Merge branch 'dev/uniprotkb'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 title: BridgeDb
 message: 'If you use this software, please cite it as below.'
 type: software
-version: 3.0.23
-date-released: '2023-08-07'
+version: 3.1.0
+date-released: '2023-11-05'
 authors:
   - given-names: Manas
     family-names: Awasthi

README.md

@@ -15,7 +15,7 @@ Using BridgeDb dependencies
 The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to 
 [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb.
 
-Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.23`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.0`:
 
 For [Maven](https://maven.apache.org/):
 
@@ -24,27 +24,27 @@ For [Maven](https://maven.apache.org/):
     <dependency>
         <groupId>org.bridgedb</groupId>
         <artifactId>org.bridgedb.bio</artifactId>
-        <version>3.0.23</version>
+        <version>3.1.0</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.23'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.0'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.23"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.0"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.0.23'
+'org.bridgedb:org.bridgedb.bio:jar:3.1.0'
 ```
 
 
@@ -133,7 +133,7 @@ To make the release, run the following commands. Mind you, this requires you
 to have an approved Sonatype (http://oss.sonatype.org/) account with push rights:
 
 ```shell
-mvn versions:set -DnewVersion=3.0.23
+mvn versions:set -DnewVersion=3.1.0
 mvn clean deploy
 ```
 
@@ -143,7 +143,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.0.23-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.1-SNAPSHOT
 mvn clean deploy
 ```
 

examples/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.0.23</version>
+    <version>3.1.0</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.bridgedb.examples</groupId>

org.bridgedb.bio/pom.xml

@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv

@@ -123,7 +123,7 @@ SubstrateDB	Sdb	http://substrate.burnham.org/	http://substrate.burnham.org/prote
 SubtiWiki	Bsu	http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page	http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id	BSU29180	gene	Bacillus subtilis	1	urn:miriam:subtiwiki	^BSU\d{5}$	SubtiWiki		subtiwiki	gene
 SUPFAM	Sf	http://supfam.org/SUPERFAMILY/	http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id	SSF57615	protein		1	urn:miriam:supfam	^\w+$	SUPFAM		supfam	protein
 SWISS-MODEL	Sw	http://swissmodel.expasy.org/	http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id	P23298	protein		1	urn:miriam:swiss-model	^\w+$	SWISS-MODEL		swiss-model	protein
-SwissLipids	Sl	http://www.swisslipids.org/	http://www.swisslipids.org/#/entity/$id/	SLM:000048885	metabolite		1		^SLM:\d+$	SwissLipids		swisslipid	metabolite
+SwissLipids	Sl	http://www.swisslipids.org/	http://www.swisslipids.org/#/entity/$id/	SLM:000048885	metabolite		1		^SLM:\d+$	SwissLipids		slm	metabolite
 Systems Biology Ontology	Sbo	http://www.ebi.ac.uk/sbo/	http://www.ebi.ac.uk/sbo/main/$id	SBO:0000262	ontology		1	urn:miriam:sbo	^SBO:\d{7}$	Systems Biology Ontology		sbo	ontology
 TAIR	A	http://arabidopsis.org/index.jsp	http://arabidopsis.org/servlets/TairObject?type=locus&name=$id	AT1G01030	gene	Arabidopsis thaliana	1	urn:miriam:tair.locus	^AT[1-5]G\d{5}$	TAIR Locus		tair.locus	gene
 TIGR	Ti	http://www.jcvi.org/		12012.t00308	gene		1	Ti		TIGR			gene
@@ -133,7 +133,7 @@ TubercuList	Tb	http://tuberculist.epfl.ch	http://tuberculist.epfl.ch/quicksearch
 UCSC Genome Browser	Uc	http://genome.ucsc.edu/	http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id	uc001tyh.1	gene		1	Uc	uc\d{3}[a-z]{3}\.\d	UCSC Genome Browser	P2576	ucsc	gene
 UMLS CUI	Cu	https://www.nlm.nih.gov/research/umls/rxnorm/index.html	https://www.ncbi.nlm.nih.gov/medgen/{$id}	760050	other	Homo sapiens	1	urn:miriam:medgen	^[CN]*\d{4,7}$	MedGen		medgen	other
 Unipathway	Up	http://www.grenoble.prabi.fr/obiwarehouse/unipathway	http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id	UPA00206	pathway		1		^UPA\d{5}$	Unipathway		upa	pathway
-Uniprot-TrEMBL	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$	UniProtKB/TrEMBL	P352	uniprot	protein
+UniProtKB	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$	UniProtKB/TrEMBL	P352	uniprot	protein
 VMH metabolite	VmhM	http://www.vmh.life	https://www.vmh.life/#metabolite/$id	h2o	metabolite		1		[a-zA-Z0-9_\(\_\)\[\]]+	VMH Life_Metabolite		vmhmetabolite	metabolite
 Wheat gene names	Wn	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/report?class=gene;name=$id	1-FEH+w3	gene	Triticum aestivum	1	Wn		Wheat gene names		graingenes.symbol	gene
 Wheat gene refs	Wr	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id	WGS-95-1333	probe	Triticum aestivum	0	Wr		Wheat gene refs		graingenes.reference	gene

