Author: mes
Date: 2010-09-21 09:28:16 -0700 (Tue, 21 Sep 2010)
New Revision: 21964
Added:
cytoscape/trunk/coreplugins/BioMartClient/src/test/resources/
cytoscape/trunk/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
Modified:
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
Log:
changed unit tests so they're not making network connections
Modified:
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
===================================================================
---
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
2010-09-21 15:23:58 UTC (rev 21963)
+++
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/BiomartStubTest.java
2010-09-21 16:28:16 UTC (rev 21964)
@@ -4,6 +4,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.io.File;
import junit.framework.TestCase;
import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
@@ -18,7 +19,8 @@
protected void setUp() throws Exception {
super.setUp();
- stub = new BiomartStub();
+ File f = new File("./src/test/resources/mart.registry.xml");
+ stub = new BiomartStub(f.toURL().toString());
stub.getRegistry();
}
@@ -27,85 +29,81 @@
}
public void testGetRegistry() throws Exception {
-// System.out.println("============ Test biomart registry
============");
-// Map<String, Map<String, String>> reg = stub.getRegistry();
-//
-// // Number of datasources. This number can be changed!
-// assertEquals(reg.keySet().size(), 22);
-
- System.out.println("============ Test biomart registry Done!
============");
+ Map<String, Map<String, String>> reg = stub.getRegistry();
+
+ assertEquals(54, reg.keySet().size());
}
public void testGetAvailableDatasets() throws Exception {
- System.out.println("============ Test biomart Available
Datasets ============");
-
Map<String, String> result =
stub.getAvailableDatasets("ensembl");
- for(String key: result.keySet()) {
- System.out.println( key + " =====> " + result.get(key));
- }
-
- System.out.println("============ Test biomart Available
Datasets DONE. ============");
+ assertTrue(result.keySet().contains("oprinceps_gene_ensembl"));
+ assertTrue(result.keySet().contains("etelfairi_gene_ensembl"));
+ assertTrue(result.keySet().contains("drerio_gene_ensembl"));
+ assertTrue(result.keySet().contains("cjacchus_gene_ensembl"));
+ assertTrue(result.keySet().contains("ocuniculus_gene_ensembl"));
+
+ assertEquals(51, result.keySet().size());
}
- public void testGetAvailableAttributes() throws Exception {
-// stub.getAvailableAttributes("oanatinus_gene_ensembl");
- }
-
-
+
+/* getAllGOAnnotations requires and actual web service to work
public void testGetAllGOAnnotations() throws Exception {
// Get Human annotation.
-// List<String[]> res = stub.getAllGOAnnotations("10090");
-// Set<String> uniqueID = new HashSet<String>();
-//
-// for(String[] line: res) {
-// uniqueID.add(line[0]);
-// for(String entry: line) {
-//
-// System.out.print(entry + "\t");
-// }
-// System.out.println("");
-// }
-// System.out.println("======== Total " + uniqueID.size() + "
annotated genes ==========");
-// res.clear();
-// uniqueID.clear();
-// uniqueID = null;
-// res = null;
+ List<String[]> res = stub.getAllGOAnnotations("10090");
+ Set<String> uniqueID = new HashSet<String>();
+
+ for(String[] line: res) {
+ uniqueID.add(line[0]);
+ for(String entry: line) {
+
+ System.out.print(entry + "\t");
+ }
+ System.out.println("");
+ }
+ System.out.println("======== Total " + uniqueID.size() + "
annotated genes ==========");
+ res.clear();
+ uniqueID.clear();
+ uniqueID = null;
+ res = null;
}
+*/
+/* sendQuery requires an actual webservice to work
public void testSendQuery() throws Exception {
-// Dataset dataset;
-// Attribute[] attrs;
-// Filter[] filters;
-//
-// dataset = new Dataset("hsapiens_gene_ensembl");
-// attrs = new Attribute[3];
-// attrs[0] = new Attribute("ensembl_gene_id");
-// attrs[1] = new Attribute("go");
-// attrs[2] = new Attribute("evidence_code");
-//
-// filters = new Filter[1];
-// filters[0] = new Filter("with_go", null);
-//
-// String query2 = XMLQueryBuilder.getQueryString(dataset, attrs,
filters);
-//
-// List<String[]> res = stub.sendQuery(query2);
-//
-//
-// Set<String> uniqueID = new HashSet<String>();
-//
-// for(String[] line: res) {
-// uniqueID.add(line[0]);
-// for(String entry: line) {
-//
-// System.out.print(entry + "\t");
-// }
-// System.out.println("");
-// }
-//
-// System.out.println("======== Total " + uniqueID.size() + "
annotated genes ==========");
+ Dataset dataset;
+ Attribute[] attrs;
+ Filter[] filters;
+ dataset = new Dataset("hsapiens_gene_ensembl");
+ attrs = new Attribute[3];
+ attrs[0] = new Attribute("ensembl_gene_id");
+ attrs[1] = new Attribute("go");
+ attrs[2] = new Attribute("evidence_code");
+
+ filters = new Filter[1];
+ filters[0] = new Filter("with_go", null);
+
+ String query2 = XMLQueryBuilder.getQueryString(dataset, attrs,
