3.jar
===================================================================
(Binary files differ)
Index: trunk/lib/sbfc-1.3.3.jar
===================================================================
--- trunk/lib/sbfc-1.3.3.jar 2014-01-17 11:29:18 UTC (rev 262)
+++ trunk/lib/sbfc-1.3.3.jar 2014-03-14 16:25:09 UTC (rev 263)
Property changes on: trunk/lib/sbfc-1.3.3.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/zip
\ No newline at end of property
Modified: trunk/src/org/sbfc/converter/sbml2graphml/Sbml2Graphml.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2graphml/Sbml2Graphml.java 2014-01-17 11:29:18 UTC (rev 262)
+++ trunk/src/org/sbfc/converter/sbml2graphml/Sbml2Graphml.java 2014-03-14 16:25:09 UTC (rev 263)
@@ -152,7 +152,12 @@
Model model = sbmlDoc.getModel();
// writing some description notes
- String comment = model.getName() + " " + model.getNotesString();
+ String comment = model.getName();
+ try {
+ comment = model.getName() + " " + model.getNotesString();
+ } catch (XMLStreamException e) {
+ e.printStackTrace();
+ }
graph += writeIndents(1) + writeDescTags(comment);
// writing the graph
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2014-03-14 16:36:07
|
Revision: 264
http://sourceforge.net/p/sbfc/code/264
Author: niko-rodrigue
Date: 2014-03-14 16:36:02 +0000 (Fri, 14 Mar 2014)
Log Message:
-----------
small updates to the sbfc bash scripts and update of the identifiers.org registry dump
Modified Paths:
--------------
trunk/identifiersUtil.sh
trunk/miriam.xml
trunk/sbfConverter.sh
trunk/sbml2sbml.sh
trunk/updateMiriamRegistry.sh
Modified: trunk/identifiersUtil.sh
===================================================================
--- trunk/identifiersUtil.sh 2014-03-14 16:25:09 UTC (rev 263)
+++ trunk/identifiersUtil.sh 2014-03-14 16:36:02 UTC (rev 264)
@@ -38,10 +38,13 @@
COMMAND="bsub $BSUB_OPTIONS -o $LOG_FILE java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml "
USE_BSUB="yes"
-if [ "`which bsub 2> /dev/null`" == "" ] ; then
+#
+# TODO : add an option to enable or not the use of the cluster, the default being not enabled so that biomodels does not need to change anything.
+#
+#if [ "`which bsub 2> /dev/null`" == "" ] ; then
COMMAND="java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml "
USE_BSUB="no"
-fi
+#fi
export CLASSPATH=
Modified: trunk/miriam.xml
===================================================================
--- trunk/miriam.xml 2014-03-14 16:25:09 UTC (rev 263)
+++ trunk/miriam.xml 2014-03-14 16:36:02 UTC (rev 264)
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Export of Identifiers.org's Registry (full) -->
-<!-- Generated: Thu Sep 26 10:25:10 BST 2013 -->
+<!-- Generated: Fri Mar 14 16:34:39 GMT 2014 -->
<!-- http://identifiers.org/registry/ -->
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2013-09-26T10:25:10+01:00" data-version="2013-09-24T14:04:20+01:00">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2014-03-14T16:34:39+00:00" data-version="2014-03-14T14:45:40+00:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
<comment>BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
<name>BIND</name>
@@ -65,7 +65,7 @@
<documentation type="URL">http://www3.oup.co.uk/nar/database/summary/646</documentation>
</documentations>
<resources>
- <resource id="MIR:00100009" state="up" reliability="96">
+ <resource id="MIR:00100009" state="up" reliability="96" primary="true">
<dataResource>http://www.ebi.ac.uk/chebi/</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id</dataEntry>
@@ -81,7 +81,7 @@
<dataInstitution>European Bioinformatics Institute, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100565" state="down" reliability="98">
+ <resource id="MIR:00100565" state="up" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
@@ -105,7 +105,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000003" pattern="^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z]))$" restricted="true">
+ <datatype id="MIR:00000003" pattern="^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" restricted="true">
<name>Ensembl</name>
<definition>Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.</definition>
<uris>
@@ -126,7 +126,7 @@
<dataInstitution>Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100561" state="up" reliability="97">
+ <resource id="MIR:00100561" state="up" reliability="99">
<dataResource>http://uswest.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://uswest.ensembl.org/id/$id</dataEntry>
@@ -134,7 +134,7 @@
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100562" state="up" reliability="97">
+ <resource id="MIR:00100562" state="up" reliability="99">
<dataResource>http://useast.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://useast.ensembl.org/id/$id</dataEntry>
@@ -142,7 +142,7 @@
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100563" state="up" reliability="97">
+ <resource id="MIR:00100563" state="up" reliability="98">
<dataResource>http://asia.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://asia.ensembl.org/id/$id</dataEntry>
@@ -156,6 +156,9 @@
<statement>While Ensembl data is nominally restricted to vertebrate species, it also includes out groups (Dorsophila, Saccharomyces and C. elegans) used in comparative analysis. These species can also be referenced through Ensembl Genomes datasets.</statement>
<link desc="Ensembl overlap">http://www.ensemblgenomes.org/info/data_access</link>
</restriction>
+ <restriction type="9" desc="Identifier multiplicity">
+ <statement>This data collection uses some 'outlier' organisms, to normalise its dataset, which are not intended to be referenced directly in this collection. In addition, those outlier organisms may be referenced using non-standard identifiers. We recommend that human data be accessed using identifiers beginning with 'ENS', and outlier organisms be referenced through the appropriate collection: WormBase (http://identifiers.org/wormbase/), SGD (http://identifiers.org/sgd/) or FlyBase (http://identifiers.org/flybase/).</statement>
+ </restriction>
</restrictions>
<tags>
<tag>eukaryotic</tag>
@@ -239,6 +242,7 @@
<element>reaction</element>
<element>event</element>
<element>rule</element>
+ <element>species</element>
</elements>
</format>
<format name="CellML">
@@ -386,7 +390,7 @@
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100507" state="down" reliability="99">
+ <resource id="MIR:00100507" state="up" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_$id</dataEntry>
@@ -576,7 +580,7 @@
<documentation type="PMID">urn:miriam:pubmed:15608177</documentation>
</documentations>
<resources>
- <resource id="MIR:00100018" state="up" reliability="96">
+ <resource id="MIR:00100018" state="up" reliability="97">
<dataResource>http://www.ebi.ac.uk/interpro/</dataResource>
<dataEntityExample>IPR000100</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/interpro/entry/$id</dataEntry>
@@ -615,7 +619,7 @@
<resource id="MIR:00100020" state="up" reliability="99">
<dataResource>http://www.genome.jp/kegg/pathway.html</dataResource>
<dataEntityExample>hsa00620</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?pathway+$id</dataEntry>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG PATHWAY Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
@@ -652,7 +656,7 @@
<resource id="MIR:00100021" state="up" reliability="100">
<dataResource>http://www.genome.jp/kegg/ligand.html</dataResource>
<dataEntityExample>C12345</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?cpd:$id</dataEntry>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG LIGAND Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
@@ -689,8 +693,8 @@
<resource id="MIR:00100022" state="up" reliability="100">
<dataResource>http://www.genome.jp/kegg/reaction/</dataResource>
<dataEntityExample>R00100</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?rn:$id</dataEntry>
- <dataInfo>KEGG LIGAND Database</dataInfo>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
+ <dataInfo>KEGG Reaction Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
@@ -731,7 +735,7 @@
<dataInstitution>National Center for Biotechnology Information</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100064" state="up" reliability="96">
+ <resource id="MIR:00100064" state="up" reliability="97">
<dataResource>http://www.hubmed.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.hubmed.org/display.cgi?uids=$id</dataEntry>
@@ -739,7 +743,7 @@
<dataInstitution>Alfred D. Eaton</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100497" state="up" reliability="100">
+ <resource id="MIR:00100497" state="up" reliability="99">
<dataResource>http://europepmc.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://europepmc.org/abstract/MED/$id</dataEntry>
@@ -1124,7 +1128,7 @@
<dataInstitution>The Jackson Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100237" state="down" reliability="98">
+ <resource id="MIR:00100237" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
@@ -1140,6 +1144,14 @@
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
+ <resource id="MIR:00100659" state="up" reliability="100">
+ <dataResource>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/</dataResource>
+ <dataEntityExample>GO:0006915</dataEntityExample>
+ <dataEntry>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/$id</dataEntry>
+ <dataInfo>GO through Amigo2 (prototype)</dataInfo>
+ <dataInstitution>Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California</dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
<resource id="MIR:00100014" obsolete="true">
<dataResource>http://ep.ebi.ac.uk/EP/GO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
@@ -1167,7 +1179,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000023" pattern="^S\d+$">
+ <datatype id="MIR:00000023" pattern="^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$" restricted="true">
<name>SGD</name>
<synonyms>
<synonym>Saccharomyces Genome Database</synonym>
@@ -1192,6 +1204,12 @@
<dataLocation>USA</dataLocation>
</resource>
</resources>
+ <restrictions>
+ <restriction type="9" desc="Identifier multiplicity">
+ <statement>This data collection can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'S\d+'.</statement>
+ <link desc="SGD identifiers nomenclature">http://www.yeastgenome.org/help/community/nomenclature-conventions</link>
+ </restriction>
+ </restrictions>
<tags>
<tag>eukaryotic</tag>
<tag>genome</tag>
@@ -1233,7 +1251,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100176" state="up" reliability="98">
+ <resource id="MIR:00100176" state="up" reliability="99">
<dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
@@ -1241,7 +1259,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100242" state="down" reliability="99">
+ <resource id="MIR:00100242" state="up" reliability="99">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
@@ -1285,7 +1303,7 @@
<resource id="MIR:00100035" state="up" reliability="100">
<dataResource>http://www.genome.jp/kegg/drug/</dataResource>
<dataEntityExample>D00123</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?dr:$id</dataEntry>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG DRUG Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
@@ -1320,7 +1338,7 @@
<resource id="MIR:00100036" state="up" reliability="100">
<dataResource>http://www.genome.jp/kegg/glycan/</dataResource>
<dataEntityExample>G00123</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?gl:$id</dataEntry>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG GLYCAN Database</dataInfo>
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
@@ -1339,7 +1357,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000027" pattern="^WBGene\d{8}$">
+ <datatype id="MIR:00000027" pattern="^(WBGene\d{8}|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" restricted="true">
<name>WormBase</name>
<definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes.</definition>
<uris>
@@ -1402,6 +1420,12 @@
<dataLocation>France</dataLocation>
</resource>
</resources>
+ <restrictions>
+ <restriction type="9" desc="Identifier multiplicity">
+ <statement>This data collection's records can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'WBGene\d{8}'.</statement>
+ <link desc="WormBase nomenclature">http://www.wormbase.org/about/userguide/nomenclature</link>