org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv

@@ -123,7 +123,7 @@ SubstrateDB	Sdb	http://substrate.burnham.org/	http://substrate.burnham.org/prote
 SubtiWiki	Bsu	http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page	http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id	BSU29180	gene	Bacillus subtilis	1	urn:miriam:subtiwiki	^BSU\d{5}$	SubtiWiki		subtiwiki	gene
 SUPFAM	Sf	http://supfam.org/SUPERFAMILY/	http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id	SSF57615	protein		1	urn:miriam:supfam	^\w+$	SUPFAM		supfam	protein
 SWISS-MODEL	Sw	http://swissmodel.expasy.org/	http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id	P23298	protein		1	urn:miriam:swiss-model	^\w+$	SWISS-MODEL		swiss-model	protein
-SwissLipids	Sl	http://www.swisslipids.org/	http://www.swisslipids.org/#/entity/$id/	SLM:000048885	metabolite		1		^SLM:\d+$	SwissLipids		swisslipid	metabolite
+SwissLipids	Sl	http://www.swisslipids.org/	http://www.swisslipids.org/#/entity/$id/	SLM:000048885	metabolite		1		^SLM:\d+$	SwissLipids		slm	metabolite
 Systems Biology Ontology	Sbo	http://www.ebi.ac.uk/sbo/	http://www.ebi.ac.uk/sbo/main/$id	SBO:0000262	ontology		1	urn:miriam:sbo	^SBO:\d{7}$	Systems Biology Ontology		sbo	ontology
 TAIR	A	http://arabidopsis.org/index.jsp	http://arabidopsis.org/servlets/TairObject?type=locus&name=$id	AT1G01030	gene	Arabidopsis thaliana	1	urn:miriam:tair.locus	^AT[1-5]G\d{5}$	TAIR Locus		tair.locus	gene
 TIGR	Ti	http://www.jcvi.org/		12012.t00308	gene		1	Ti		TIGR			gene
@@ -133,7 +133,7 @@ TubercuList	Tb	http://tuberculist.epfl.ch	http://tuberculist.epfl.ch/quicksearch
 UCSC Genome Browser	Uc	http://genome.ucsc.edu/	http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id	uc001tyh.1	gene		1	Uc	uc\d{3}[a-z]{3}\.\d	UCSC Genome Browser	P2576	ucsc	gene
 UMLS CUI	Cu	https://www.nlm.nih.gov/research/umls/rxnorm/index.html	https://www.ncbi.nlm.nih.gov/medgen/{$id}	760050	other	Homo sapiens	1	urn:miriam:medgen	^[CN]*\d{4,7}$	MedGen		medgen	other
 Unipathway	Up	http://www.grenoble.prabi.fr/obiwarehouse/unipathway	http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id	UPA00206	pathway		1		^UPA\d{5}$	Unipathway		upa	pathway
-Uniprot-TrEMBL	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$	UniProtKB/TrEMBL	P352	uniprot	protein
+UniProtKB	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$	UniProtKB/TrEMBL	P352	uniprot	protein
 VMH metabolite	VmhM	http://www.vmh.life	https://www.vmh.life/#metabolite/$id	h2o	metabolite		1		[a-zA-Z0-9_\(\_\)\[\]]+	VMH Life_Metabolite		vmhmetabolite	metabolite
 Wheat gene names	Wn	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/report?class=gene;name=$id	1-FEH+w3	gene	Triticum aestivum	1	Wn		Wheat gene names		graingenes.symbol	gene
 Wheat gene refs	Wr	http://wheat.pw.usda.gov/	http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id	WGS-95-1333	probe	Triticum aestivum	0	Wr		Wheat gene refs		graingenes.reference	gene