filters);
+
+ List<String[]> res = stub.sendQuery(query2);
+
+
+ Set<String> uniqueID = new HashSet<String>();
+
+ for(String[] line: res) {
+ uniqueID.add(line[0]);
+ for(String entry: line) {
+
+ System.out.print(entry + "\t");
+ }
+ System.out.println("");
+ }
+
+ System.out.println("======== Total " + uniqueID.size() + "
annotated genes ==========");
+
}
+ */
}
Modified:
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
===================================================================
---
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
2010-09-21 15:23:58 UTC (rev 21963)
+++
cytoscape/trunk/coreplugins/BioMartClient/src/test/java/edu/ucsd/bioeng/idekerlab/biomartclient/tests/QueryBuilderUtilTest.java
2010-09-21 16:28:16 UTC (rev 21964)
@@ -3,6 +3,7 @@
import java.io.BufferedReader;
import java.util.List;
import java.util.Map;
+import java.io.File;
import edu.ucsd.bioeng.idekerlab.biomartclient.BiomartStub;
import edu.ucsd.bioeng.idekerlab.biomartclient.utils.QueryBuilderUtil;
@@ -11,11 +12,12 @@
public class QueryBuilderUtilTest extends TestCase {
BiomartStub stub;
+ private final String queryString = "<?xml version=\"1.0\"
encoding=\"UTF-8\"?><Query count=\"\" datasetConfigVersion=\"0.6\"
formatter=\"TSV\" header=\"1\" uniqueRows=\"1\"
virtualSchemaName=\"default\"><Dataset
name=\"hsapiens_gene_ensembl\"><Attribute
name=\"ensembl_gene_id\"/></Dataset></Query>";
protected void setUp() throws Exception {
super.setUp();
- stub = new BiomartStub();
-
+ File f = new File("./src/test/resources/mart.registry.xml");
+ stub = new BiomartStub(f.toURL().toString());
}
protected void tearDown() throws Exception {
@@ -24,19 +26,7 @@
public void testGetAllAliases() throws Exception {
- BufferedReader reader =
stub.sendQuery(QueryBuilderUtil.getAllAliases(null));
- String line;
- while ((line = reader.readLine()) != null)
- System.out.println(line);
-
- Map<String, String> ds = stub.getAvailableDatasets("ensembl");
- int count = 1;
- for(String e: ds.keySet()) {
- if(e.endsWith("gene_ensembl")) {
- System.out.println("Datasource " + count + " =
" + e + "-" + ds.get(e));
- count++;
- }
-
- }
+ String query= QueryBuilderUtil.getAllAliases(null);
+ assertEquals( queryString, query );
}
}
Added:
cytoscape/trunk/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
===================================================================
---
cytoscape/trunk/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
(rev 0)
+++
cytoscape/trunk/coreplugins/BioMartClient/src/test/resources/mart.registry.xml
2010-09-21 16:28:16 UTC (rev 21964)
@@ -0,0 +1,57 @@
+
+<MartRegistry>
+ <MartURLLocation database="ensembl_mart_59" default="1" displayName="ENSEMBL
GENES 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="ensembl" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="snp_mart_59" default="0" displayName="ENSEMBL
VARIATION 59 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="snp" path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="1" />
+ <MartURLLocation database="functional_genomics_mart_59" default="0"
displayName="ENSEMBL FUNCTIONAL GENOMICS 59 (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="functional_genomics"
path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1"
/>
+ <MartURLLocation database="vega_mart_59" default="0" displayName="VEGA 38
(SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="vega"
path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1"
/>
+ <MartURLLocation database="genomic_features_mart_59" default="0"
displayName="ENSEMBL GENOMIC FEATURES 59 (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="genomic_features"
path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="0"
/>
+ <MartURLLocation database="ontology_mart_59" default="0"
displayName="ENSEMBL ONTOLOGY 59 (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="ontology" path="/biomart/martservice"
port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="sequence_mart_59" default="0"
displayName="ENSEMBL SEQUENCE 59 (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="sequence" path="/biomart/martservice"
port="80" serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="bacterial_mart_6" default="0"
displayName="ENSEMBL BACTERIA 6 (EBI UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="bacterial_mart_6"
path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1"
/>
+ <MartURLLocation database="bacterial_sequence_mart_6" default="0"
displayName="" host="www.biomart.org" includeDatasets="" martUser=""
name="bacterial_sequence_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="fungal_mart_6" default="0" displayName="ENSEMBL
FUNGAL 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="fungal_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="fungal_sequence_mart_6" default="0"
displayName="" host="www.biomart.org" includeDatasets="" martUser=""