+ </restriction>
+ </restrictions>
<tags>
<tag>expression</tag>
<tag>genome</tag>
@@ -1446,7 +1470,7 @@
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100044" state="up" reliability="88">
+ <resource id="MIR:00100044" state="up" reliability="87">
<dataResource>http://pfam.sbc.su.se/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sbc.su.se/family/$id</dataEntry>
@@ -1492,7 +1516,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000029" pattern="^[A-Z]+\d+(\.\d+)?$">
+ <datatype id="MIR:00000029" pattern="^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$">
<name>Nucleotide Sequence Database</name>
<synonyms>
<synonym>International Nucleotide Sequence Database Collaboration</synonym>
@@ -1512,6 +1536,7 @@
<documentation type="PMID">urn:miriam:pubmed:12436968</documentation>
<documentation type="URL">http://www.ebi.ac.uk/embl/Contact/collaboration.html</documentation>
<documentation type="URL">http://insdc.org/</documentation>
+ <documentation type="URL">http://www.ddbj.nig.ac.jp/sub/acc_def-e.html</documentation>
</documentations>
<resources>
<resource id="MIR:00100049" state="up" reliability="99">
@@ -1527,10 +1552,10 @@
<dataEntityExample>X58356</dataEntityExample>
<dataEntry>http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$id</dataEntry>
<dataInfo>INSDC through DDBJ</dataInfo>
- <dataInstitution>DNA Data Bank of Japan</dataInstitution>
+ <dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100487" state="probably up" reliability="96">
+ <resource id="MIR:00100487" state="probably up" reliability="97">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>X58356</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
@@ -1617,15 +1642,15 @@
<documentation type="URL">http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep_format.shtml</documentation>
</documentations>
<resources>
- <resource id="MIR:00100051" state="up" reliability="96" primary="true">
+ <resource id="MIR:00100051" state="up" reliability="97" primary="true">
<dataResource>http://www.wormbase.org/db/seq/protein</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
- <dataEntry>http://www.wormbase.org/db/seq/protein?name=$id</dataEntry>
+ <dataEntry>http://www.wormbase.org/db/seq/protein?name=WP:$id</dataEntry>
<dataInfo>Wormpep (Master)</dataInfo>
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100052" state="up" reliability="91">
+ <resource id="MIR:00100052" state="up" reliability="92">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
<dataEntry>http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id</dataEntry>
@@ -1866,7 +1891,7 @@
<documentation type="URL">http://www.informatics.jax.org/mgihome/projects/overview.shtml#aboutMGD</documentation>
</documentations>
<resources>
- <resource id="MIR:00100062" state="up" reliability="99">
+ <resource id="MIR:00100062" state="up" reliability="98">
<dataResource>http://www.informatics.jax.org/</dataResource>
<dataEntityExample>MGI:2442292</dataEntityExample>
<dataEntry>http://www.informatics.jax.org/marker/$id</dataEntry>
@@ -2026,7 +2051,7 @@
<dataResource>http://www.uniprot.org/uniparc/</dataResource>
<dataEntityExample>UPI000000000A</dataEntityExample>
<dataEntry>http://www.uniprot.org/uniparc/$id</dataEntry>
- <dataInfo>UniPrac through UniProt</dataInfo>
+ <dataInfo>UniParc through UniProt</dataInfo>
<dataInstitution>UniProt Consortium</dataInstitution>
<dataLocation>USA, UK and Switzerland</dataLocation>
</resource>
@@ -2043,7 +2068,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000042" pattern="^MINT\-\d{1,5}$">
+ <datatype id="MIR:00000042" pattern="^MINT\-\d{1,7}$">
<name>MINT</name>
<definition>The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.</definition>
<uris>
@@ -2055,7 +2080,7 @@
<documentation type="PMID">urn:miriam:pubmed:17135203</documentation>
</documentations>
<resources>
- <resource id="MIR:00100070" state="up" reliability="98">
+ <resource id="MIR:00100070" state="up" reliability="99">
<dataResource>http://mint.bio.uniroma2.it/mint/</dataResource>
<dataEntityExample>MINT-10000</dataEntityExample>
<dataEntry>http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id</dataEntry>
@@ -2063,6 +2088,14 @@
<dataInstitution>University of Rome Tor Vergata, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
+ <resource id="MIR:00100654" state="up" reliability="97">
+ <dataResource>http://www.ebi.ac.uk/intact/</dataResource>
+ <dataEntityExample>MINT-7905142</dataEntityExample>
+ <dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:$id</dataEntry>
+ <dataInfo>MINT subset through IntAct</dataInfo>
+ <dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
+ <dataLocation>UK</dataLocation>
+ </resource>
</resources>
<tags>
<tag>interaction</tag>
@@ -2086,7 +2119,7 @@
<documentation type="PMID">urn:miriam:pubmed:15221759</documentation>
</documentations>
<resources>
- <resource id="MIR:00100071" state="down" reliability="91">
+ <resource id="MIR:00100071" state="down" reliability="85">
<dataResource>http://www.ebi.ac.uk/IPI</dataResource>
<dataEntityExample>IPI00000001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ipi&id=$id&format=default&style=html</dataEntry>
@@ -2194,7 +2227,15 @@
<documentation type="DOI">urn:miriam:doi:10.1093%2Fnar%2Fgkg038</documentation>
</documentations>
<resources>
- <resource id="MIR:00100074" state="up" reliability="99">
+ <resource id="MIR:00100653" state="up" reliability="100" primary="true">
+ <dataResource>http://pir0.georgetown.edu/resid/</dataResource>
+ <dataEntityExample>AA0001</dataEntityExample>
+ <dataEntry>http://pir0.georgetown.edu/cgi-bin/resid?id=$id</dataEntry>
+ <dataInfo>RESID at Georgetown University</dataInfo>
+ <dataInstitution>Georgetown University Medical Center, Washington</dataInstitution>
+ <dataLocation>USA</dataLocation>
+ </resource>
+ <resource id="MIR:00100074" obsolete="true">
<dataResource>http://www.ebi.ac.uk/RESID/</dataResource>
<dataEntityExample>AA0001</dataEntityExample>
<dataEntry>http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id']</dataEntry>
@@ -2346,7 +2387,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100078" state="up" reliability="74">
+ <resource id="MIR:00100078" state="up" reliability="76">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>AT1G01030</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?type=locus&name=$id</dataEntry>
@@ -2460,7 +2501,7 @@
<documentation type="PMID">urn:miriam:pubmed:18451766</documentation>
</documentations>
<resources>
- <resource id="MIR:00100081" state="up" reliability="99">
+ <resource id="MIR:00100081" state="up" reliability="97">
<dataResource>http://www.peptideatlas.org/</dataResource>
<dataEntityExample>PAp00000009</dataEntityExample>
<dataEntry>https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$id</dataEntry>
@@ -2538,7 +2579,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100235" state="down" reliability="99">
+ <resource id="MIR:00100235" state="up" reliability="97">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>ECO:0000006</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/ECO/$id</dataEntry>
@@ -2613,7 +2654,7 @@
<documentation type="PMID">urn:miriam:pubmed:14681421</documentation>
</documentations>
<resources>
- <resource id="MIR:00100085" state="up" reliability="98">
+ <resource id="MIR:00100085" state="up" reliability="97">
<dataResource>http://pathway.yeastgenome.org/</dataResource>
<dataEntityExample>PWY3O-214</dataEntityExample>
<dataEntry>http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id</dataEntry>
@@ -2672,7 +2713,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000059" pattern="^S\d{2}\.\d{3}$">
+ <datatype id="MIR:00000059" pattern="^[SCTAGMNU]\d{2}\.\d{3}$">
<name>MEROPS</name>
<definition>The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.</definition>
<uris>
@@ -2789,7 +2830,7 @@
<documentation type="PMID">urn:miriam:pubmed:15059838</documentation>
</documentations>
<resources>
- <resource id="MIR:00100090" state="down" reliability="97">
+ <resource id="MIR:00100090" state="up" reliability="97">
<dataResource>http://ligand-depot.rutgers.edu/index.html</dataResource>
<dataEntityExample>ABC</dataEntityExample>
<dataEntry>http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid</dataEntry>
@@ -2801,8 +2842,8 @@
<dataResource>http://ligand-expo.rcsb.org/</dataResource>
<dataEntityExample>ABC</dataEntityExample>
<dataEntry>http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid</dataEntry>
- <dataInfo>Ligand Expo at RCSB PDB</dataInfo>
- <dataInstitution>Research Collaboratory for Structural Bioinformatics (RCSB), San Diego, California</dataInstitution>
+ <dataInfo>Ligand Expo at Rutgers</dataInfo>
+ <dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
</resources>
@@ -2831,7 +2872,7 @@
<documentation type="PMID">urn:miriam:pubmed:14681355</documentation>
</documentations>
<resources>
- <resource id="MIR:00100091" state="up" reliability="92">
+ <resource id="MIR:00100091" state="up" reliability="93">
<dataResource>http://aclame.ulb.ac.be/</dataResource>
<dataEntityExample>mge:2</dataEntityExample>
<dataEntry>http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$id</dataEntry>
@@ -2864,7 +2905,7 @@
<documentation type="URL">http://www.worldcat.org/whatis/default.jsp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100092" state="down" reliability="93">
+ <resource id="MIR:00100092" state="up" reliability="92">
<dataResource>http://isbndb.com/</dataResource>
<dataEntityExample>9781584885658</dataEntityExample>
<dataEntry>http://isbndb.com/search-all.html?kw=$id</dataEntry>
@@ -2898,7 +2939,7 @@
<datatype id="MIR:00000065" pattern="^\d+$">
<name>PRIDE</name>
- <definition>The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.</definition>
+ <definition>The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.</definition>
<uris>
<uri type="URN">urn:miriam:pride</uri>
<uri type="URL">http://identifiers.org/pride/</uri>
@@ -2911,10 +2952,10 @@
<documentation type="PMID">urn:miriam:pubmed:18428683</documentation>
</documentations>
<resources>
- <resource id="MIR:00100094" state="up" reliability="97">
+ <resource id="MIR:00100094" state="down" reliability="96">
<dataResource>http://www.ebi.ac.uk/pride/</dataResource>
<dataEntityExample>1</dataEntityExample>
- <dataEntry>http://www.ebi.ac.uk/pride/experimentLink.do?experimentAccessionNumber=$id</dataEntry>
+ <dataEntry>http://www.ebi.ac.uk/pride/archive/assays/$id</dataEntry>
<dataInfo>PRIDE at EBI</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
@@ -2993,7 +3034,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100236" state="down" reliability="93">
+ <resource id="MIR:00100236" state="up" reliability="91">
<dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>FMA:67112</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/FMA_subset/$id</dataEntry>
@@ -3028,9 +3069,9 @@
<documentation type="PMID">urn:miriam:pubmed:19147664</documentation>
</documentations>
<resources>
- <resource id="MIR:00100098" state="up" reliability="99">
+ <resource id="MIR:00100098" state="up" reliability="98">
<dataResource>http://matrixdb.ibcp.fr/</dataResource>
- <dataEntityExample>P00747_P07355</dataEntityExample>
+ <dataEntityExample>P00747__P07355</dataEntityExample>
<dataEntry>http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association</dataEntry>
<dataInfo>MatrixDB Association</dataInfo>
<dataInstitution>Institut de Biologie et Chimie des Protéines, Lyon University</dataInstitution>
@@ -3094,8 +3135,7 @@
<datatype id="MIR:00000070" pattern="^\w+:[\w\d\.-]*$">
<name>KEGG Genes</name>
- <definition>KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.
-</definition>
+ <definition>KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.</definition>
<uris>
<uri type="URN">urn:miriam:kegg.genes</uri>
<uri type="URL">http://identifiers.org/kegg.genes/</uri>
@@ -3109,7 +3149,7 @@
<resource id="MIR:00100100" state="up" reliability="100">
<dataResource>http://www.genome.jp/kegg/genes.html</dataResource>
<dataEntityExample>syn:ssr3451</dataEntityExample>
- <dataEntry>http://www.genome.jp/dbget-bin/www_bget?$id</dataEntry>
+ <dataEntry>http://www.kegg.jp/entry/$id</dataEntry>
<dataInfo>KEGG GENES Database</dataIn...
