Author: kono Date: 2012-08-08 16:55:24 -0700 (Wed, 08 Aug 2012) New Revision: 30139
Modified: core3/impl/trunk/linkout-impl/pom.xml core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/NodeLinkoutTaskFactory.java core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java core3/impl/trunk/linkout-impl/src/main/resources/linkout.props Log: fixes #1350 Links updated. Modified: core3/impl/trunk/linkout-impl/pom.xml =================================================================== --- core3/impl/trunk/linkout-impl/pom.xml 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/pom.xml 2012-08-08 23:55:24 UTC (rev 30139) @@ -1,5 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> <parent> <groupId>org.cytoscape</groupId> <artifactId>impl-parent</artifactId> @@ -12,16 +13,14 @@ </properties> <modelVersion>4.0.0</modelVersion> - <groupId>org.cytoscape</groupId> <artifactId>linkout-impl</artifactId> - <name>Cytoscape Linkout Impl (${project.artifactId})</name> <packaging>bundle</packaging> <repositories> - <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots --> + <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots --> <repository> <id>cytoscape_snapshots</id> <snapshots> @@ -93,11 +92,6 @@ <groupId>org.cytoscape</groupId> <artifactId>swing-application-api</artifactId> </dependency> - <dependency> - <groupId>org.springframework</groupId> - <artifactId>spring-beans</artifactId> - <version>${spring.version}</version> - </dependency> </dependencies> </project> Modified: core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java =================================================================== --- core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/CyActivator.java 2012-08-08 23:55:24 UTC (rev 30139) @@ -19,8 +19,6 @@ public class CyActivator extends AbstractCyActivator { - private static final Logger logger = LoggerFactory.getLogger(CyActivator.class); - public CyActivator() { super(); } @@ -33,11 +31,11 @@ SynchronousTaskManager synTaskMngrServRef = getService(bc, SynchronousTaskManager.class); PropsReader linkoutProps = new PropsReader("linkout","linkout.props",CyProperty.SavePolicy.CONFIG_DIR); - - LinkOut linkout = new LinkOut(linkoutProps,cyServiceRegistrarServiceRef,openBrowserServiceRef,cyApplicationConfigurationServiceRef, synTaskMngrServRef); + final LinkOut linkout = new LinkOut(linkoutProps,cyServiceRegistrarServiceRef,openBrowserServiceRef,cyApplicationConfigurationServiceRef, synTaskMngrServRef); Properties linkoutPropsProps = new Properties(); linkoutPropsProps.setProperty("cyPropertyName","linkout"); + registerService(bc,linkoutProps,CyProperty.class, linkoutPropsProps); registerService(bc, linkout, PropertyUpdatedListener.class, linkoutPropsProps); registerServiceListener(bc, linkout, "addCommanLineLinkOut", "removeCommanLineLinkOut", CyProperty.class); Modified: core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java =================================================================== --- core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkOut.java 2012-08-08 23:55:24 UTC (rev 30139) @@ -36,29 +36,15 @@ package org.cytoscape.linkout.internal; -import org.cytoscape.application.CyApplicationConfiguration; -import org.cytoscape.application.swing.CyEdgeViewContextMenuFactory; -import org.cytoscape.application.swing.CyNodeViewContextMenuFactory; +import static org.cytoscape.work.ServiceProperties.EDGE_DYNAMIC_LINKOUTS_MENU; +import static org.cytoscape.work.ServiceProperties.EDGE_LINKOUTS_MENU; +import static org.cytoscape.work.ServiceProperties.MENU_GRAVITY; +import static org.cytoscape.work.ServiceProperties.NODE_DYNAMIC_LINKOUTS_MENU; +import static org.cytoscape.work.ServiceProperties.NODE_LINKOUTS_MENU; +import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU; -import org.cytoscape.property.CyProperty; -import org.cytoscape.property.PropertyUpdatedEvent; -import org.cytoscape.property.PropertyUpdatedListener; - -import org.cytoscape.service.util.CyServiceRegistrar; - -import org.cytoscape.task.NodeViewTaskFactory; -import org.cytoscape.task.EdgeViewTaskFactory; - -import org.cytoscape.util.swing.OpenBrowser; - -import static org.cytoscape.work.ServiceProperties.