name="fungal_sequence_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="metazoa_genomic_features_mart_6" default="0"
displayName="" host="www.biomart.org" includeDatasets="" martUser=""
name="metazoa_genomic_features_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="metazoa_mart_6" default="1" displayName="ENSEMBL
METAZOA 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="metazoa_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="metazoa_sequence_mart_6" default="0"
displayName="" host="www.biomart.org" includeDatasets="" martUser=""
name="metazoa_sequence_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="plant_mart_6" default="0" displayName="ENSEMBL
PLANT 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="plant_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="plant_sequence_mart_6" default="0" displayName=""
host="www.biomart.org" includeDatasets="" martUser=""
name="plant_sequence_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="protist_mart_6" default="1" displayName="ENSEMBL
PROTISTS 6 (EBI UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="protist_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="protist_sequence_mart_6" default="0"
displayName="" host="www.biomart.org" includeDatasets="" martUser=""
name="protist_sequence_mart_6" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
+ <MartURLLocation database="msd_mart_4" default="0" displayName="MSD
PROTOTYPE (EBI UK)" host="www.biomart.org" includeDatasets="" martUser=""
name="msd" path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="1" />
+ <MartURLLocation database="utlp" default="" displayName="HIGH THROUGHPUT
GENE TARGETING AND TRAPPING (SANGER UK)" host="www.sanger.ac.uk"
includeDatasets="" martUser="" name="htgt" path="/htgt/biomart/martservice"
port="80" redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="test_reactome_mart" default="1"
displayName="REACTOME (CSHL US)" host="banon.cshl.edu"
includeDatasets="complex,pathway,reaction,interaction" martUser=""
name="REACTOME" path="/biomart/martservice" port="5555" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="wormmart_215" default="1" displayName="WORMBASE
215 (CSHL US)" host="www.wormbase.org" includeDatasets="" martUser=""
name="wormbase215" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="WS215 --latest" visible="1" />
+ <MartURLLocation default="0" displayName="DICTYBASE (NORTHWESTERN US)"
host="www.dictybase.org" includeDatasets="" martUser="" name="dicty"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="dictyMart" visible="1" />
+ <MartURLLocation database="biomart" default="1" displayName="MGI (JACKSON
LABORATORY US)" host="biomart.informatics.jax.org" includeDatasets="markers"
name="biomart" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="rgd__mart" default="" displayName="RGD GENES (MCW
US)" host="rote.hmgc.mcw.edu" includeDatasets="" martUser="" name="rgd__mart"
path="/biomart/martservice" port="9999" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ipi_rat__mart" default="" displayName="RGD IPI
MART (MCW US)" host="rote.hmgc.mcw.edu" includeDatasets="" martUser=""
name="ipi_rat__mart" path="/biomart/martservice" port="9999" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="SSLP__mart" default="" displayName="RGD
MICROSATELLITE MARKERS (MCW US)" host="rote.hmgc.mcw.edu" includeDatasets=""
martUser="" name="SSLP__mart" path="/biomart/martservice" port="9999"
redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="g4public" default="" displayName="HGNC (EBI UK)"
host="www.genenames.org" includeDatasets="" name="g4public"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="pride_mart_1" default="1" displayName="PRIDE (EBI
UK)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="pride"
path="/pride/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="SPMART" default="" displayName="UNIPROT (EBI UK)"
host="www.ebi.ac.uk" includeDatasets="" martUser="" name="uniprot_mart"
path="/uniprot/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ensembl_expressionmart_48" default="1"
displayName="EURATMART (EBI UK)" host="www.ebi.ac.uk" includeDatasets=""
martUser="" name="ensembl_expressionmart_48"
path="/euratools/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="biomartDB" default="" displayName="PARAMECIUM
GENOME (CNRS FRANCE)" host="paramecium.cgm.cnrs-gif.fr"
includeDatasets="macronuclear" martUser="" name="biomartDB"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="tdb_biomart_new" default=""
displayName="EUREXPRESS (MRC EDINBURGH UK)" host="biomart.eurexpress.org"
includeDatasets="template" martUser="" name="Eurexpress Biomart"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="pepseekerGOLD_mart06" default="0"
displayName="PEPSEEKER (UNIVERSITY OF MANCHESTER UK)"