[truncated message content] |
|
From: <nik...@us...> - 2014-03-17 16:44:36
|
Revision: 266
http://sourceforge.net/p/sbfc/code/266
Author: niko-rodrigue
Date: 2014-03-17 16:44:32 +0000 (Mon, 17 Mar 2014)
Log Message:
-----------
changed the read SBML method name
Modified Paths:
--------------
trunk/lib/sbfc-1.3.3.jar
trunk/src/org/sbfc/converter/models/SBMLModel.java
Modified: trunk/lib/sbfc-1.3.3.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/models/SBMLModel.java
===================================================================
--- trunk/src/org/sbfc/converter/models/SBMLModel.java 2014-03-17 16:17:11 UTC (rev 265)
+++ trunk/src/org/sbfc/converter/models/SBMLModel.java 2014-03-17 16:44:32 UTC (rev 266)
@@ -114,9 +114,9 @@
public SBMLDocument modelFromFile(String fileName) throws ReadModelError {
-
+
try {
- document = JSBML.readSBML(fileName);
+ document = JSBML.readSBMLFromFile(fileName);
this.fileName = fileName;
} catch (XMLStreamException e) {
e.printStackTrace();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2014-06-04 12:55:28
|
Revision: 267
http://sourceforge.net/p/sbfc/code/267
Author: niko-rodrigue
Date: 2014-06-04 12:55:24 +0000 (Wed, 04 Jun 2014)
Log Message:
-----------
removed a very old version of the Woodstox xml library that was creating conflicts. Updated the identifiers.org registry xml dump. Added a bit more output to the console when problems are encountered in the Converter class
Modified Paths:
--------------
trunk/miriam.xml
trunk/src/org/sbfc/converter/Converter.java
Removed Paths:
-------------
trunk/lib/wstx-asl-2.8.jar
Deleted: trunk/lib/wstx-asl-2.8.jar
===================================================================
(Binary files differ)
Modified: trunk/miriam.xml
===================================================================
--- trunk/miriam.xml 2014-03-17 16:44:32 UTC (rev 266)
+++ trunk/miriam.xml 2014-06-04 12:55:24 UTC (rev 267)
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Export of Identifiers.org's Registry (full) -->
-<!-- Generated: Fri Mar 14 16:34:39 GMT 2014 -->
+<!-- Generated: Wed Jun 04 12:50:34 BST 2014 -->
<!-- http://identifiers.org/registry/ -->
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2014-03-14T16:34:39+00:00" data-version="2014-03-14T14:45:40+00:00">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2014-06-04T12:50:34+01:00" data-version="2014-06-03T16:02:07+01:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
<comment>BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
<name>BIND</name>
@@ -74,15 +74,15 @@
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100158" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CHEBI</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>ChEBI through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100565" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100565" state="up" reliability="98">
+ <dataResource>http://bioportal.bioontology.org/ontologies/CHEBI</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
<dataInfo>ChEBI through BioPortal</dataInfo>
@@ -142,7 +142,7 @@
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100563" state="up" reliability="98">
+ <resource id="MIR:00100563" state="up" reliability="99">
<dataResource>http://asia.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://asia.ensembl.org/id/$id</dataEntry>
@@ -259,7 +259,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000005" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
+ <datatype id="MIR:00000005" pattern="^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
<name>UniProt Knowledgebase</name>
<synonyms>
<synonym>UniProtKB</synonym>
@@ -390,8 +390,8 @@
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100507" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100507" state="up" reliability="98">
+ <dataResource>http://bioportal.bioontology.org/ontologies/NCBITAXON</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_$id</dataEntry>
<dataInfo>Taxonomy through BioPortal</dataInfo>
@@ -438,7 +438,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100107" state="up" reliability="94">
+ <resource id="MIR:00100107" state="up" reliability="92">
<dataResource>http://biomodels.caltech.edu/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://biomodels.caltech.edu/$id</dataEntry>
@@ -446,6 +446,14 @@
<dataInstitution>California Institute of Technology</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
+ <resource id="MIR:00100674" state="down" reliability="56">
+ <dataResource>http://cu.biomodels.bio2rdf.org/</dataResource>
+ <dataEntityExample>BIOMD0000000048</dataEntityExample>
+ <dataEntry>http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id</dataEntry>
+ <dataInfo>BioModels Database through Bio2RDF</dataInfo>
+ <dataInstitution>Bio2RDF, Carleton University, Ottawa, Ontario</dataInstitution>
+ <dataLocation>Canada</dataLocation>
+ </resource>
</resources>
<tags>
<tag>model</tag>
@@ -905,7 +913,7 @@
<documentation type="PMID">urn:miriam:pubmed:15608231</documentation>
</documentations>
<resources>
- <resource id="MIR:00100026" state="up" reliability="99">
+ <resource id="MIR:00100026" state="probably up" reliability="95">
<dataResource>http://www.reactome.org/</dataResource>
<dataEntityExample>REACT_1590</dataEntityExample>
<dataEntry>http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$id</dataEntry>
@@ -1129,14 +1137,14 @@
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100237" state="up" reliability="97">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataResource>http://bioportal.bioontology.org/ontologies/GO</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
<dataInfo>GO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100585" state="up" reliability="100">
+ <resource id="MIR:00100585" state="up" reliability="97">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>GO:0000003</dataEntityExample>
<dataEntry>http://www.pantherdb.org/panther/category.do?categoryAcc=$id</dataEntry>
@@ -1152,6 +1160,14 @@
<dataInstitution>Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
+ <resource id="MIR:00100675" state="up" reliability="100">
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO</dataResource>
+ <dataEntityExample>GO:0006915</dataEntityExample>
+ <dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
+ <dataInfo>GO through OLS</dataInfo>
+ <dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
+ <dataLocation>UK</dataLocation>
+ </resource>
<resource id="MIR:00100014" obsolete="true">
<dataResource>http://ep.ebi.ac.uk/EP/GO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
@@ -1252,7 +1268,7 @@
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100176" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SBO</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>SBO through OLS</dataInfo>
@@ -1260,7 +1276,7 @@
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100242" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataResource>http://bioportal.bioontology.org/ontologies/SBO</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
<dataInfo>SBO through BioPortal</dataInfo>
@@ -1470,7 +1486,7 @@
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100044" state="up" reliability="87">
+ <resource id="MIR:00100044" state="up" reliability="84">
<dataResource>http://pfam.sbc.su.se/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sbc.su.se/family/$id</dataEntry>
@@ -1555,7 +1571,7 @@
<dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100487" state="probably up" reliability="97">
+ <resource id="MIR:00100487" state="probably up" reliability="98">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>X58356</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
@@ -1650,7 +1666,7 @@
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100052" state="up" reliability="92">
+ <resource id="MIR:00100052" obsolete="true">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
<dataEntry>http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id</dataEntry>
@@ -1741,6 +1757,10 @@
<datatype id="MIR:00000033" pattern="^\d+$">
<name>PubChem-substance</name>
+ <synonyms>
+ <synonym>PubChem Substance</synonym>
+ <synonym>PubChem SID</synonym>
+ </synonyms>
<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.</definition>
<uris>
<uri type="URN">urn:miriam:pubchem.substance</uri>
@@ -1776,6 +1796,10 @@
<datatype id="MIR:00000034" pattern="^\d+$">
<name>PubChem-compound</name>
+ <synonyms>
+ <synonym>PubChem Compound</synonym>
+ <synonym>PubChem CID</synonym>
+ </synonyms>
<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.</definition>
<uris>
<uri type="URN">urn:miriam:pubchem.compound</uri>
@@ -2088,7 +2112,7 @@
<dataInstitution>University of Rome Tor Vergata, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
- <resource id="MIR:00100654" state="up" reliability="97">
+ <resource id="MIR:00100654" state="up" reliability="98">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>MINT-7905142</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:$id</dataEntry>
@@ -2141,7 +2165,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000044" pattern="^DIP[\:\-]\d{3}[EN]$">
+ <datatype id="MIR:00000044" pattern="^DIP(\:)?\-\d{1,}[ENXS]$">
<name>Database of Interacting Proteins</name>
<synonyms>
<synonym>DIP</synonym>
@@ -2387,7 +2411,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100078" state="up" reliability="76">
+ <resource id="MIR:00100078" state="up" reliability="77">
<dataResource>http://arabidopsis.org/index.jsp</dataResource>
<dataEntityExample>AT1G01030</dataEntityExample>
<dataEntry>http://arabidopsis.org/servlets/TairObject?type=locus&name=$id</dataEntry>
@@ -2572,15 +2596,15 @@
</documentations>
<resources>
<resource id="MIR:00100083" state="up" reliability="97">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=ECO&termId=ECO:0000000</dataResource>
<dataEntityExample>ECO:0000006</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Evidence Codes via the Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100235" state="up" reliability="97">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100235" state="up" reliability="96">
+ <dataResource>http://bioportal.bioontology.org/ontologies/ECO</dataResource>
<dataEntityExample>ECO:0000006</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/ECO/$id</dataEntry>
<dataInfo>Evidence Code Ontology through BioPortal</dataInfo>
@@ -2611,16 +2635,16 @@
<documentation type="URL">http://psidev.sourceforge.net/mod/data/PSI-MOD.obo</documentation>
</documentations>
<resources>
- <resource id="MIR:00100084" state="up" reliability="97">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <resource id="MIR:00100084" state="up" reliability="98">
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD</dataResource>
<dataEntityExample>MOD:00001</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Protein modifications ontology via the Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100239" state="up" reliability="100">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100239" state="down" reliability="99">
+ <dataResource>http://bioportal.bioontology.org/ontologies/PSIMOD</dataResource>
<dataEntityExample>MOD:00001</dataEntityExample>
<dataEntry>http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=$id</dataEntry>
<dataInfo>Protein modifications ontology through BioPortal</dataInfo>
@@ -2725,7 +2749,7 @@
<documentation type="PMID">urn:miriam:pubmed:17991683</documentation>
</documentations>
<resources>
- <resource id="MIR:00100087" state="up" reliability="99">
+ <resource id="MIR:00100087" state="up" reliability="98">
<dataResource>http://merops.sanger.ac.uk/index.htm</dataResource>
<dataEntityExample>S01.001</dataEntityExample>
<dataEntry>http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$id</dataEntry>
@@ -2905,7 +2929,7 @@
<documentation type="URL">http://www.worldcat.org/whatis/default.jsp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100092" state="up" reliability="92">
+ <resource id="MIR:00100092" state="up" reliability="93">
<dataResource>http://isbndb.com/</dataResource>
<dataEntityExample>9781584885658</dataEntityExample>
<dataEntry>http://isbndb.com/search-all.html?kw=$id</dataEntry>
@@ -2952,7 +2976,7 @@
<documentation type="PMID">urn:miriam:pubmed:18428683</documentation>
</documentations>
<resources>
- <resource id="MIR:00100094" state="down" reliability="96">
+ <resource id="MIR:00100094" state="up" reliability="96">
<dataResource>http://www.ebi.ac.uk/pride/</dataResource>
<dataEntityExample>1</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/pride/archive/assays/$id</dataEntry>
@@ -2985,7 +3009,7 @@
<documentation type="URL">http://www.jsbi.org/journal/GIW04/GIW04P058.pdf</documentation>
</documentations>
<resources>
- <resource id="MIR:00100095" state="up" reliability="93">
+ <resource id="MIR:00100095" state="up" reliability="94">
<dataResource>http://www.3dmet.dna.affrc.go.jp/</dataResource>
<dataEntityExample>B00162</dataEntityExample>
<dataEntry>http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id</dataEntry>
@@ -3027,15 +3051,15 @@
</documentations>
<resources>
<resource id="MIR:00100097" state="up" reliability="97">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=FMA</dataResource>
<dataEntityExample>FMA:67112</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Foundational Model of Anatomy via Ontology Lookup Service (OLS)</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100236" state="up" reliability="91">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100236" state="up" reliability="92">
+ <dataResource>http://bioportal.bioontology.org/ontologies/FMA</dataResource>
<dataEntityExample>FMA:67112</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/FMA_subset/$id</dataEntry>
<dataInfo>Foundational Model of Anatomy through BioPortal</dataInfo>