*; -import org.cytoscape.work.SynchronousTaskManager; -import org.cytoscape.work.TaskFactory; - - import java.io.File; import java.io.FileInputStream; - import java.util.ArrayList; import java.util.HashMap; import java.util.List; @@ -67,6 +53,17 @@ import javax.swing.SwingUtilities; +import org.cytoscape.application.CyApplicationConfiguration; +import org.cytoscape.application.swing.CyEdgeViewContextMenuFactory; +import org.cytoscape.application.swing.CyNodeViewContextMenuFactory; +import org.cytoscape.property.CyProperty; +import org.cytoscape.property.PropertyUpdatedEvent; +import org.cytoscape.property.PropertyUpdatedListener; +import org.cytoscape.service.util.CyServiceRegistrar; +import org.cytoscape.task.EdgeViewTaskFactory; +import org.cytoscape.task.NodeViewTaskFactory; +import org.cytoscape.util.swing.OpenBrowser; +import org.cytoscape.work.SynchronousTaskManager; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -108,34 +105,27 @@ private final Map<String, NodeLinkoutTaskFactory> cpropKey2NodeVTF; private final Map<String, EdgeLinkoutTaskFactory> cpropKey2EdgeVTF; - /** - * Creates a new LinkOut object. - * - * @param props DOCUMENT ME! - * @param registrar DOCUMENT ME! - * @param browser DOCUMENT ME! - * @param config DOCUMENT ME! - */ + public LinkOut(CyProperty<Properties> propService, CyServiceRegistrar registrar, OpenBrowser browser, - final CyApplicationConfiguration config, final SynchronousTaskManager synTaskManager) { + final CyApplicationConfiguration config, final SynchronousTaskManager synTaskManager) { this.props = propService.getProperties(); this.registrar = registrar; this.browser = browser; this.config = config; this.synTaskManager = synTaskManager; - + propKey2EdgeVTF = new HashMap<String, EdgeLinkoutTaskFactory>(); propKey2NodeVTF = new HashMap<String, NodeLinkoutTaskFactory>(); - + cpropKey2EdgeVTF = new HashMap<String, EdgeLinkoutTaskFactory>(); cpropKey2NodeVTF = new HashMap<String, NodeLinkoutTaskFactory>(); - + readLocalProperties(); addStaticNodeLinks(); addStaticEdgeLinks(); - // This has been disabled until we can figure out the right way to + // This has been disabled until we can figure out the right way to // construct these menus and add them to the existing Linkout menu. // The current approach is not used (as far as we know) and adds // significant confusion in the UI @@ -189,7 +179,7 @@ logger.debug("Bad URL for propKey: " + propKey); continue; } - EdgeViewTaskFactory evtf = new EdgeLinkoutTaskFactory(browser,url); + final EdgeViewTaskFactory evtf = new EdgeLinkoutTaskFactory(browser,url); registrar.registerService(evtf, EdgeViewTaskFactory.class, dict); propKey2EdgeVTF.put(propKey, (EdgeLinkoutTaskFactory) evtf); } @@ -206,11 +196,12 @@ p = p + marker.length(); Properties dict = new Properties(); String menuKey; - if (marker.equals(NODEMARKER)) + if (marker.equals(NODEMARKER)) { menuKey = NODE_LINKOUTS_MENU + "." + propKey.substring(p); - else + } else { menuKey = EDGE_LINKOUTS_MENU + "." + propKey.substring(p); - + } + dict.setProperty(PREFERRED_MENU, menuKey); dict.setProperty(MENU_GRAVITY, "-1"); // Alphabetic ordering return dict; @@ -288,9 +279,6 @@ @Override public void run() { - // TODO Auto-generated method stub - - if (e.getSource().getName().equals("linkout") ) //when linkout prop is