host="www.ispider.manchester.ac.uk" includeDatasets="peptide" martUser=""
name="pepseekerGOLD_mart06" path="/pepseeker/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="pepseekerGOLD" visible="1" />
+ <MartURLLocation database="datacippotato_martpot_001" default=""
displayName="DB_POTATO (INTERNATIONAL POTATO CENTER-CIP)"
host="germplasmdb.cip.cgiar.org" includeDatasets="" martUser=""
name="Potato_01" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="datacipsweet_martsweet_001" default=""
displayName="DB_SWEETPOTATO (INTERNATIONAL POTATO CENTER-CIP)"
host="germplasmdb.cip.cgiar.org" includeDatasets="" martUser=""
name="Sweetpotato_01" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="phytozome_mart_v5" default=""
displayName="PHYTOZOME (JGI/CIG US)" host="www.phytozome.net"
includeDatasets="" martUser="" name="phytozome_mart"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="zome_mart" visible="1" />
+ <MartURLLocation database="sequence_mart_v5" default=""
displayName="Sequences" host="www.phytozome.net"
includeDatasets="sequence_phytozome" martUser="" name="sequence_mart"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="zome_mart" visible="0" />
+ <MartURLLocation database="mart_cyanobase_1" default="1"
displayName="CYANOBASE 1 (KAZUSA JAPAN)" host="mart.kazusa.or.jp"
includeDatasets="" martUser="default" name="cyanobase_1"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="hapmart_27_36" default="1" displayName="HAPMAP 27
(NCBI US)" host="hapmap.ncbi.nlm.nih.gov" includeDatasets=""
name="HapMap_rel27" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="rel27_NCBI_Build36" visible="1" />
+ <MartURLLocation database="cosp" default="1" displayName="COSMIC (SANGER
UK)" host="www.sanger.ac.uk" includeDatasets="" martUser="" name="CosmicMart"
path="/genetics/CGP/cosmic/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="cildb_all_v2" default="" displayName="CILDB
INPARANOID AND FILTERED BEST HIT (CNRS FRANCE)" host="cildb.cgm.cnrs-gif.fr"
includeDatasets="" name="cildb_all_v2" path="/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="cildb_inp_v2" default="" displayName="CILDB
INPARANOID (CNRS FRANCE)" host="cildb.cgm.cnrs-gif.fr" includeDatasets=""
name="cildb_inp_v2" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="marker_mart_30_55" default=""
displayName="GRAMENE 30 MARKERS (CSHL/CORNELL US)" host="www.gramene.org"
includeDatasets="" martUser="" name="GRAMENE_MARKER_30"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="map_mart_30_55" default="" displayName="GRAMENE
30 MAPPINGS (CSHL/CORNELL US)" host="www.gramene.org" includeDatasets=""
martUser="" name="GRAMENE_MAP_30" path="/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="qtl_mart_30_55" default="" displayName="GRAMENE
30 QTL DB (CSHL/CORNELL US)" host="www.gramene.org" includeDatasets=""
martUser="" name="QTL_MART" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="genes" default="" displayName="INTOGEN GENES"
host="biomart.intogen.org" includeDatasets="" martUser="" name="genes"
path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="oncomodules" default="" displayName="INTOGEN
ONCOMODULES" host="biomart.intogen.org" includeDatasets="" martUser=""
name="oncomodules" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="gmap_japonica" default="1" displayName="RICE-MAP
JAPONICA (PEKING UNIVESITY CHINA)" host="ricemart.cbi.edu.cn"
includeDatasets="" martUser="" name="gmap_japonica" path="/biomart/martservice"
port="80" redirect="1" serverVirtualSchema="gmap_japonica" visible="1" />
+ <MartURLLocation database="europhenome_annotation_1_3_3_20100414" default=""
displayName="EUROPHENOME" host="www.i-dcc.org" includeDatasets="europhenome"
martUser="" name="europhenomeannotations" path="/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="emma_biomart" default="" displayName="THE
EUROPEAN MOUSE MUTANT ARCHIVE (EMMA)" host="www.i-dcc.org" includeDatasets=""
martUser="" name="emma_biomart" path="/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="ikmc_mart_alt" default="" displayName="IKMC GENES
AND PRODUCTS (I-DCC)" host="www.i-dcc.org" includeDatasets="" martUser=""
name="ikmc" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+ <MartURLLocation database="gmap_indica" default="1" displayName="RICE-MAP
INDICA (PEKING UNIVERSITY CHINA)" host="ricemart.cbi.edu.cn" includeDatasets=""
martUser="" name="gmap_indica" path="/biomart/martservice" port="80"
redirect="1" serverVirtualSchema="gmap_indica" visible="1" />
+ <MartURLLocation database="ensembl_latest" default=""
displayName="PANCREATIC EXPRESSION DATABASE (INSTITUTE OF CANCER UK)"
host="www.pancreasexpression.org" includeDatasets="" martUser=""
name="Ensembl56" path="/biomart/martservice" port="80" redirect="1"
serverVirtualSchema="default" visible="1" />
+</MartRegistry>
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