@@ -3247,7 +3271,7 @@
<documentation type="URL">http://www.pathwaycommons.org/pc/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100103" state="up" reliability="95">
+ <resource id="MIR:00100103" state="up" reliability="94">
<dataResource>http://www.pathwaycommons.org/pc/</dataResource>
<dataEntityExample>485991</dataEntityExample>
<dataEntry>http://www.pathwaycommons.org/pc/record2.do?id=$id</dataEntry>
@@ -3286,7 +3310,7 @@
<documentation type="PMID">urn:miriam:pubmed:15713731</documentation>
</documentations>
<resources>
- <resource id="MIR:00100104" state="up" reliability="96">
+ <resource id="MIR:00100104" state="down" reliability="96">
<dataResource>http://pbil.univ-lyon1.fr/databases/hovergen.php</dataResource>
<dataEntityExample>HBG004341</dataEntityExample>
<dataEntry>http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$id&db=HOVERGEN</dataEntry>
@@ -3322,7 +3346,7 @@
<documentation type="URL">http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100105" state="up" reliability="94">
+ <resource id="MIR:00100105" state="up" reliability="95">
<dataResource>http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp</dataResource>
<dataEntityExample>37</dataEntityExample>
<dataEntry>http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id</dataEntry>
@@ -3469,7 +3493,7 @@
<documentation type="PMID">urn:miriam:pubmed:17991680</documentation>
</documentations>
<resources>
- <resource id="MIR:00100110" state="up" reliability="94">
+ <resource id="MIR:00100110" state="up" reliability="95">
<dataResource>http://zfin.org</dataResource>
<dataEntityExample>ZDB-GENE-041118-11</dataEntityExample>
<dataEntry>http://zfin.org/action/marker/view/$id</dataEntry>
@@ -3556,7 +3580,7 @@
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100241" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataResource>http://bioportal.bioontology.org/ontologies/SO</dataResource>
<dataEntityExample>SO:0000704</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SO/$id</dataEntry>
<dataInfo>Sequence Ontology through BioPortal</dataInfo>
@@ -3564,7 +3588,7 @@
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100628" state="up" reliability="100">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SO</dataResource>
<dataEntityExample>SO:0000704</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Sequence Ontology through Ontology Lookup Service (OLS)</dataInfo>
@@ -3978,7 +4002,7 @@
<documentation type="PMID">urn:miriam:pubmed:11752352</documentation>
</documentations>
<resources>
- <resource id="MIR:00100123" state="up" reliability="97">
+ <resource id="MIR:00100123" state="down" reliability="94">
<dataResource>http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp</dataResource>
<dataEntityExample>DAP000773</dataEntityExample>
<dataEntry>http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id</dataEntry>
@@ -4012,7 +4036,7 @@
<documentation type="PMID">urn:miriam:pubmed:11752352</documentation>
</documentations>
<resources>
- <resource id="MIR:00100124" state="up" reliability="97">
+ <resource id="MIR:00100124" state="down" reliability="94">
<dataResource>http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp</dataResource>
<dataEntityExample>TTDS00056</dataEntityExample>
<dataEntry>http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id</dataEntry>
@@ -4046,7 +4070,7 @@
<documentation type="URL">http://senselab.med.yale.edu/NeuronDB/default.asp</documentation>
</documentations>
<resources>
- <resource id="MIR:00100125" state="up" reliability="97">
+ <resource id="MIR:00100125" state="up" reliability="96">
<dataResource>http://senselab.med.yale.edu/NeuronDB/</dataResource>
<dataEntityExample>265</dataEntityExample>
<dataEntry>http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id</dataEntry>
@@ -4392,7 +4416,7 @@
<documentation type="URL">http://www.smpdb.ca/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100137" state="up" reliability="99">
+ <resource id="MIR:00100137" state="down" reliability="96">
<dataResource>http://www.smpdb.ca/pathways</dataResource>
<dataEntityExample>SMP00001</dataEntityExample>
<dataEntry>http://pathman.smpdb.ca/pathways/$id/pathway</dataEntry>
@@ -4502,7 +4526,7 @@
<documentation type="URL">http://teddyontology.sourceforge.net/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100140" state="up" reliability="98">
+ <resource id="MIR:00100140" state="down" reliability="95">
<dataResource>http://teddyontology.sourceforge.net/</dataResource>
<dataEntityExample>TEDDY_0000066</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/TEDDY/$id</dataEntry>
@@ -4531,8 +4555,8 @@
<documentation type="URL">http://www.ebi.ac.uk/compneur-srv/kisao/</documentation>
</documentations>
<resources>
- <resource id="MIR:00100141" state="up" reliability="98">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100141" state="up" reliability="97">
+ <dataResource>http://bioportal.bioontology.org/ontologies/KISAO</dataResource>
<dataEntityExample>KISAO_0000057</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/KISAO/kisao:$id</dataEntry>
<dataInfo>KiSAO via NCBO's Bioportal</dataInfo>
@@ -4560,15 +4584,15 @@
</documentations>
<resources>
<resource id="MIR:00100142" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI</dataResource>
<dataEntityExample>MI:0308</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Molecular Interactions Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100564" state="up" reliability="89">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100564" state="down" reliability="90">
+ <dataResource>http://bioportal.bioontology.org/ontologies/PPIO</dataResource>
<dataEntityExample>MI:0308</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PPIO/$id</dataEntry>
<dataInfo>PSI Molecular Interactions Ontology through BioPortal</dataInfo>
@@ -4609,15 +4633,15 @@
</documentations>
<resources>
<resource id="MIR:00100143" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CL</dataResource>
<dataEntityExample>CL:0000232</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Cell Type Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100234" state="up" reliability="97">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100234" state="up" reliability="96">
+ <dataResource>http://bioportal.bioontology.org/ontologies/CL</dataResource>
<dataEntityExample>CL:0000232</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CL/$id</dataEntry>
<dataInfo>Cell Type Ontology through BioPortal</dataInfo>
@@ -4656,15 +4680,15 @@
</documentations>
<resources>
<resource id="MIR:00100144" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO</dataResource>
<dataEntityExample>BTO:0000146</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>Brenda Tissue Ontology through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100233" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <resource id="MIR:00100233" state="down" reliability="99">
+ <dataResource>http://bioportal.bioontology.org/ontologies/BTO</dataResource>
<dataEntityExample>BTO:0000146</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/BTO/$id</dataEntry>
<dataInfo>Brenda Tissue Ontology through BioPortal</dataInfo>
@@ -4701,7 +4725,7 @@
</documentations>
<resources>
<resource id="MIR:00100145" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PATO</dataResource>
<dataEntityExample>PATO:0001998</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>PATO through OLS</dataInfo>
@@ -4709,7 +4733,7 @@
<dataLocation>UK</dataLocation>
</resource>
<resource id="MIR:00100238" state="up" reliability="96">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataResource>http://bioportal.bioontology.org/ontologies/PATO</dataResource>
<dataEntityExample>PATO:0001998</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/PATO/$id</dataEntry>
<dataInfo>PATO through BioPortal</dataInfo>
@@ -4955,7 +4979,7 @@
<documentation type="PMID">urn:miriam:pubmed:18984618</documentation>
</documentations>
<resources>
- <resource id="MIR:00100152" state="up" reliability="100">
+ <resource id="MIR:00100152" state="up" reliability="99">
<dataResource>http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd</dataResource>
<dataEntityExample>cd00400</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$id</dataEntry>
@@ -4991,7 +5015,7 @@
<documentation type="PMID">urn:miriam:pubmed:15892874</documentation>
</documentations>
<resources>
- <resource id="MIR:00100153" state="up" reliability="98">
+ <resource id="MIR:00100153" state="up" reliability="99">
<dataResource>http://www.obofoundry.org/ro/</dataResource>
<dataEntityExample>OBO_REL:is_a</dataEntityExample>
<dataEntry>http://www.obofoundry.org/ro/#$id</dataEntry>
@@ -5064,7 +5088,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100663" state="up" reliability="33">
+ <resource id="MIR:00100663" state="up" reliability="84">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>IM-19210-3</dataEntityExample>
<dataEntry>https://imexcentral.org/icentral/imex/rec/$id</dataEntry>
@@ -5099,7 +5123,7 @@
<documentation type="URL">http://irefindex.uio.no/wiki/iRefIndex</documentation>
</documentations>
<resources>
- <resource id="MIR:00100156" state="up" reliability="96">
+ <resource id="MIR:00100156" state="up" reliability="97">
<dataResource>http://wodaklab.org/iRefWeb/</dataResource>
<dataEntityExample>617102</dataEntityExample>
<dataEntry>http://wodaklab.org/iRefWeb/interaction/show/$id</dataEntry>
@@ -5190,7 +5214,7 @@
</resources>
</datatype>
- <datatype id="MIR:00000126" pattern="^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO)\d+$">
+ <datatype id="MIR:00000126" pattern="^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$">
<name>NeuroLex</name>
<synonyms>
<synonym>BIRNLex</synonym>
@@ -5215,7 +5239,7 @@
<dataLocation>USA</dataLocation>
</resource>
<resource id="MIR:00100183" state="up" reliability="99">
- <dataResource>http://bioportal.bioontology.org/</dataResource>
+ <dataResource>http://bioportal.bioontology.org/ontologies/BIRNLEX</dataResource>
<dataEntityExample>birnlex_1672</dataEntityExample>
<dataEntry>http://pur...
[truncated message content] |
|
From: <nik...@us...> - 2014-09-05 13:59:51
|
Revision: 268
http://sourceforge.net/p/sbfc/code/268
Author: niko-rodrigue
Date: 2014-09-05 13:59:43 +0000 (Fri, 05 Sep 2014)
Log Message:
-----------
updated the jsbml jar file to correct a bug when reading/writing annotation without indentation or newline
Modified Paths:
--------------
trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java
Added Paths:
-----------
trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar
Removed Paths:
-------------
trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
Deleted: trunk/lib/jsbml-1.0-beta-with-dependencies-20140314.jar
===================================================================
(Binary files differ)
Added: trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar
===================================================================
(Binary files differ)
Index: trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar
===================================================================
--- trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar 2014-06-04 12:55:24 UTC (rev 267)
+++ trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar 2014-09-05 13:59:43 UTC (rev 268)
Property changes on: trunk/lib/jsbml-1.0-beta-with-dependencies-20140905.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java 2014-06-04 12:55:24 UTC (rev 267)
+++ trunk/src/org/sbfc/converter/sbml2sbml/IdentifiersUtil.java 2014-09-05 13:59:43 UTC (rev 268)
@@ -212,7 +212,7 @@
if (args.length < 2) {
System.out.println(
- "Usage : java org.sbml.jsbml.xml.stax.SBMLWriter [-m|-i|-u] sbmlFileName [suffix]");
+ "Usage : java org.sbfc.converter.sbml2sbml.IdentifiersUtil [-m|-i|-u] sbmlFileName [suffix]");
System.out.println("\n\t\tThe order of the options is important.");
System.out.println("\n\t\t-m will update the given sbml file to use miriam urn-uris");
System.out.println("\n\t\t-i will update the given sbml file to use miriam url-uris (identifiers.org urls)");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2014-10-22 14:54:47
|
Revision: 270
http://sourceforge.net/p/sbfc/code/270
Author: niko-rodrigue
Date: 2014-10-22 14:54:29 +0000 (Wed, 22 Oct 2014)
Log Message:
-----------
added the script used by the sbfc online application
Modified Paths:
--------------
trunk/miriam.xml
trunk/sbfConverter.sh
Added Paths:
-----------
trunk/sbfConverterOnline.sh
Modified: trunk/miriam.xml
===================================================================
--- trunk/miriam.xml 2014-09-05 14:10:55 UTC (rev 269)
+++ trunk/miriam.xml 2014-10-22 14:54:29 UTC (rev 270)
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Export of Identifiers.org's Registry (full) -->
-<!-- Generated: Fri Sep 05 15:01:31 BST 2014 -->
+<!-- Generated: Fri Mar 14 16:34:39 GMT 2014 -->
<!-- http://identifiers.org/registry/ -->
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2014-09-05T15:01:31+01:00" data-version="2014-08-12T14:38:46+01:00">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="2014-03-14T16:34:39+00:00" data-version="2014-03-14T14:45:40+00:00">
<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
<comment>BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
<name>BIND</name>
@@ -74,15 +74,15 @@
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100158" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CHEBI</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>ChEBI through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100565" state="up" reliability="92">
- <dataResource>http://bioportal.bioontology.org/ontologies/CHEBI</dataResource>
+ <resource id="MIR:00100565" state="up" reliability="99">
