[WIP] preparing for 3.0.30

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: 3.0.29
-date-released: 2025-07-28
+version: 3.0.30
+date-released: 2026-01-05
 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](https://search.maven.org/artifact/org.bridgedb/bridgedb-bundle), 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 `3.0.29`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.30`:
 
 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>3.0.29</version>
+        <version>3.0.30</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.29'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.30'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.29"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.30"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.0.29'
+'org.bridgedb:org.bridgedb.bio:jar:3.0.30'
 ```
 
 
@@ -135,7 +135,7 @@ 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=3.0.29
+mvn versions:set -DnewVersion=3.0.30
 mvn clean deploy
 ```
 
@@ -145,7 +145,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.0.30-SNAPSHOT
+mvn versions:set -DnewVersion=3.0.31-SNAPSHOT
 mvn clean deploy
 ```
 

examples/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.0.29</version>
+    <version>3.0.30</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>3.0.29</version>
+  	<version>3.0.30</version>
   </parent>
 
 	<build>

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

@@ -85,7 +85,7 @@ NCI Pathway Interaction Database	Pid	http://pid.nci.nih.gov/	http://pid.nci.nih.
 OMIM	Om	http://omim.org/	http://omim.org/entry/$id	603903	gene		0	urn:miriam:mim	^[*#+%^]?\d{6}$	OMIM	P492	omim	gene,disease
 OpenTargets	Opt	https://www.opentargets.org/	https://genetics.opentargets.org/gene/$id	ENSG00000169174	gene		1		^ENS[A-Z]*[FPTG]\d{11}$				gene
 ORCID	orcid	https://orcid.org	https://orcid.org/$id	0000-0002-5355-2576	other	Homo sapiens	1	urn:miriam:orcid	^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$	ORCID	P496	orcid	other,author
-Orphanet	On	http://www.orpha.net/consor/	https://identifiers.org/orphanet:$id	85163	other	Homo sapiens	1	urn:miriam:orphanet	^\d+$	Bio2RDF		orphanet	other
+Orphanet	On	http://www.orpha.net/consor/	https://identifiers.org/orphanet:$id	85163	other	Homo sapiens	1	urn:miriam:orphanet	^\d+$	Bio2RDF		orpha	other
 Oryzabase	Ob	http://www.shigen.nig.ac.jp/rice/oryzabase	http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id	468	gene	Oryza sativa	1	Ob		Oryzabase		oryzabase.gene	gene
 Other	O				gene		1	O		Other			other
 Pathway Commons	Pc	http://www.pathwaycommons.org/pc/	http://www.pathwaycommons.org/pc/record2.do?id=$id	485991	pathway		1	urn:miriam:pathwaycommons	^\d+$	Pathway Commons		pathwaycommons	pathway
@@ -123,7 +123,8 @@ SUPFAM	Sf	http://supfam.org/SUPERFAMILY/	http://supfam.org/SUPERFAMILY/cgi-bin/s
 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		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	https://www.arabidopsis.org/	https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id	AT1G01030	gene	Arabidopsis thaliana	1	urn:miriam:tair.locus	^AT[1-5]G\d{5}$	TAIR Locus		tair.locus	gene
+TAIR	A	https://www.arabidopsis.org/	https://www.arabidopsis.org/locus?accession=$id	2200950	gene	Arabidopsis thaliana	1	urn:miriam:tair.locus	^\d+$	TAIR Locus		tair.locus	gene
+TAIR gene name	Agn	https://www.arabidopsis.org/	https://www.arabidopsis.org/locus?name=$id	AT1G01030	gene	Arabidopsis thaliana	1	urn:miriam:tair.name	^AT[1-5]G\d{5}$	TAIR gene name		araport	gene
 TIGR	Ti	http://www.jcvi.org/		12012.t00308	gene		1	Ti		TIGR			gene
 TTD Drug	Td	http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp	http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id	DAP000773	metabolite		1	urn:miriam:ttd.drug	^DAP\d+$	TTD Drug		ttd.drug	metabolite
 TTD Target	Tt	http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp	http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id	TTDS00056	protein		1	urn:miriam:ttd.target	^TTDS\d+$	TTD Target		ttd.target	protein