org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java

@@ -14,6 +14,13 @@
 */
 package org.bridgedb.bio;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNotSame;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileInputStream;
@@ -24,14 +31,8 @@
 import java.lang.reflect.Method;
 import java.util.HashSet;
 import java.util.Set;
-import java.util.regex.Pattern;
 
 import org.bridgedb.DataSource;
-import org.bridgedb.DataSourcePatterns;
-import org.junit.BeforeClass;
-import org.junit.jupiter.api.BeforeAll;
-
-import static org.junit.jupiter.api.Assertions.*;
 
 
 /**
@@ -40,11 +41,6 @@
  */
 public class DataSourceTxtTest {
 
-	@BeforeAll
-	public static void setUpSources() {
-		DataSourceTxt.init();
-	}
-
 	@org.junit.jupiter.api.Test
 	public void testUniqueSystemCodes() {
 		Set<String> codes = new HashSet<String>();

org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java

@@ -0,0 +1,58 @@
+/* Copyright (c)  2023  Egon Willighagen
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and limitations under the License.
+ */
+package org.bridgedb.bio;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.bridgedb.DataSource;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+public class UniProtKBTest {
+
+	@BeforeAll
+	public static void setUpSources() {
+		DataSourceTxt.init();
+	}
+
+	@Test
+    public void getBySystemCode() {
+        DataSource ds1 = DataSource.getExistingBySystemCode("S");
+        assertNotNull(ds1);
+        assertEquals("S", ds1.getSystemCode());
+        assertEquals("UniProtKB", ds1.getFullName());
+    }
+
+	@Test
+    public void getByFullName_TrEMBL() {
+        DataSource ds1 = DataSource.getExistingByFullName("Uniprot-TrEMBL");
+        assertNotNull(ds1);
+        assertEquals("S", ds1.getSystemCode());
+        assertEquals("UniProtKB", ds1.getFullName());
+	}
+
+	@Test
+    public void getByFullName_SwissProt() {
+        DataSource ds1 = DataSource.getExistingByFullName("Uniprot-SwissProt");
+        assertNotNull(ds1);
+        assertEquals("S", ds1.getSystemCode());
+        assertEquals("UniProtKB", ds1.getFullName());
+    }
+
+	@Test
+    public void getByFullName_UniProtKB() {
+        DataSource ds1 = DataSource.getExistingByFullName("UniProtKB");
+        assertNotNull(ds1);
+        assertEquals("S", ds1.getSystemCode());
+        assertEquals("UniProtKB", ds1.getFullName());
+    }
+}

org.bridgedb.file.orthoxml/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.gui/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.rdb.construct/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.rdb/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.rdf/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
     <build>

org.bridgedb.rdf/resources/BioDataSource.ttl

@@ -1263,7 +1263,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ;
 	dcterms:alternative "UniProtKB/Swiss-Prot" .
 
 bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ;
-	bridgeDB:fullName "Uniprot-TrEMBL" ;
+	bridgeDB:fullName "UniProtKB" ;
 	bridgeDB:systemCode "S" ;
 	bridgeDB:mainUrl "http://www.uniprot.org/" ;
 	bridgeDB:idExample "P62158" ;

org.bridgedb.rdf/resources/DataSource.ttl

@@ -1135,7 +1135,7 @@ bridgeDB:DataSource_Uniprot_Enzyme a bridgeDB:DataSource ;
 	bridgeDB:hasPrimaryUriPattern <http://purl.uniprot.org/enzyme/$id> .
 
 bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ;
-	bridgeDB:fullName "Uniprot-TrEMBL" ;
+	bridgeDB:fullName "UniProtKB" ;
 	bridgeDB:alternativeFullName "Uniprot/TrEMBL" ;
 	bridgeDB:systemCode "S" ;
 	bridgeDB:mainUrl "http://www.uniprot.org/" ;

org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl

@@ -6202,7 +6202,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ;
 	bridgeDB:hasUriPattern <http://www.uniprot.org/uniprot/$id> .
 
 bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ;
-	bridgeDB:fullName "Uniprot-TrEMBL" ;
+	bridgeDB:fullName "UniProtKB" ;
 	bridgeDB:systemCode "S" ;
 	bridgeDB:mainUrl "http://www.uniprot.org/" ;
 	bridgeDB:idExample "P62158" ;

org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt

@@ -540,7 +540,7 @@ Unipathway	Up	http://www.grenoble.prabi.fr/obiwarehouse/unipathway	http://www.gr
 Uniprot Enzyme	Enzyme		http://purl.uniprot.org/enzyme/$id		unknown		1			
 UniProt Isoform	uniprot.isoform		http://www.uniprot.org/uniprot/$id	Q5BJF6-3	unknown		1	urn:miriam:uniprot.isoform	^([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+)$	
 Uniprot-SwissProt	Sp	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	CALM_HUMAN	protein		1		^[A-Z0-9]+_[A-Z]+$	UniProtKB/Swiss-Prot
-Uniprot-TrEMBL	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$	UniProtKB/TrEMBL
+UniProtKB	S	http://www.uniprot.org/	http://www.uniprot.org/uniprot/$id	P62158	protein		1	urn:miriam:uniprot	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$	UniProtKB/TrEMBL
 UniSTS	unists		http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id	456789	unknown		1	urn:miriam:unists	^\d+$	
 Unit Ontology	unit		http://purl.bioontology.org/ontology/UO/$id	UO:0000080	unknown		1	urn:miriam:unit	^UO:\d{7}?	
 Unite	unite		http://unite.ut.ee/bl_forw.php?nimi=$id	UDB000691	unknown		1	urn:miriam:unite	^UDB\d{6}$	

org.bridgedb.sql/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
         <build>

org.bridgedb.tools.batchmapper/pom.xml

@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>
@@ -33,19 +33,19 @@
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb</artifactId>
-                        <version>3.0.23</version>
+                        <version>3.1.0</version>
                         <scope>compile</scope>
                 </dependency>
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb.bio</artifactId>
-			<version>3.0.23</version>
+			<version>3.1.0</version>
 			<scope>compile</scope>
 		</dependency>
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb.rdb</artifactId>
-                        <version>3.0.23</version>
+                        <version>3.1.0</version>
                         <scope>compile</scope>
                 </dependency>
 	</dependencies>

org.bridgedb.tools.info/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>

org.bridgedb.tools.qc/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>
@@ -90,7 +90,7 @@
                 <dependency>
                         <groupId>com.google.guava</groupId>
                         <artifactId>guava</artifactId>
-                        <version>[32.0.1-jre,)</version>
+                        <version>[32.0.0-jre,)</version>
                 </dependency>
                 <dependency>
                         <groupId>org.apache.derby</groupId>

org.bridgedb.tools.voidtool/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
 	<build>
@@ -90,7 +90,7 @@
                 <dependency>
                         <groupId>com.google.guava</groupId>
                         <artifactId>guava</artifactId>
-                        <version>[30.0-jre,)</version>
+                        <version>[32.0-jre,)</version>
                 </dependency>
                 <dependency>
                         <groupId>org.apache.derby</groupId>

org.bridgedb.uri.api/pom.xml

@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.23</version>
+  	<version>3.1.0</version>
   </parent>
 
         <build>