+ <dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>CHEBI:36927</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
<dataInfo>ChEBI through BioPortal</dataInfo>
@@ -142,7 +142,7 @@
<dataInstitution></dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100563" state="up" reliability="99">
+ <resource id="MIR:00100563" state="up" reliability="98">
<dataResource>http://asia.ensembl.org/</dataResource>
<dataEntityExample>ENSG00000139618</dataEntityExample>
<dataEntry>http://asia.ensembl.org/id/$id</dataEntry>
@@ -213,7 +213,7 @@
<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100003" state="down" reliability="99">
+ <resource id="MIR:00100003" state="up" reliability="99">
<dataResource>http://enzyme.expasy.org/</dataResource>
<dataEntityExample>1.1.1.1</dataEntityExample>
<dataEntry>http://enzyme.expasy.org/EC/$id</dataEntry>
@@ -259,23 +259,21 @@
</annotation>
</datatype>
- <datatype id="MIR:00000005" pattern="^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
+ <datatype id="MIR:00000005" pattern="^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$">
<name>UniProt Knowledgebase</name>
<synonyms>
<synonym>UniProtKB</synonym>
<synonym>UniProt</synonym>
- <synonym>Protein Knowledgebase</synonym>
</synonyms>
<definition>The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.</definition>
<uris>
<uri type="URN">urn:miriam:uniprot</uri>
<uri type="URL">http://identifiers.org/uniprot/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/uniprot//</uri>
+ <uri type="URL" deprecated="true">http://www.uniprot.org/</uri>
<uri type="URN" deprecated="true">urn:lsid:uniprot.org:uniprot</uri>
- <uri type="URL" deprecated="true">http://www.uniprot.org/</uri>
<uri type="URN" deprecated="true">urn:lsid:uniprot.org</uri>
</uris>
- <namespace>//identifiers.org/uniprot/</namespace>
+ <namespace>uniprot</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381842</documentation>
<documentation type="PMID">urn:miriam:pubmed:23161681</documentation>
@@ -358,12 +356,10 @@
</synonyms>
<definition>The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.</definition>
<uris>
- <uri type="URL">http://identifiers.org/taxonomy/</uri>
<uri type="URN">urn:miriam:taxonomy</uri>
<uri type="URL">http://identifiers.org/taxonomy/</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/Taxonomy/</uri>
<uri type="URL" deprecated="true">http://www.taxonomy.org/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/taxonomy</uri>
</uris>
<namespace>taxonomy</namespace>
<documentations>
@@ -374,7 +370,7 @@
<dataResource>http://www.ncbi.nlm.nih.gov/Taxonomy/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id</dataEntry>
- <dataInfo>NCBI Taxonomy</dataInfo>
+ <dataInfo>Taxonomy at NCBI</dataInfo>
<dataInstitution>National Center for Biotechnology Information</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
@@ -382,34 +378,26 @@
<dataResource>http://www.uniprot.org/taxonomy/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.uniprot.org/taxonomy/$id</dataEntry>
- <dataInfo>UniProt</dataInfo>
- <dataInstitution>UniProt Consortium</dataInstitution>
- <dataLocation>USA, UK and Switzerland</dataLocation>
+ <dataInfo>Taxonomy at Uniprot</dataInfo>
+ <dataInstitution>European Bioinformatics Institute</dataInstitution>
+ <dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100299" state="probably up" reliability="98">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/Taxon:$id</dataEntry>
- <dataInfo>European Nucleotide Archive (ENA)</dataInfo>
+ <dataInfo>Taxonomy at European Nucleotide Archive (ENA)</dataInfo>
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100507" state="down" reliability="94">
- <dataResource>http://bioportal.bioontology.org/ontologies/NCBITAXON</dataResource>
+ <resource id="MIR:00100507" state="up" reliability="99">
+ <dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>9606</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/obo:NCBITaxon_$id</dataEntry>
- <dataInfo>BioPortal</dataInfo>
+ <dataInfo>Taxonomy through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100695" state="up" reliability="97">
- <dataResource>http://taxonomy.bio2rdf.org/fct/</dataResource>
- <dataEntityExample>9606</dataEntityExample>
- <dataEntry>http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<tags>
<tag>taxonomy</tag>
@@ -434,11 +422,9 @@
<uris>
<uri type="URN">urn:miriam:biomodels.db</uri>
<uri type="URL">http://identifiers.org/biomodels.db/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/biomodels.db//</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/biomodels/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/biomodels</uri>
</uris>
- <namespace>//identifiers.org/biomodels.db/</namespace>
+ <namespace>biomodels.db</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381960</documentation>
<documentation type="PMID">urn:miriam:pubmed:20587024</documentation>
@@ -448,26 +434,18 @@
<dataResource>http://www.ebi.ac.uk/biomodels/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/biomodels-main/$id</dataEntry>
- <dataInfo>BioModels Database</dataInfo>
+ <dataInfo>BioModels, a Database of Annotated Published Models</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100107" state="up" reliability="92">
+ <resource id="MIR:00100107" state="up" reliability="94">
<dataResource>http://biomodels.caltech.edu/</dataResource>
<dataEntityExample>BIOMD0000000048</dataEntityExample>
<dataEntry>http://biomodels.caltech.edu/$id</dataEntry>
- <dataInfo>Caltech mirror</dataInfo>
+ <dataInfo>Mirror of BioModels Database</dataInfo>
<dataInstitution>California Institute of Technology</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100674" state="up" reliability="82">
- <dataResource>http://cu.biomodels.bio2rdf.org/fct/</dataResource>
- <dataEntityExample>BIOMD0000000048</dataEntityExample>
- <dataEntry>http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<tags>
<tag>model</tag>
@@ -595,12 +573,9 @@
<uris>
<uri type="URN">urn:miriam:interpro</uri>
<uri type="URL">http://identifiers.org/interpro/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/interpro//</uri>
<uri type="URL" deprecated="true">http://www.ebi.ac.uk/interpro/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/interpro</uri>
- <uri type="URL" deprecated="true">http://purl.uniprot.org/interpro/</uri>
</uris>
- <namespace>//identifiers.org/interpro/</namespace>
+ <namespace>interpro</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608177</documentation>
</documentations>
@@ -613,14 +588,6 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100697" state="unknown" reliability="0">
- <dataResource>http://interpro.bio2rdf.org/fct/</dataResource>
- <dataEntityExample>IPR000100</dataEntityExample>
- <dataEntry>http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<tags>
<tag>domain</tag>
@@ -750,19 +717,17 @@
<name>PubMed</name>
<definition>PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.</definition>
<uris>
- <uri type="URL">http://identifiers.org/pubmed/</uri>
<uri type="URN">urn:miriam:pubmed</uri>
<uri type="URL">http://identifiers.org/pubmed/</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/PubMed/</uri>
<uri type="URL" deprecated="true">http://www.pubmed.gov/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/pubmed</uri>
</uris>
<namespace>pubmed</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:16381840</documentation>
</documentations>
<resources>
- <resource id="MIR:00100023" state="up" reliability="99">
+ <resource id="MIR:00100023" state="up" reliability="99" primary="true">
<dataResource>http://www.ncbi.nlm.nih.gov/PubMed/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://www.ncbi.nlm.nih.gov/pubmed/$id</dataEntry>
@@ -782,18 +747,10 @@
<dataResource>http://europepmc.org/</dataResource>
<dataEntityExample>16333295</dataEntityExample>
<dataEntry>http://europepmc.org/abstract/MED/$id</dataEntry>
- <dataInfo>Europe PMC</dataInfo>
+ <dataInfo>PubMed through Europe PubMed Central</dataInfo>
<dataInstitution>Europe PubMed Central partners</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100702" state="unknown" reliability="0">
- <dataResource>http://pubmed.bio2rdf.org/fct</dataResource>
- <dataEntityExample>23735196</dataEntityExample>
- <dataEntry>http://pubmed.bio2rdf.org/describe/?url=http://bio2rdf.org/pubmed:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
<resource id="MIR:00100028" obsolete="true">
<dataResource>http://www.ebi.ac.uk/Databases/MEDLINE/medline.html</dataResource>
<dataEntityExample>16333295</dataEntityExample>
@@ -845,11 +802,9 @@
<uris>
<uri type="URN">urn:miriam:omim</uri>
<uri type="URL">http://identifiers.org/omim/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/omim//</uri>
<uri type="URL" deprecated="true">http://www.ncbi.nlm.nih.gov/OMIM/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/omim</uri>
</uris>
- <namespace>//identifiers.org/omim/</namespace>
+ <namespace>omim</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608251</documentation>
</documentations>
@@ -878,14 +833,6 @@
<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
<dataLocation>UK</dataLocation>
</resource>
- <resource id="MIR:00100694" state="up" reliability="100">
- <dataResource>http://omim.bio2rdf.org/fct</dataResource>
- <dataEntityExample>603903</dataEntityExample>
- <dataEntry>http://omim.bio2rdf.org/describe/?url=http://bio2rdf.org/omim:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<tags>
<tag>disorder</tag>
@@ -958,10 +905,10 @@
<documentation type="PMID">urn:miriam:pubmed:15608231</documentation>
</documentations>
<resources>
- <resource id="MIR:00100026" state="probably up" reliability="95">
+ <resource id="MIR:00100026" state="up" reliability="99">
<dataResource>http://www.reactome.org/</dataResource>
<dataEntityExample>REACT_1590</dataEntityExample>
- <dataEntry>http://www.reactome.org/PathwayBrowser/#$id</dataEntry>
+ <dataEntry>http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$id</dataEntry>
<dataInfo>Reactome, a curated knowledgebase of biological pathways</dataInfo>
<dataInstitution>Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory and European Bioinformatics Institute</dataInstitution>
<dataLocation>Canada / USA / United Kingdom</dataLocation>
@@ -1145,14 +1092,11 @@
</synonyms>
<definition>The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.</definition>
<uris>
- <uri type="URL">http://identifiers.org/go/</uri>
<uri type="URN">urn:miriam:go</uri>
<uri type="URL">http://identifiers.org/go/</uri>
- <uri type="URL" deprecated="true">http://identifiers.org/obo.go/</uri>
<uri type="URL" deprecated="true">http://www.geneontology.org/</uri>
<uri type="URN" deprecated="true">urn:miriam:obo.go</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/</uri>
- <uri type="URL" deprecated="true">http://purl.obolibrary.org/obo/</uri>
+ <uri type="URL" deprecated="true">http://identifiers.org/obo.go/</uri>
</uris>
<namespace>go</namespace>
<documentations>
@@ -1168,7 +1112,7 @@
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100013" state="up" reliability="99" primary="true">
+ <resource id="MIR:00100013" state="up" reliability="98" primary="true">
<dataResource>http://amigo.geneontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=$id</dataEntry>
@@ -1184,15 +1128,15 @@
<dataInstitution>The Jackson Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100237" state="up" reliability="95">
- <dataResource>http://bioportal.bioontology.org/ontologies/GO</dataResource>
+ <resource id="MIR:00100237" state="up" reliability="97">
+ <dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
<dataInfo>GO through BioPortal</dataInfo>
<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100585" state="up" reliability="97">
+ <resource id="MIR:00100585" state="up" reliability="100">
<dataResource>http://www.pantherdb.org/</dataResource>
<dataEntityExample>GO:0000003</dataEntityExample>
<dataEntry>http://www.pantherdb.org/panther/category.do?categoryAcc=$id</dataEntry>
@@ -1200,7 +1144,7 @@
<dataInstitution>Keck School of Medicine, University of Southern California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100659" state="down" reliability="86">
+ <resource id="MIR:00100659" state="up" reliability="100">
<dataResource>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
<dataEntry>http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/$id</dataEntry>
@@ -1208,14 +1152,6 @@
<dataInstitution>Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100675" state="up" reliability="100">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO</dataResource>
- <dataEntityExample>GO:0006915</dataEntityExample>
- <dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
- <dataInfo>GO through OLS</dataInfo>
- <dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
- <dataLocation>UK</dataLocation>
- </resource>
<resource id="MIR:00100014" obsolete="true">
<dataResource>http://ep.ebi.ac.uk/EP/GO/</dataResource>
<dataEntityExample>GO:0006915</dataEntityExample>
@@ -1252,11 +1188,9 @@
<uris>
<uri type="URN">urn:miriam:sgd</uri>
<uri type="URL">http://identifiers.org/sgd/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/sgd//</uri>
<uri type="URL" deprecated="true">http://www.yeastgenome.org/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/sgd</uri>
</uris>
- <namespace>//identifiers.org/sgd/</namespace>
+ <namespace>sgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:14681421</documentation>
</documentations>
@@ -1269,14 +1203,6 @@
<dataInstitution>Stanford University</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100703" state="unknown" reliability="0">
- <dataResource>http://sgd.bio2rdf.org/fct</dataResource>
- <dataEntityExample>S000006169</dataEntityExample>
- <dataEntry>http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<restrictions>
<restriction type="9" desc="Identifier multiplicity">
@@ -1326,15 +1252,15 @@