changed { final Properties props = (Properties) e.getSource().getProperties(); Modified: core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java =================================================================== --- core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/LinkoutTask.java 2012-08-08 23:55:24 UTC (rev 30139) @@ -1,24 +1,16 @@ package org.cytoscape.linkout.internal; - -import java.util.List; -import java.util.ArrayList; -import java.util.regex.Pattern; import java.util.regex.Matcher; +import java.util.regex.Pattern; import org.cytoscape.model.CyIdentifiable; -import org.cytoscape.model.CyTable; -import org.cytoscape.model.CyColumn; -import org.cytoscape.model.CyRow; import org.cytoscape.model.CyNetwork; import org.cytoscape.util.swing.OpenBrowser; import org.cytoscape.work.AbstractTask; import org.cytoscape.work.TaskMonitor; - import org.slf4j.Logger; import org.slf4j.LoggerFactory; - public class LinkoutTask extends AbstractTask { private static final Logger logger = LoggerFactory.getLogger(LinkoutTask.class); @@ -28,10 +20,10 @@ private final OpenBrowser browser; private final CyNetwork network; - private static final String REGEX = "%.+%"; - private static final Pattern regexPattern = Pattern.compile(REGEX); + private static final String REGEX = "%.+%"; + private static final Pattern regexPattern = Pattern.compile(REGEX); - public LinkoutTask(String link, OpenBrowser browser, CyNetwork network, CyIdentifiable... tableEntries ) { + public LinkoutTask(String link, OpenBrowser browser, CyNetwork network, CyIdentifiable... tableEntries) { this.link = link; this.tableEntries = tableEntries; this.browser = browser; @@ -45,12 +37,12 @@ // This absurdity is to support backwards compatibility // with 2.x formatted links. - if ( tableEntries.length == 1 ) { + if (tableEntries.length == 1) { url = substituteAttributes(url, tableEntries[0], "ID"); - } else if ( tableEntries.length == 2 ) { + } else if (tableEntries.length == 2) { url = substituteAttributes(url, tableEntries[0], "ID1"); url = substituteAttributes(url, tableEntries[1], "ID2"); - } else if ( tableEntries.length == 3 ) { + } else if (tableEntries.length == 3) { url = substituteAttributes(url, tableEntries[0], "ID1"); url = substituteAttributes(url, tableEntries[1], "ID2"); url = substituteAttributes(url, tableEntries[2], "ID"); @@ -62,28 +54,28 @@ } private String substituteAttributes(String url, CyIdentifiable tableEntry, String id) { - + // Replace %ATTRIBUTE.NAME% mark with the value of the attribute final Matcher mat = regexPattern.matcher(url); - - while (mat.find()) { + + while (mat.find()) { String attrName = url.substring(mat.start() + 1, mat.end() - 1); - String replaceName = attrName; - - // handle the default case where ID, ID1, ID2 is now the "name" column - if ( attrName.equals(id) ) - attrName = "name"; - + String replaceName = attrName; + + // handle the default case where ID, ID1, ID2 is now the "name" + // column + if (attrName.equals(id)) + attrName = CyNetwork.NAME; + Object raw = network.getRow(tableEntry).getRaw(attrName); - if ( raw == null ) { + if (raw == null) continue; - } - String attrValue = raw.toString(); - url = url.replace("%" + replaceName + "%", attrValue); - mat = regexPattern.matcher(url); + String attrValue = raw.toString(); + url = url.replace("%" + replaceName + "%", attrValue); + mat = regexPattern.matcher(url); } - - return url; + + return url; } } Modified: core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/NodeLinkoutTaskFactory.java =================================================================== --- core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/NodeLinkoutTaskFactory.java 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/NodeLinkoutTaskFactory.java 