<dataLocation>United Kingdom</dataLocation>
</resource>
<resource id="MIR:00100176" state="up" reliability="99">
- <dataResource>http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SBO</dataResource>
+ <dataResource>http://www.ebi.ac.uk/ontology-lookup/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ontology-lookup/?termId=$id</dataEntry>
<dataInfo>SBO through OLS</dataInfo>
<dataInstitution>European Bioinformatics Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100242" state="up" reliability="96">
- <dataResource>http://bioportal.bioontology.org/ontologies/SBO</dataResource>
+ <resource id="MIR:00100242" state="up" reliability="99">
+ <dataResource>http://bioportal.bioontology.org/</dataResource>
<dataEntityExample>SBO:0000262</dataEntityExample>
<dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
<dataInfo>SBO through BioPortal</dataInfo>
@@ -1435,11 +1361,9 @@
<name>WormBase</name>
<definition>WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes.</definition>
<uris>
- <uri type="URL">http://identifiers.org/wormbase/</uri>
<uri type="URN">urn:miriam:wormbase</uri>
<uri type="URL">http://identifiers.org/wormbase/</uri>
<uri type="URL" deprecated="true">http://www.wormbase.org/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/wormbase</uri>
</uris>
<namespace>wormbase</namespace>
<documentations>
@@ -1463,14 +1387,6 @@
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100704" state="unknown" reliability="0">
- <dataResource>http://wormbase.bio2rdf.org/fct</dataResource>
- <dataEntityExample>WBGene00000001</dataEntityExample>
- <dataEntry>http://wormbase.bio2rdf.org/describe/?url=http://bio2rdf.org/wormbase:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
<resource id="MIR:00100039" obsolete="true">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>WBGene00000001</dataEntityExample>
@@ -1546,15 +1462,7 @@
<documentation type="PMID">urn:miriam:pubmed:9223186</documentation>
</documentations>
<resources>
- <resource id="MIR:00100685" state="up" reliability="100">
- <dataResource>http://pfam.xfam.org/</dataResource>
- <dataEntityExample>PF01234</dataEntityExample>
- <dataEntry>http://pfam.xfam.org/family/$id</dataEntry>
- <dataInfo>Pfam at EMBL-EBI</dataInfo>
- <dataInstitution>EMBL-EBI, Wellcome Trust Genome Campus, Hinxton</dataInstitution>
- <dataLocation>UK</dataLocation>
- </resource>
- <resource id="MIR:00100043" obsolete="true">
+ <resource id="MIR:00100043" state="up" reliability="99">
<dataResource>http://pfam.sanger.ac.uk/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sanger.ac.uk/family/$id/</dataEntry>
@@ -1562,7 +1470,7 @@
<dataInstitution>Wellcome Trust Sanger Institute</dataInstitution>
<dataLocation>United Kingdom</dataLocation>
</resource>
- <resource id="MIR:00100044" obsolete="true">
+ <resource id="MIR:00100044" state="up" reliability="87">
<dataResource>http://pfam.sbc.su.se/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.sbc.su.se/family/$id</dataEntry>
@@ -1570,7 +1478,7 @@
<dataInstitution>Karolinska Institutet</dataInstitution>
<dataLocation>Sweden</dataLocation>
</resource>
- <resource id="MIR:00100045" obsolete="true">
+ <resource id="MIR:00100045" state="up" reliability="99">
<dataResource>http://pfam.janelia.org/</dataResource>
<dataEntityExample>PF01234</dataEntityExample>
<dataEntry>http://pfam.janelia.org/family/$id</dataEntry>
@@ -1647,7 +1555,7 @@
<dataInstitution>DNA Data Bank of Japan, Mishima, Shizuoka</dataInstitution>
<dataLocation>Japan</dataLocation>
</resource>
- <resource id="MIR:00100487" state="probably up" reliability="98">
+ <resource id="MIR:00100487" state="probably up" reliability="97">
<dataResource>http://www.ebi.ac.uk/ena/</dataResource>
<dataEntityExample>X58356</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/ena/data/view/$id</dataEntry>
@@ -1742,7 +1650,7 @@
<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100052" obsolete="true">
+ <resource id="MIR:00100052" state="up" reliability="92">
<dataResource>http://wormbase.sanger.ac.uk/</dataResource>
<dataEntityExample>CE28239</dataEntityExample>
<dataEntry>http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id</dataEntry>
@@ -1801,7 +1709,7 @@
<documentation type="PMID">urn:miriam:pubmed:16381852</documentation>
</documentations>
<resources>
- <resource id="MIR:00100056" state="down" reliability="99">
+ <resource id="MIR:00100056" state="up" reliability="99">
<dataResource>http://www.expasy.org/prosite/</dataResource>
<dataEntityExample>PS00001</dataEntityExample>
<dataEntry>http://prosite.expasy.org/$id</dataEntry>
@@ -1833,10 +1741,6 @@
<datatype id="MIR:00000033" pattern="^\d+$">
<name>PubChem-substance</name>
- <synonyms>
- <synonym>PubChem Substance</synonym>
- <synonym>PubChem SID</synonym>
- </synonyms>
<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.</definition>
<uris>
<uri type="URN">urn:miriam:pubchem.substance</uri>
@@ -1848,7 +1752,7 @@
<documentation type="PMID">urn:miriam:pubmed:17170002</documentation>
</documentations>
<resources>
- <resource id="MIR:00100058" state="up" reliability="96">
+ <resource id="MIR:00100058" state="up" reliability="95">
<dataResource>http://pubchem.ncbi.nlm.nih.gov/</dataResource>
<dataEntityExample>100101</dataEntityExample>
<dataEntry>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$id</dataEntry>
@@ -1872,10 +1776,6 @@
<datatype id="MIR:00000034" pattern="^\d+$">
<name>PubChem-compound</name>
- <synonyms>
- <synonym>PubChem Compound</synonym>
- <synonym>PubChem CID</synonym>
- </synonyms>
<definition>PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.</definition>
<uris>
<uri type="URN">urn:miriam:pubchem.compound</uri>
@@ -1983,11 +1883,9 @@
<uris>
<uri type="URN">urn:miriam:mgd</uri>
<uri type="URL">http://identifiers.org/mgd/</uri>
- <uri type="URL">http://identifiers.org///identifiers.org/mgd//</uri>
<uri type="URL" deprecated="true">http://mousegenome.org/</uri>
- <uri type="URL" deprecated="true">http://bio2rdf.org/mgi:</uri>
</uris>
- <namespace>//identifiers.org/mgd/</namespace>
+ <namespace>mgd</namespace>
<documentations>
<documentation type="PMID">urn:miriam:pubmed:15608240</documentation>
<documentation type="URL">http://www.informatics.jax.org/mgihome/projects/overview.shtml#aboutMGD</documentation>
@@ -2001,14 +1899,6 @@
<dataInstitution>The Jackson Laboratory</dataInstitution>
<dataLocation>USA</dataLocation>
</resource>
- <resource id="MIR:00100696" obsolete="true">
- <dataResource>http://mgi.bio2rdf.org/fct</dataResource>
- <dataEntityExample>2442292</dataEntityExample>
- <dataEntry>http://mgi.bio2rdf.org/describe/?url=http://bio2rdf.org/mgi:$id</dataEntry>
- <dataInfo>Bio2RDF</dataInfo>
- <dataInstitution>Bio2RDF.org</dataInstitution>
- <dataLocation></dataLocation>
- </resource>
</resources>
<tags>
<tag>expression</tag>
@@ -2198,7 +2088,7 @@
<dataInstitution>University of Rome Tor Vergata, Rome</dataInstitution>
<dataLocation>Italy</dataLocation>
</resource>
- <resource id="MIR:00100654" state="up" reliability="95">
+ <resource id="MIR:00100654" state="up" reliability="97">
<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
<dataEntityExample>MINT-7905142</dataEntityExample>
<dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:$id</dataEntry>
@@ -2251,7 +2141,7 @@
</annotation>
</datatype>
- <datatype id="MIR:00000044" pattern="^DIP(\:)?\-\d{1,}[ENXS]$">
+ <datatype id="MIR:00000044" pattern="^DIP[\:\-]\d{3}[EN]$">
<name>Database of Interacting Proteins</name>
<synonyms>
<synonym>DIP</synonym>
@@ -2497,7 +2387,7 @@
<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
</documentations>
<resources>
- <resource id="MIR:00100078" state="up" reliability="78">
+ <resource id="MIR:00100078" state="up" reliability="76">
<dataResource>http://ara...
[truncated message content] |
|
From: <nik...@us...> - 2014-11-24 14:56:30
|
Revision: 271
http://sourceforge.net/p/sbfc/code/271
Author: niko-rodrigue
Date: 2014-11-24 14:56:22 +0000 (Mon, 24 Nov 2014)
Log Message:
-----------
corrected a bug in sbml2xpp, when a species was modified by rules the 'init' value was not always set properly
Modified Paths:
--------------
trunk/build.xml
trunk/lib/sbfc-1.3.3.jar
trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2014-10-22 14:54:29 UTC (rev 270)
+++ trunk/build.xml 2014-11-24 14:56:22 UTC (rev 271)
@@ -12,9 +12,9 @@
</tstamp>
<property name="Name" value="System Biology Format Converter"/>
<property name="name" value="sbfc"/>
- <property name="version" value="1.3.3"/>
+ <property name="version" value="1.3.4"/>
- <property name="sbml2xpp.version" value="1.2"/>
+ <property name="sbml2xpp.version" value="1.3"/>
<property name="sbml2octave.version" value="1.0"/>
<property name="sbml2biopax.version" value="3.1.1"/>
Modified: trunk/lib/sbfc-1.3.3.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java 2014-10-22 14:54:29 UTC (rev 270)
+++ trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java 2014-11-24 14:56:22 UTC (rev 271)
@@ -41,7 +41,6 @@
import org.sbfc.converter.models.XPPModel;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.AlgebraicRule;
-import org.sbml.jsbml.AssignmentRule;
import org.sbml.jsbml.CVTerm;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.Delay;
@@ -55,7 +54,6 @@
import org.sbml.jsbml.Model;
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.Parameter;
-import org.sbml.jsbml.RateRule;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Rule;
import org.sbml.jsbml.SBMLException;
@@ -64,6 +62,7 @@
import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.StoichiometryMath;
import org.sbml.jsbml.Trigger;
+import org.sbml.jsbml.Variable;
import org.sbml.jsbml.util.compilers.FormulaCompilerNoPiecewise;
@@ -332,7 +331,7 @@
if (rule instanceof AlgebraicRule) {
rulemath = printAlgebraicRule(rule);
} else {
- rulemath = printRule(rule);
+ rulemath = printRule((ExplicitRule) rule);
}
if (rulemath == null) {
@@ -939,26 +938,18 @@
/**
- * using libSBML changes the Rules(mathML) to Infix notation
+ * Changes the Rules(mathML) to Infix notation, using jsbml.
*
* @param rule
* @return
* @throws SBMLException
*/
- private String printRule(Rule rule) throws SBMLException {
+ private String printRule(ExplicitRule rule) throws SBMLException {
StringBuilder ruleStr = new StringBuilder();
- String variableId = null;
+ String variableId = rule.getVariable();
+ Variable variable = rule.getVariableInstance();
- /*Getting VariableId*/
- if(rule.isRate()) {
- variableId = ((RateRule)rule).getVariable();
-
- }
- else if(rule.isAssignment()) {
- variableId = ((AssignmentRule)rule).getVariable();
- }
-
String xppId = XPPID.getXPPId(variableId);
String mathMLStr = rule.getMath().toFormula();
mathMLStr = replaceIdInsideFormula(mathMLStr);
@@ -971,33 +962,24 @@
if (matchMath(mathMLStr, ruleStr)) {
- // mathMLStr = translatePiecewise(mathMLStr);
+ // Get the initial value
+ // TODO - check that 'init' is allowed for assignmentRule
+ if (variable.isSetValue()) {
+ String initialValue = "" + variable.getValue();
+ ruleStr.append("init " + xppId + "=" + initialValue + "\n");
+ }
+
+ if (rule.isRate())
+ {
+ ruleStr.append("d" + xppId + "/dt=" + mathMLStr + "\n");
+ }
+ else if (rule.isAssignment())
+ {
+ ruleStr.append("" + xppId + "=" + mathMLStr + "\n");
+ ruleStr.append("aux " + xppId + "=" + xppId + "\n");
+ }
- if (rule.isRate()) {
-
- // Get the initial values or have that done before ?
- RateRule variable = (RateRule)rule;
- String initialValue = "TODO";
- if (variable.getVariableInstance() instanceof Compartment) {
- initialValue = "" + ((Compartment) variable.getVariableInstance()).getSize();
- } else if (variable.getVariableInstance() instanceof Species) {
-
- // TODO : check which one of InitialAmount or InitialConcentration we should use !!!
- initialValue = "" + ((Species) variable.getVariableInstance()).getInitialAmount();
-
- } else if(variable.getVariableInstance() instanceof Parameter) {
- initialValue = "" + ((Parameter) variable.getVariableInstance()).getValue();
- }
-
- ruleStr.append("init " + xppId + "=" + initialValue + "\n");
- ruleStr.append("d" + xppId + "/dt=" + mathMLStr + "\n");
-
- } else if (rule.isAssignment()) {
- ruleStr.append("" + xppId + "=" + mathMLStr + "\n");
- ruleStr.append("aux " + xppId + "=" + xppId + "\n");
- }
-
} else {
// Print a warning to say that there are some unsupported functions
System.out.println("Rule " + variableId + " ignored : there are some unsupported functions !!");
@@ -1005,7 +987,6 @@
}
return ruleStr.toString();
-
}
/**
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|
|
From: <nik...@us...> - 2014-11-24 15:13:30
|
Revision: 273
http://sourceforge.net/p/sbfc/code/273
Author: niko-rodrigue
Date: 2014-11-24 15:13:23 +0000 (Mon, 24 Nov 2014)
Log Message:
-----------
'init' not allowed for assignmentRule in xppaut
Modified Paths:
--------------
trunk/lib/sbfc-1.3.4.jar
trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java
Modified: trunk/lib/sbfc-1.3.4.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java 2014-11-24 14:59:52 UTC (rev 272)
+++ trunk/src/org/sbfc/converter/sbml2xpp/SBML2XPP.java 2014-11-24 15:13:23 UTC (rev 273)
@@ -962,9 +962,8 @@
if (matchMath(mathMLStr, ruleStr)) {
- // Get the initial value
- // TODO - check that 'init' is allowed for assignmentRule
- if (variable.isSetValue()) {
+ // Get the initial value ('init' is not allowed for assignmentRule)
+ if (variable.isSetValue() && rule.isRate()) {
String initialValue = "" + variable.getValue();
ruleStr.append("init " + xppId + "=" + initialValue + "\n");
}
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|
|
From: <nik...@us...> - 2015-05-26 15:31:29
|
Revision: 334
http://sourceforge.net/p/sbfc/code/334
Author: niko-rodrigue
Date: 2015-05-26 15:31:27 +0000 (Tue, 26 May 2015)
Log Message:
-----------
updated the README in the trunk folder.
Added Paths:
-----------
trunk/README.md
Removed Paths:
-------------
trunk/README
Deleted: trunk/README
===================================================================
--- trunk/README 2015-05-26 15:17:08 UTC (rev 333)
+++ trunk/README 2015-05-26 15:31:27 UTC (rev 334)
@@ -1,45 +0,0 @@
- S B F C Framework
-
-The System Biology Format Converter (SBFC) aims is to provide a generic
-framework that potentially allows any conversion between two formats.
-Interoperability between formats is a recurring issue in Systems Biology.
-Although there are various tools available to convert models from one format
-to another, most of them have been independently developed and cannot easily
-be combined, specially to provide support for more formats. The framework is
-written in Java and can be used as a standalone executable. This is a
-collaborative project and we hope that developers will provide support for
-more formats by creating new modules.SBFC allows anyone to easily add new
-converters and to integrate existing converters with a minimum of changes.
-It also allow to combine several existing converters.
-
-SBFC is a free, open-source programming library.
-
-For more information about the SBFC Framework, please visit the
-SBFC website at
- http://sbfc.sourceforge.net/
-
-
-Thank you for your interest in SBFC!
-
-The SBFC Team.
-
-
-
-
-_____/\\\\\\\\\\\______/\\\\\\\\\\\\\_______/\\\\\\\\\\\\\\\____/\\\\\\\\\_
- ___/\\\/////////\\\___\/\\\/////////\\\____\/\\\///////////___/\\\////////__
- __\//\\\______\///____\/\\\_______\/\\\____\/\\\____________/\\\/___________
- ___\////\\\___________\/\\\\\\\\\\\\\\_____\/\\\\\\\\\\\___/\\\_____________
- ______\////\\\________\/\\\/////////\\\____\/\\\///////___\/\\\_____________
- _________\////\\\_____\/\\\_______\/\\\____\/\\\__________\//\\\____________
- __/\\\______\//\\\____\/\\\_______\/\\\____\/\\\__________\///\\\__________
- _\///\\\\\\\\\\\/_____\/\\\\\\\\\\\\\/_____\/\\\____________\////\\\\\\\\\_
- ___\///////////_______\/////////////_______\///_______________\/////////__
-
- ___ ___ ___ ___
- / __| o O O | _ ) o O O | __| o O O / __|
- \__ \ o | _ \ o | _| o | (__
- |___/ TS__[O] |___/ TS__[O] _|_|_ TS__[O] \___|
-_|"""""| {======|_|"""""| {======|_| """ | {======|_|"""""|
-"`-0-0-'./o--000'"`-0-0-'./o--000'"`-0-0-'./o--000'"`-0-0-'
-
Copied: trunk/README.md (from rev 325, trunk/README)
===================================================================
--- trunk/README.md (rev 0)
+++ trunk/README.md 2015-05-26 15:31:27 UTC (rev 334)
@@ -0,0 +1,39 @@
+ S B F C Framework
+
+The **System Biology Format Converter** (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats.
+
+The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. It also allow to combine several existing converters.
+SBFC is a free, open-source programming library.
+
+For more information about the SBFC Framework, please visit the SBFC website at
+
+<http://sbfc.sourceforge.net/>
+
+Please report problems with SBFC using the tracker at <http://sourceforge.net/p/sbfc/bugs/>
+
+Mailing list for discussing SBFC is at <https://sourceforge.net/p/sbfc/mailman/sbfc-devel/>. Please use this mailing list to contact the core SBFC developers directly.
+
+---
+
+## How to use SBFC
+
+## How to compile and develope with SBFC
+
+
+Thank you for your interest in SBFC!
+
+The SBFC Team.
+
+
+
+<pre>
+_____/\\\\\\\\\\\______/\\\\\\\\\\\\\_______/\\\\\\\\\\\\\\\____/\\\\\\\\\_
+ ___/\\\/////////\\\___\/\\\/////////\\\____\/\\\///////////___/\\\////////__
+ __\//\\\______\///____\/\\\_______\/\\\____\/\\\____________/\\\/___________
+ ___\////\\\___________\/\\\\\\\\\\\\\\_____\/\\\\\\\\\\\___/\\\_____________
+ ______\////\\\________\/\\\/////////\\\____\/\\\///////___\/\\\_____________
+ _________\////\\\_____\/\\\_______\/\\\____\/\\\__________\//\\\____________
+ __/\\\______\//\\\____\/\\\_______\/\\\____\/\\\__________\///\\\__________
+ _\///\\\\\\\\\\\/_____\/\\\\\\\\\\\\\/_____\/\\\____________\////\\\\\\\\\_
+ ___\///////////_______\/////////////_______\///_______________\/////////__
+</pre>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-07-02 12:19:09
|
Revision: 359
http://sourceforge.net/p/sbfc/code/359
Author: pdp10
Date: 2015-07-02 12:19:06 +0000 (Thu, 02 Jul 2015)
Log Message:
-----------
added sbml2matlab converter
Added Paths:
-----------
trunk/sbml2matlab.sh
trunk/src/org/sbfc/converter/sbml2matlab/
trunk/src/org/sbfc/converter/sbml2matlab/SBML2Matlab.java
Added: trunk/sbml2matlab.sh
===================================================================
--- trunk/sbml2matlab.sh (rev 0)
+++ trunk/sbml2matlab.sh 2015-07-02 12:19:06 UTC (rev 359)
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+## Example script to use the System Biology Format Converter to convert an SBML model to Matlab.
+
+#RESOLVE_LINK=`readlink -e $0` // the option '-e' does not exist on tomcat-11/12
+RESOLVE_LINK=`readlink -f $0`
+
+SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
+
+${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel SBML2Matlab $1
+
Property changes on: trunk/sbml2matlab.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Added: trunk/src/org/sbfc/converter/sbml2matlab/SBML2Matlab.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2matlab/SBML2Matlab.java (rev 0)
+++ trunk/src/org/sbfc/converter/sbml2matlab/SBML2Matlab.java 2015-07-02 12:19:06 UTC (rev 359)
@@ -0,0 +1,106 @@
+/*
+ * $Id: SBML2Matlab.java 294 2015-03-26 16:24:02Z pdp10 $
+ * $URL: svn+ssh://pdp10@svn.code.sf.net/p/sbfc/code/trunk/src/org/sbfc/converter/sbml2matlab/SBML2Matlab.java $
+ *
+ *
+ * ==============================================================================
+ * Copyright (c) 2010 the copyright is held jointly by the individual
+ * authors. See the file AUTHORS for the list of authors
+ *
+ * This file is part of The System Biology Format Converter (SBFC).
+ *
+ * SBFC is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * SBFC is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with SBFC. If not, see<http://www.gnu.org/licenses/>.
+ *
+ * ==============================================================================
+ *
+ */
+
+package org.sbfc.converter.sbml2matlab;
+
+import org.sbfc.converter.sbml2octave.SBML2Octave;
+
+
+
+
+/**
+ * Convert an SBML file into an Matlab file.
+ *
+ * @author Piero Dalle Pezze
+ *
+ * @version 1.0
+ *
+ */
+public class SBML2Matlab extends SBML2Octave {
+
+ /**
+ * <b>Constructor SBML2Octave.</b><br/> Main method of the biological model
+ * export from <a href="http://sbml.org/"><b>SBML</b></a> (Systems Biology
+ * Markup Language) to Matlab</a>.
+
+ *
+ */
+ public SBML2Matlab() {
+ super();
+
+ }
+
+ // The following protected methods differ between Octave and Matlab.
+ // These are overridden in the converter SBML2Matlab
+ protected String headerString() {
+ return "% This file works with MATLAB and is automatically generated with \n" +
+ "% the System Biology Format Converter (http://sbfc.sourceforge.net/)\n" +
+ "% from an SBML file.\n" +
+ // TODO : put the version used
+ "%\n" +
+ "% The conversion system has the following limitations:\n" +
+ "% - You may have to re order some reactions and Assignment Rules definition\n" +
+ "% - Delays are not taken into account\n" +
+ "% - You should change the lsode parameters (start, end, steps) to get better results\n%\n\n";
+ // This seems not to be any longer required by Octave
+// "%\n% NOTE for Octave users ONLY:\n" +
+// "% To prevent Octave from thinking that this is a function file, \n" +
+// "% the following line should be uncommented (instead comment it if using Matlab): \n" +
+// "%1;\n\n";
+ }
+
+ protected String xdotFunctionSignature() {
+ return "% Depending on whether you are using Octave or Matlab,\n" +
+ "% you should comment / uncomment one of the following blocks.\n" +
+ "% This should also be done for the definition of the function f below.\n" +
+ "% Start Matlab code\n" +
+ "function xdot=f(t,x)\n" +
+ "% End Matlab code\n\n" +
+
+ "% Start Octave code\n" +
+ "%function xdot=f(x,t)\n" +
+ "% End Octave code\n\n";
+ }
+
+ protected String odeSolverCode() {
+ return "% Depending on whether you are using Octave or Matlab,\n" +
+ "% you should comment / uncomment one of the following blocks.\n" +
+ "% This should also be done for the definition of the function f below.\n" +
+ "% Start Matlab code\n" +
+ "\ttspan=[0:0.01:100];\n" +
+ "\topts = odeset('AbsTol',1e-3);\n" +
+ "\t[t,x]=ode23tb(@f,tspan,x0,opts);\n" +
+ "% End Matlab code\n\n" +
+
+ "% Start Octave code\n" +
+ "%\tt=linspace(0,100,100);\n" +
+ "%\tx=lsode('f',x0,t);\n" +
+ "% End Octave code\n\n";
+ }
+
+}
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|
|
From: <nik...@us...> - 2015-07-06 10:30:30
|
Revision: 373
http://sourceforge.net/p/sbfc/code/373
Author: niko-rodrigue
Date: 2015-07-06 10:30:28 +0000 (Mon, 06 Jul 2015)
Log Message:
-----------
added first prototype of windows bat files
Added Paths:
-----------
trunk/sbfConverter.bat
trunk/sbml2octave.bat
Added: trunk/sbfConverter.bat
===================================================================
--- trunk/sbfConverter.bat (rev 0)
+++ trunk/sbfConverter.bat 2015-07-06 10:30:28 UTC (rev 373)
@@ -0,0 +1,10 @@
+@echo off
+
+MODEL_NAME=$1
+CONVERTER_NAME=$2
+file=$3
+
+java -Dmiriam.xml.export=miriam.xml -classpath lib\*.jar org.sbfc.converter.Converter %MODEL_NAME% %CONVERTER_NAME% %file%
+
+
+pause
\ No newline at end of file
Added: trunk/sbml2octave.bat
===================================================================
--- trunk/sbml2octave.bat (rev 0)
+++ trunk/sbml2octave.bat 2015-07-06 10:30:28 UTC (rev 373)
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## Example script to use the System Biology Format Converter to convert an SBML model into octave.
+
+sbfConverter.bat SBMLModel SBML2Octave $1
+
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|
|
From: <nik...@us...> - 2015-07-06 13:51:09
|
Revision: 375
http://sourceforge.net/p/sbfc/code/375
Author: niko-rodrigue
Date: 2015-07-06 13:51:06 +0000 (Mon, 06 Jul 2015)
Log Message:
-----------
updated the bat files so that it works on windows + some minor corrections to code
Modified Paths:
--------------
trunk/sbfConverter.bat
trunk/sbml2octave.bat
trunk/src/org/sbfc/converter/Converter.java
trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
Modified: trunk/sbfConverter.bat
===================================================================
--- trunk/sbfConverter.bat 2015-07-06 13:49:51 UTC (rev 374)
+++ trunk/sbfConverter.bat 2015-07-06 13:51:06 UTC (rev 375)
@@ -1,10 +1,17 @@
-@echo off
+rem @echo off
-MODEL_NAME=$1
-CONVERTER_NAME=$2
-file=$3
+set CONVERTER_HOME=%~dp0
-java -Dmiriam.xml.export=miriam.xml -classpath lib\*.jar org.sbfc.converter.Converter %MODEL_NAME% %CONVERTER_NAME% %file%
+set MODEL_NAME=%1
+set CONVERTER_NAME=%2
+set file=%3
+set CLASSPATH=%CONVERTER_HOME%lib\*;.