2012-08-08 23:55:24 UTC (rev 30139) @@ -14,7 +14,7 @@ private String link; private final OpenBrowser browser; - public NodeLinkoutTaskFactory(OpenBrowser browser, String link) { + public NodeLinkoutTaskFactory(final OpenBrowser browser, final String link) { super(); this.link = link; this.browser = browser; Modified: core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java =================================================================== --- core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/java/org/cytoscape/linkout/internal/PropsReader.java 2012-08-08 23:55:24 UTC (rev 30139) @@ -7,5 +7,4 @@ PropsReader(String name, String fileName, SavePolicy sp) { super(name, fileName, sp); } -} - +} \ No newline at end of file Modified: core3/impl/trunk/linkout-impl/src/main/resources/linkout.props =================================================================== --- core3/impl/trunk/linkout-impl/src/main/resources/linkout.props 2012-08-08 23:20:31 UTC (rev 30138) +++ core3/impl/trunk/linkout-impl/src/main/resources/linkout.props 2012-08-08 23:55:24 UTC (rev 30139) @@ -1,34 +1,28 @@ -#Linkout Property File -#12/5/2007 Links re-organized by Keiichiro Ono ([email protected]) +#Linkout Property File +#08/08/2012 Links updated by Keiichiro Ono ([email protected]) -#nodelinkouturl.yeast.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=4932 -#nodelinkouturl.Biological\ resources.iHOP=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID% -nodelinkouturl.Entrez.All\ Databases\ (Global\ search\ by\ free\ keyword)=http://www.ncbi.nlm.nih.gov/sites/gquery?GlobalQuery.GQueryCluster.GQuerySearchBox.Term=%ID% -nodelinkouturl.Entrez.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract -nodelinkouturl.Entrez.Protein=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept -nodelinkouturl.Entrez.Nucleotide=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=nucleotide&term\=%ID%&doptcmdl\=GenBank -nodelinkouturl.Entrez.OMIM=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=omim&term\=%ID%&doptcmdl\=Synopsis -nodelinkouturl.Entrez.Structure=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=structure&term\=%ID%&doptcmdl\=Brief -nodelinkouturl.Entrez.Gene=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Search&term=%ID% +################# Node Links ################ -nodelinkouturl.iHOP.yeast=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=4932 -nodelinkouturl.iHOP.human=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=9606 +nodelinkouturl.Web\ Search.Google=http://www.google.com/search?hl=en&q=%ID%&btnG=Google+Search +nodelinkouturl.Web\ Search.Wikipedia=http://en.wikipedia.org/wiki/%ID% -nodelinkouturl.Search\ Engines.Google=http://www.google.com/search?hl=en&q=%ID%&btnG=Google+Search -nodelinkouturl.Search\ Engines.Ask=http://www.ask.com/web?q=%ID%&qsrc=0&o=0 +nodelinkouturl.Sequences\ and\ Proteins.Entrez\ Gene=http://www.ncbi.nlm.nih.gov/gene/%ID% +nodelinkouturl.Sequences\ and\ Proteins.Entrez\ Genome=http://www.ncbi.nlm.nih.gov/genome?term=%ID% +nodelinkouturl.Sequences\ and\ Proteins.Ensembl\ Gene\ View.yeast=http://www.ensembl.org/Saccharomyces_cerevisiae/geneview?gene=%ID% +nodelinkouturl.Sequences\ and\ Proteins.Ensembl\ Gene\ View.human=http://www.ensembl.org/Homo_sapiens/geneview?gene=%ID% +nodelinkouturl.Sequences\ and\ Proteins.Ensembl\ Gene\ View.fly=http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=%ID% +nodelinkouturl.Sequences\ and\ Proteins.Ensembl\ Gene\ View.mouse=http://www.ensembl.org/Mus_musculus/geneview?gene=%ID% +nodelinkouturl.Sequences\ and\ Proteins.Ensembl\ Gene\ View.worm=http://www.ensembl.org/Caenorhabditis_elegans/geneview?gene=%ID% +nodelinkouturl.Sequences\ and\ Proteins.UniProt=http://beta.uniprot.org/uniprot/%ID% +nodelinkouturl.Sequences\ and\ Proteins.Entrez Protein=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept -nodelinkouturl.UniProt.PIR=http://www.pir.uniprot.org/cgi-bin/upEntry?id=%ID% -nodelinkouturl.UniProt.KB\ Beta=http://beta.uniprot.org/uniprot/%ID% +nodelinkouturl.Publications.