+echo "classpath= %CLASSPATH% "
+echo %~dp0
+
+java -Dmiriam.xml.export=miriam.xml -classpath %CLASSPATH% org.sbfc.converter.Converter %MODEL_NAME% %CONVERTER_NAME% %file%
+
+
pause
\ No newline at end of file
Modified: trunk/sbml2octave.bat
===================================================================
--- trunk/sbml2octave.bat 2015-07-06 13:49:51 UTC (rev 374)
+++ trunk/sbml2octave.bat 2015-07-06 13:51:06 UTC (rev 375)
@@ -1,6 +1,6 @@
-#!/bin/bash
+@echo off
-## Example script to use the System Biology Format Converter to convert an SBML model into octave.
+rem Example script to use the System Biology Format Converter to convert an SBML model into octave.
-sbfConverter.bat SBMLModel SBML2Octave $1
+sbfConverter.bat SBMLModel SBML2Octave %1
Modified: trunk/src/org/sbfc/converter/Converter.java
===================================================================
--- trunk/src/org/sbfc/converter/Converter.java 2015-07-06 13:49:51 UTC (rev 374)
+++ trunk/src/org/sbfc/converter/Converter.java 2015-07-06 13:51:06 UTC (rev 375)
@@ -117,8 +117,8 @@
converterType = "URL2URN";
}
- System.out.println("INSIDE converter type: " + converterType);
- System.out.println("INSIDE convert package: " + converterPackage);
+ logger.debug("getPackageClassPath - converter type: " + converterType);
+ logger.debug("getPackageClassPath - convert package: " + converterPackage);
// Explicitly avoid creating convertType and ConvertPackage as Converter static data fields.
return new Converter().new ConverterData(converterType, converterPackage);
@@ -149,11 +149,6 @@
converterType = data.getConverterType();
converterPackage = data.getConverterPackage();
- //System.out.println("converter type: " + converterType);
- //System.out.println("convert package: " + converterPackage);
-
-
-
//Instantiating the converter
GeneralConverter converter=null;
try {
Modified: trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 13:49:51 UTC (rev 374)
+++ trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 13:51:06 UTC (rev 375)
@@ -1337,7 +1337,7 @@
if (!hasRule && !hasEvent(parameter.getId())) {
paramStr.append("% Warning parameter " + parameter.getId()
- + " is not constant, it should be controled by a Rule and/or events" + "\n");
+ + " is not constant, it should be controlled by a Rule and/or events" + "\n");
}
if (!hasRule) {
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|
|
From: <nik...@us...> - 2015-07-06 14:25:36
|
Revision: 376
http://sourceforge.net/p/sbfc/code/376
Author: niko-rodrigue
Date: 2015-07-06 14:25:33 +0000 (Mon, 06 Jul 2015)
Log Message:
-----------
updated the jsbml jar file + corrected bat files + updated log4j.properties
Modified Paths:
--------------
trunk/lib/sbfc-1.3.5.jar
trunk/log4j.properties
trunk/sbfConverter.bat
trunk/sbml2octave.bat
trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
Added Paths:
-----------
trunk/lib/jsbml-1.0-with-dependencies.jar
trunk/sbml2xpp.bat
Removed Paths:
-------------
trunk/lib/jsbml-1.0-rc1-with-dependencies.jar
Deleted: trunk/lib/jsbml-1.0-rc1-with-dependencies.jar
===================================================================
(Binary files differ)
Added: trunk/lib/jsbml-1.0-with-dependencies.jar
===================================================================
(Binary files differ)
Index: trunk/lib/jsbml-1.0-with-dependencies.jar
===================================================================
--- trunk/lib/jsbml-1.0-with-dependencies.jar 2015-07-06 13:51:06 UTC (rev 375)
+++ trunk/lib/jsbml-1.0-with-dependencies.jar 2015-07-06 14:25:33 UTC (rev 376)
Property changes on: trunk/lib/jsbml-1.0-with-dependencies.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/lib/sbfc-1.3.5.jar
===================================================================
(Binary files differ)
Modified: trunk/log4j.properties
===================================================================
--- trunk/log4j.properties 2015-07-06 13:51:06 UTC (rev 375)
+++ trunk/log4j.properties 2015-07-06 14:25:33 UTC (rev 376)
@@ -2,7 +2,6 @@
# INFO should be default logging level
#log4j.rootCategory=INFO, DefaultFile
log4j.rootCategory=INFO, console
-log4j.logger.uk.ac.ebi.miriam=ERROR, MiriamWSLibFile
log4j.logger.org.sbml=INFO
# 'DefaultFile' configuration
@@ -13,15 +12,7 @@
log4j.appender.DefaultFile.layout=org.apache.log4j.PatternLayout
log4j.appender.DefaultFile.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n
-# 'MiriamWSLibFile' configuration
-# log4j.appender.MiriamWSLibFile.Threshold=ERROR
-log4j.appender.MiriamWSLibFile.layout=org.apache.log4j.PatternLayout
-log4j.appender.MiriamWSLibFile.layout.ConversionPattern=%d %-5p %-17c{2} (%13F:%L) %3x - %m%n
-log4j.appender.MiriamWSLibFile=org.apache.log4j.FileAppender
-log4j.appender.MiriamWSLibFile.File=./log/miriamws.log
-log4j.appender.A.Append=true
-
#
# Console Display
#
@@ -33,7 +24,8 @@
# Comment this line or put it at the DEBUG level to get the message from the SimpleSBaseChangeListener
-# log4j.logger.org.sbml.jsbml.util.compilers=DEBUG
+log4j.logger.org.sbml.jsbml.util=WARN
+log4j.logger.org.sbml.jsbml.test=WARN
# comment the following line to get the debug messages from sbfc
-log4j.logger.org.sbfc=DEBUG
+#log4j.logger.org.sbfc=DEBUG
Modified: trunk/sbfConverter.bat
===================================================================
--- trunk/sbfConverter.bat 2015-07-06 13:51:06 UTC (rev 375)
+++ trunk/sbfConverter.bat 2015-07-06 14:25:33 UTC (rev 376)
@@ -1,4 +1,4 @@
-rem @echo off
+@echo off
set CONVERTER_HOME=%~dp0
@@ -6,10 +6,10 @@
set CONVERTER_NAME=%2
set file=%3
-set CLASSPATH=%CONVERTER_HOME%lib\*;.
+set CLASSPATH=%CONVERTER_HOME%.;%CONVERTER_HOME%lib\*
-echo "classpath= %CLASSPATH% "
-echo %~dp0
+rem echo "classpath= %CLASSPATH% "
+rem echo %~dp0
java -Dmiriam.xml.export=miriam.xml -classpath %CLASSPATH% org.sbfc.converter.Converter %MODEL_NAME% %CONVERTER_NAME% %file%
Modified: trunk/sbml2octave.bat
===================================================================
--- trunk/sbml2octave.bat 2015-07-06 13:51:06 UTC (rev 375)
+++ trunk/sbml2octave.bat 2015-07-06 14:25:33 UTC (rev 376)
@@ -2,5 +2,7 @@
rem Example script to use the System Biology Format Converter to convert an SBML model into octave.
-sbfConverter.bat SBMLModel SBML2Octave %1
+set CONVERTER_HOME=%~dp0
+%CONVERTER_HOME%\sbfConverter.bat SBMLModel SBML2Octave %*
+
Added: trunk/sbml2xpp.bat
===================================================================
--- trunk/sbml2xpp.bat (rev 0)
+++ trunk/sbml2xpp.bat 2015-07-06 14:25:33 UTC (rev 376)
@@ -0,0 +1,8 @@
+@echo off
+
+rem Example script to use the System Biology Format Converter to convert an SBML model into XPP.
+
+set CONVERTER_HOME=%~dp0
+
+%CONVERTER_HOME%\sbfConverter.bat SBMLModel SBML2XPP %*
+
Modified: trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 13:51:06 UTC (rev 375)
+++ trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 14:25:33 UTC (rev 376)
@@ -585,6 +585,8 @@
// Leave this at the end.
+ octaveModel +="% adding few functions representing operators used in SBML but not present directly \n";
+ octaveModel +="% in either matlab or octave. \n";
octaveModel +="function z=pow(x,y),z=x^y;end\n" + "function z=root(x,y),z=y^(1/x);end\n";
octaveModel +="function z = piecewise(varargin)\n"
+"\tnumArgs = nargin;\n"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-07-06 14:39:12
|
Revision: 377
http://sourceforge.net/p/sbfc/code/377
Author: niko-rodrigue
Date: 2015-07-06 14:39:10 +0000 (Mon, 06 Jul 2015)
Log Message:
-----------
corrected the initial value for RareRule on Species
Modified Paths:
--------------
trunk/lib/sbfc-1.3.5.jar
trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
Modified: trunk/lib/sbfc-1.3.5.jar
===================================================================
(Binary files differ)
Modified: trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 14:25:33 UTC (rev 376)
+++ trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 14:39:10 UTC (rev 377)
@@ -997,9 +997,17 @@
initialValue = "" + ((Compartment) variable.getVariableInstance()).getSize();
} else if (variable.getVariableInstance() instanceof Species) {
- // TODO : check which one of InitialAmount or InitialConcentration we should use !!!
- initialValue = "" + ((Species) variable.getVariableInstance()).getInitialAmount();
+ Species s = (Species) variable.getVariableInstance();
+ if (s.isSetInitialAmount()) {
+ initialValue = "" + s.getInitialAmount();
+ } else if (s.isSetInitialConcentration()) {
+ initialValue = "" + s.getInitialConcentration();
+ } // TODO - we should handle the case where no initial value is given (or value is given through initialAssigment)
+ else {
+ initialValue = "NaN";
+ }
+
} else if(variable.getVariableInstance() instanceof Parameter) {
initialValue = "" + ((Parameter) variable.getVariableInstance()).getValue();
}
@@ -1077,6 +1085,7 @@
String id = OctaveID.getOctaveId(species.getId());
// TODO : check why we are not using these two boolean anymore.
+ // TODO - indeed, we should probably use them to prevent adding unnecessary entries in the xdot list
// boolean isAffectedByRule = false;
// boolean isAffectedByAssignmenRule = false;
boolean needInit = true;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-07-07 15:03:32
|
Revision: 378
http://sourceforge.net/p/sbfc/code/378
Author: niko-rodrigue
Date: 2015-07-07 15:03:29 +0000 (Tue, 07 Jul 2015)
Log Message:
-----------
started to update the license information.
Modified Paths:
--------------
trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
Added Paths:
-----------
trunk/COPYING.txt
trunk/LICENSE.txt
Added: trunk/COPYING.txt
===================================================================
--- trunk/COPYING.txt (rev 0)
+++ trunk/COPYING.txt 2015-07-07 15:03:29 UTC (rev 378)
@@ -0,0 +1,504 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
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+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ <signature of Ty Coon>, 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+
Added: trunk/LICENSE.txt
===================================================================
--- trunk/LICENSE.txt (rev 0)
+++ trunk/LICENSE.txt 2015-07-07 15:03:29 UTC (rev 378)
@@ -0,0 +1,37 @@
+ Licensing and Distribution Terms for SBFC,
+ the System Biology Format Converter. Please visit
+ <http://sbfc.sf.net> to have more information about SBFC.
+
+Copyright (C) 2009-2015 jointly by the following organizations:
+ 1. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ 2. The Babraham Institute, Cambridge, UK
+ 3. Department of Bioinformatics, BiGCaT, Maastricht University
+
+SBFC is free software; you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as
+published by the Free Software Foundation; either version 2.1
+of the License, or any later version.
+
+This software is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software
+and documentation provided hereunder is on an "as is" basis, and
+the copyright holders have no obligations to provide maintenance,
+support, updates, enhancements or modifications. In no event
+shall the copyright holders be liable to any party for direct,
+indirect, special, incidental or consequential damages, including
+lost profits, arising out of the use of this software and its
+documentation, even if the copyright holders have been advised of
+the possibility of such damage. See the GNU Lesser General Public
+License for more details.
+
+You should have received a copy of the GNU Lesser General
+Public License along with this library in the file named
+"COPYING.txt" included with the software distribution. A copy
+is also available online at the Internet address
+http://sbfc.sf.net/mediawiki/index.php/COPYING for your
+convenience. You may also write to obtain a copy from the Free
+Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
+MA 02111-1307 USA.
+
+
Modified: trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-06 14:39:10 UTC (rev 377)
+++ trunk/src/org/sbfc/converter/sbml2octave/SBML2Octave.java 2015-07-07 15:03:29 UTC (rev 378)
@@ -2,30 +2,26 @@
* $Id$
* $URL$
*
- *
- * ==============================================================================
- * Copyright (c) 2010 the copyright is held jointly by the individual
- * authors. See the file AUTHORS for the list of authors
- *
+ * ==========================================================================
* This file is part of The System Biology Format Converter (SBFC).
+ * Please visit <http://sbfc....
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