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract +nodelinkouturl.Publications.OMIM=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=omim&term\=%ID%&doptcmdl\=Synopsis -nodelinkouturl.Other\ Biological\ DB.GeneCards=http://www.genecards.org/cgi-bin/carddisp.pl?gene=%ID%&alias=yes -nodelinkouturl.Other\ Biological\ DB.Pfam=http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%ID% -nodelinkouturl.Other\ Biological\ DB.InterPro=http://www.ebi.ac.uk/interpro/IEntry?ac=%ID% - - nodelinkouturl.Model\ Organism\ DB.MGI\ (mouse)=http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%ID%&selectedQuery=Genes+and+Markers nodelinkouturl.Model\ Organism\ DB.WormBase\ (worm)=http://www.wormbase.org/db/gene/gene?name=%ID% -nodelinkouturl.Model\ Organism\ DB.SGD\ (yeast)=http\://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID% +nodelinkouturl.Model\ Organism\ DB.SGD\ (yeast)=http://db.yeastgenome.org/cgi-bin/locus.pl?locus=%ID% nodelinkouturl.Model\ Organism\ DB.FlyBase\ (fly)=http://flybase.bio.indiana.edu/.bin/fbidq.html?%ID% nodelinkouturl.Model\ Organism\ DB.HGNC\ (human)=http://www.genenames.org/data/hgnc_data.php?hgnc_id=%ID% @@ -36,54 +30,34 @@ nodelinkouturl.Ontology.Gene\ Ontology\ (QuickGO\ by\ ID)=http://www.ebi.ac.uk/ego/DisplayGoTerm?id=%ID% nodelinkouturl.Ontology.Gene\ Ontology\ (QuickGO\ by\ name)=http://www.ebi.ac.uk/ego/GSearch?query=%ID%&mode=name&ontology=all_ont -#Ensembl -nodelinkouturl.Ensembl\ Gene\ View.yeast=http://www.ensembl.org/Saccharomyces_cerevisiae/geneview?gene=%ID% -nodelinkouturl.Ensembl\ Gene\ View.human=http://www.ensembl.org/Homo_sapiens/geneview?gene=%ID% -nodelinkouturl.Ensembl\ Gene\ View.fly=http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=%ID% -nodelinkouturl.Ensembl\ Gene\ View.mouse=http://www.ensembl.org/Mus_musculus/geneview?gene=%ID% -nodelinkouturl.Ensembl\ Gene\ View.worm=http://www.ensembl.org/Caenorhabditis_elegans/geneview?gene=%ID% +#Global Search +nodelinkouturl.Global\ Database\ Search.EBI=http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&requestFrom=ebi_index&query=%ID% +nodelinkouturl.Global\ Database\ Search.NCBI=http://www.ncbi.nlm.nih.gov/gquery/?term=%ID% -#EB-eye -nodelinkouturl.EBI\ Tools.All\ the\ EBI\ (Global\ search\ by\ free\ keyword)=http://www.ebi.ac.uk/ebisearch/search.ebi?query=%ID%&db=allebi -nodelinkouturl.EBI\ Tools.Dasty2\ (Visualize\ protein\ sequence\ feature\ information)=http://www.ebi.ac.uk/dasty/display.html?q=%ID%&label=BIOSAPIENS&t=3 -nodelinkouturl.EBI\ Tools.PRIDE\ (PRoteomics\ IDEntifications\ database)=http://www.ebi.ac.uk/pride/simpleSearch.do?simpleSearchValue=%ID% +#Structure +nodelinkouturl.Structure\ Databases.PDBe=http://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=%ID% +nodelinkouturl.Structure\ Databases.NCBI\ Structure=http://www.ncbi.nlm.nih.gov/structure/?term=%ID% -#Reactome links -nodelinkouturl.Reactome.ReactomeID=http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%ID% -nodelinkouturl.Reactome.Entrez=http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%ID% -nodelinkouturl.Reactome.UniProt=http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%ID% -nodelinkouturl.Reactome.SGD=http://www.reactome.org/cgi-bin/link?SOURCE=SGD&ID=%ID%&FOCUS_SPECIES=Saccharomyces+cerevisiae -nodelinkouturl.Reactome.RefSeq=http://www.reactome.org/cgi-bin/link?SOURCE=RefSeq&ID=%ID% -nodelinkouturl.Reactome.Wormbase=http://www.reactome.org/cgi-bin/link?SOURCE=Wormbase&ID=%ID%&FOCUS_SPECIES=Caenorhabditis+elegans -#Network/Pathway databases -nodelinkouturl.Interaction\ Databases.HPRD=http://www.hprd.org/resultsQuery?multiplefound=&prot_name=%ID%&external=Ref_seq&accession_id=&hprd=&gene_symbol=&chromo_locus=&function=&ptm_type=&localization=&domain=&motif=&expression=&prot_start=&prot_end=&limit=0&mole_start=&mole_end=&disease=&query_submit=Search -nodelinkouturl.Interaction\ Databases.IntAct=http://www.ebi.ac.uk/intact/search/do/search?searchString=%ID%&filter=ac -nodelinkouturl.Interaction\ Databases.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=0 +#Pathway databases +nodelinkouturl.Pathway\ Databases.Reactome=http://www.reactome.org/cgi-bin/search2?OPERATOR=ALL&SPECIES=ALL&QUERY=%ID% +nodelinkouturl.Pathway\ Databases.Wikipathways=http://www.wikipathways.org//index.php?query=%ID%&title=Special%3ASearchPathways&doSearch=1&sa=Search +nodelinkouturl.Pathway\ Databases.KEGG\ Pathways=http://www.kegg.jp/kegg-bin/search_pathway_text?map=map&keyword=%ID%&mode=1&viewImage=true +nodelinkouturl.Pathway\ Databases.Pathway\ Commons=http://www.pathwaycommons.org/pc/webservice.do?version=3.0&snapshot_id=GLOBAL_FILTER_SETTINGS&record_type=PATHWAY&q=%ID%&format=html&cmd=get_by_keyword -#EBI Links -nodelinkouturl.Array\ Express.All\ Species=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=&displayInsitu=on&exp_query= -nodelinkouturl.Array\ Express.human=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=Homo+sapiens&displayInsitu=on&exp_query= -nodelinkouturl.Array\ Express.yeast=http://www.ebi.ac.uk/microarray-as/aew/DW?queryFor=gene&gene_query=%ID%&species=Saccharomyces+cerevisiae&displayInsitu=on&exp_query= +# Arrays +nodelinkouturl.Array\ Experiments.GEO\ DataSets=http://www.ncbi.nlm.nih.gov/gds/?term=%ID% +nodelinkouturl.Array\ Experiments.ArrayExpress=http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=%ID% -#KEGG Links -nodelinkouturl.KEGG.All\ Species\ (use\ KEGG\ ID)=http://www.kegg.jp/dbget-bin/www_bget?%ID% -nodelinkouturl.KEGG.human\ (use\ NCBI\ GeneID)=http://www.kegg.jp/dbget-bin/www_bget?hsa:%ID% -nodelinkouturl.KEGG.yeast\ (use\ ORF\ name)=http://www.kegg.jp/dbget-bin/www_bget?sce:%ID% -nodelinkouturl.KEGG.mouse\ (use\ NCBI\ GeneID)=http://www.genome.jp/dbget-bin/www_bget?mmu:%ID% +############## Edge Links ##################### -#Edge Links -edgelinkouturl.iHop.yeast=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID1%&ncbi_tax_id_1=4932&syns_2=%ID2%&ncbi_tax_id_2=4932 -edgelinkouturl.iHop.human=http://www.ihop-net.org/UniPub/iHOP/in?syns_1=%ID1%&ncbi_tax_id_1=9606&syns_2=%ID2%&ncbi_tax_id_2=9606 +edgelinkouturl.Publications.Pubmed\ (search\ by\ Pubmed\ ID)=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract -edgelinkouturl.Entrez.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%&doptcmdl\=Abstract +edgelinkouturl.Ontology.Molecular\ Interaction\ (PSI-MI\ Term)=http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A%ID% -edgelinkouturl.Ontology.Molecular\ Interaction\ (PSI-MI)=http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A%ID% - - #Interaction Database Links -edgelinkouturl.Network\ Database.IntAct=http://www.ebi.ac.uk/intact/search/do/search?searchString=%ID%&filter=ac -edgelinkouturl.Network\ Database.BioGRID=http://www.thebiogrid.org/SearchResults/summary/%ID% +edgelinkouturl.Interaction\ Databases.IntAct=http://www.ebi.ac.uk/intact/search/do/search?searchString=%ID%&filter=ac +edgelinkouturl.Interaction\ Databases.BioGRID=http://www.thebiogrid.org/SearchResults/summary/%ID% #Attribute name for user-embedded URLs Linkout.externalLinkName=Linkout.ExternalLinks -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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