bridgedb · egonw · Oct 3, 2024 · Oct 3, 2024 · Jul 26, 2025 · Jul 26, 2025
diff --git a/CITATION.cff b/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: 3.0.28
-date-released: 2024-09-27
+version: 3.0.29
+date-released: 2025-07-28
 authors:
   - given-names: Manas
     family-names: Awasthi

diff --git a/README.md b/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 `3.0.28`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.29`:
 
 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>3.0.28</version>
+        <version>3.0.29</version>
     </dependency>
 </dependencies>
 ```
 
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.28'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.29'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.28"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.29"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.0.28'
+'org.bridgedb:org.bridgedb.bio:jar:3.0.29'
 ```
 
 
@@ -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=3.0.28
+mvn versions:set -DnewVersion=3.0.29
 mvn clean deploy
 ```
 
@@ -145,7 +145,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.0.29-SNAPSHOT
+mvn versions:set -DnewVersion=3.0.30-SNAPSHOT
 mvn clean deploy
 ```
 

diff --git a/common-bundles/com.google.collect_1.0.0.v201105210816.jar b/common-bundles/com.google.collect_1.0.0.v201105210816.jar
diff --git a/common-bundles/commons-collections-3.2.1.jar b/common-bundles/commons-collections-3.2.1.jar
diff --git a/common-bundles/javax.activation_1.1.0.v201105071233.jar b/common-bundles/javax.activation_1.1.0.v201105071233.jar
diff --git a/examples/pom.xml b/examples/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.0.28</version>
+    <version>3.0.29</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.bridgedb.examples</groupId>

diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml
@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.0.28</version>
+  	<version>3.0.29</version>
   </parent>
 
 	<build>
@@ -56,7 +56,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>${maven-jar.version}</version>
                 <configuration>
                     <archive>
                         <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>

diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
@@ -23,23 +23,22 @@ dbSNP	Sn	http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp	http://www.ncbi.nlm.nih
 DrugBank	Dr	http://www.drugbank.ca/	http://www.drugbank.ca/drugs/$id	DB00001	metabolite		1	urn:miriam:drugbank	^D(B|BSALT|BCAT)(\d{1})?\d{5}$	DrugBank	P715	drugbank	metabolite
 DOI	Pbd	https://doi.org/	https://doi.org/$id	10.1038/s41597-020-0477-8	publication		1	urn:miriam:doi	^\d{2}\.\d{4}.*$	Digital Object Identifier	P356	doi	publication
 EcoCyc	Eco	http://ecocyc.org/	http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id	1.1.1.127-RXN	interaction	Escherichia coli	1	Eco	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+-RXN	EcoCyc		ecocyc	interaction
-EcoGene	Ec	http://ecogene.org/	http://ecogene.org/geneInfo.php?eg_id=$id	EG10173	gene	Escherichia coli	1	urn:miriam:ecogene	^EG\d+$	EcoGene		ecogene	gene
 EMBL	Em	http://www.ebi.ac.uk/embl/	http://www.ebi.ac.uk/ena/data/view/$id	X58356	gene		1	urn:miriam:ena.embl	^[A-Z]+[0-9]+$	European Nucleotide Archive		ena.embl	gene
 Ensembl	En	http://www.ensembl.org/	https://www.ensembl.org/id/$id	ENSG00000139618	gene		1	urn:miriam:ensembl	^ENS[A-Z]*[FPTG]\d{11}$	Ensembl	P594	ensembl	gene
 Entrez Gene	L	http://www.ncbi.nlm.nih.gov/gene	http://www.ncbi.nlm.nih.gov/gene/$id	100010	gene		1	urn:miriam:ncbigene	^\d+$	Entrez Gene	P351	ncbigene	gene
-Enzyme Nomenclature	E	http://www.ebi.ac.uk/intenz/	http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id	1.1.1.1	gene		1	urn:miriam:ec-code	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$	Enzyme Nomenclature	P591	eccode	gene
+Enzyme Nomenclature	E	http://www.ebi.ac.uk/intenz/	http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id	1.1.1.1	gene		1	urn:miriam:ec-code	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$	Enzyme Nomenclature	P591	ec	gene
 EPA CompTox	Ect	https://comptox.epa.gov/dashboard	https://comptox.epa.gov/dashboard/$id	DTXSID7020637	metabolite		1	Ect	^DTXSID(\d{2})?\d{7}\d?$	EPA CompTox Dashboard	P3117	comptox	metabolite
 European Registry of Materials	Nmerm	https://nanocommons.github.io/identifiers/		ERM00000064	material		0		^ERM\d{8}$	European Registry of Materials		erm	material
 FlyBase	F	http://flybase.org/	http://flybase.org/reports/$id.html	FBgn0011293	gene	Drosophila melanogaster	1	urn:miriam:fb	^FB\w{2}\d{7}$	FlyBase	P3852	flybase	gene
 GenBank	G	http://www.ncbi.nlm.nih.gov/genbank/	http://www.ncbi.nlm.nih.gov/nuccore/$id	NW_004190323	gene		0	urn:miriam:insdc	(\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5})	GenBank		insdc	gene
 Gene Wiki	Gw	http://en.wikipedia.org/wiki/Portal:Gene_Wiki	http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id	1017	gene		0	urn:miriam:genewiki	\d+	Gene Wiki	P351	genewiki	gene
 GeneOntology	T	http://www.ebi.ac.uk/QuickGO/	http://www.ebi.ac.uk/QuickGO/GTerm?id=$id	GO:0006915	ontology		0	urn:miriam:go	^GO:\d{7}$	Gene Ontology	P686	go	ontology
-Gramene Arabidopsis	EnAt	https://www.gramene.org/	https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id	ATMG01360	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}	Gramene Arabidopsis			gene
+Gramene Arabidopsis	EnAt	https://www.gramene.org/	https://plants.ensembl.org/id/$id	ATMG01360	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}	Gramene Arabidopsis		ensembl.plant	gene
 Gramene Genes DB	Gg	https://www.gramene.org/	https://archive.gramene.org/db/genes/search_gene?acc=$id	GR:0060184	gene		1	Gg	GR:\d+	Gramene Genes		gramene.gene	gene
 Gramene Literature	Gl	https://www.gramene.org/	https://www.gramene.org/db/literature/pub_search?ref_id=$id	6200	gene		0	Gl		Gramene Literature		gramene.reference	gene
-Gramene Maize	EnZm	https://www.ensembl.org	https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id	GRMZM2G174107	gene		1	EnZm		Gramene Maize			gene
+Gramene Maize	EnZm	https://www.ensembl.org	https://plants.ensembl.org/id/$id	GRMZM2G174107	gene		1	EnZm	^GRMZM2G\d+$	Gramene Maize		ensembl.plant	gene
 Gramene Pathway	Gp	https://www.gramene.org/pathway		AAH72400	pathway		1	Gp		Gramene Pathway			pathway
-Gramene Rice	EnOj	https://www.gramene.org/	http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id	Os05g0113900	gene		1	EnOj		Gramene Rice			gene
+Gramene Rice	EnOj	https://www.gramene.org/	https://plants.ensembl.org/id/$id	Os05g0113900	gene		1	EnOj	^Os\d.*$	Gramene Rice		ensembl.plant	gene
 Guide to Pharmacology	Gpl	http://www.guidetopharmacology.org/	https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id	1627	gene		1		^\d+$	Guide to Pharmacology Targets	P5458	iuphar.receptor	gene
 Guide to Pharmacology Targets	Gpt	http://www.guidetopharmacology.org/	https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id	256	metabolite		1		^\d+$	Guide to Pharmacology	P595	iuphar.ligand	metabolite
 HGNC	H	http://www.genenames.org	https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id	DAPK1	gene	Homo sapiens	1	urn:miriam:hgnc.symbol	^[A-Za-z0-9]+	HGNC Symbol	P353	hgnc.symbol	gene
@@ -70,7 +69,7 @@ LIPID MAPS	Lm	http://www.lipidmaps.org	https://www.lipidmaps.org/data/structure/
 LipidBank	Lb	http://lipidbank.jp/index.html	http://lipidbank.jp/cgi-bin/detail.cgi?id=$id	BBA0001	metabolite		1	urn:miriam:lipidbank	^\w+\d+$	LipidBank		lipidbank	metabolite
 MACiE	Ma	http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html	http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id	M0001	protein		1	urn:miriam:macie	^M\d{4}$	MACiE		macie	protein
 MaizeGDB	Mg	https://maizegdb.org/	https://maizegdb.org/gene_center/gene/$id	acc1	gene	Zea mays	1	Mg		MaizeGDB		maizegdb.locus	gene
-MatrixDB	Md	http://matrixdb.ibcp.fr/	http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association	P00747_P07355	interaction		1	urn:miriam:matrixdb.association	^([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]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$	MatrixDB		matrixdb.association	interaction
+MatrixDB	Md	http://matrixdb.univ-lyon1.fr/	http://matrixdb.univ-lyon1.fr/association/$id	P00747_P07355	interaction		1	urn:miriam:matrixdb.association	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$	MatrixDB		matrixdb.association	interaction
 MeSH	Me	http://id.nlm.nih.gov/mesh/	http://id.nlm.nih.gov/mesh/$id	C000100	other		1	urn:miriam:mesh	^(C|D)\d{6}$	Medical Subject Headings		mesh	disease,metabolite,gene,other
 MetaboLights Compounds	Ml	http://www.ebi.ac.uk/metabolights/	http://www.ebi.ac.uk/metabolights/$id	MTBLC17170	metabolite		1	Ml	^MTBLC\d{1,6}$	MetaboLights Compounds	P3890	metabolights	metabolite
 MetaCyc	Mc	http://www.metacyc.org/	http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id	D-GLUTAMATE-OXIDASE-RXN	interaction		1	Mc		MetaCyc		metacyc.reaction	interaction
@@ -111,7 +110,7 @@ RESID	Res	http://www.ebi.ac.uk/RESID/	http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
 Rfam	Rf		https://rfam.org/family/$id	RF00066	gene		1	Rf	RF\d+	RFAM		rfam	gene
 RGD	R	https://rgd.mcw.edu/	https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id	2018	gene	Rattus norvegicus	1	urn:miriam:rgd	^\d{4,7}$	Rat Genome Database	P3853	rgd	gene
 Rhea	Rh	http://www.ebi.ac.uk/rhea/	http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id	12345	interaction		1	urn:miriam:rhea	^\d{5}$	Rhea		rhea	interaction
-Rice Ensembl Gene	Os	https://www.gramene.org/Oryza_sativa	https://www.gramene.org/Oryza_sativa/geneview?gene=$id	Os04g54800	gene	Oryza sativa	1	Os		Rice Ensembl Gene			gene
+Rice Ensembl Gene	Os	https://www.gramene.org/Oryza_sativa	https://plants.ensembl.org/id/$id	Os04g54800	gene	Oryza sativa	1	Os	^Os.*$	Rice Ensembl Gene		ensembl.plant	gene
 SGD	D	http://www.yeastgenome.org/	http://www.yeastgenome.org/locus/$id	S000028457	gene	Saccharomyces cerevisiae	1	urn:miriam:sgd	^S\d+$	SGD	P3406	sgd	gene
 Small Molecule Pathway Database	Sm	http://www.smpdb.ca/pathways	https://smpdb.ca/view/$id	SMP00001	pathway		1	urn:miriam:smpdb	^SMP\d{5}$	Small Molecule Pathway Database		smpdb	pathway
 SMART	Sma	http://smart.embl-heidelberg.de/	http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id	SM00015	protein		1	urn:miriam:smart	^SM\d{5}$	SMART	P3524	smart	protein

diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
@@ -23,23 +23,22 @@ dbSNP	Sn	http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp	http://www.ncbi.nlm.nih
 DrugBank	Dr	http://www.drugbank.ca/	http://www.drugbank.ca/drugs/$id	DB00001	metabolite		1	urn:miriam:drugbank	^D(B|BSALT|BCAT)(\d{1})?\d{5}$	DrugBank	P715	drugbank	metabolite
 DOI	Pbd	https://doi.org/	https://doi.org/$id	10.1038/s41597-020-0477-8	publication		1	urn:miriam:doi	^\d{2}\.\d{4}.*$	Digital Object Identifier	P356	doi	publication
 EcoCyc	Eco	http://ecocyc.org/	http://ecocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=$id	1.1.1.127-RXN	interaction	Escherichia coli	1	Eco	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+-RXN	EcoCyc		ecocyc	interaction
-EcoGene	Ec	http://ecogene.org/	http://ecogene.org/geneInfo.php?eg_id=$id	EG10173	gene	Escherichia coli	1	urn:miriam:ecogene	^EG\d+$	EcoGene		ecogene	gene
 EMBL	Em	http://www.ebi.ac.uk/embl/	http://www.ebi.ac.uk/ena/data/view/$id	X58356	gene		1	urn:miriam:ena.embl	^[A-Z]+[0-9]+$	European Nucleotide Archive		ena.embl	gene
 Ensembl	En	http://www.ensembl.org/	https://www.ensembl.org/id/$id	ENSG00000139618	gene		1	urn:miriam:ensembl	^ENS[A-Z]*[FPTG]\d{11}$	Ensembl	P594	ensembl	gene
 Entrez Gene	L	http://www.ncbi.nlm.nih.gov/gene	http://www.ncbi.nlm.nih.gov/gene/$id	100010	gene		1	urn:miriam:ncbigene	^\d+$	Entrez Gene	P351	ncbigene	gene
-Enzyme Nomenclature	E	http://www.ebi.ac.uk/intenz/	http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id	1.1.1.1	gene		1	urn:miriam:ec-code	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$	Enzyme Nomenclature	P591	eccode	gene
+Enzyme Nomenclature	E	http://www.ebi.ac.uk/intenz/	http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id	1.1.1.1	gene		1	urn:miriam:ec-code	^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$	Enzyme Nomenclature	P591	ec	gene
 EPA CompTox	Ect	https://comptox.epa.gov/dashboard	https://comptox.epa.gov/dashboard/$id	DTXSID7020637	metabolite		1	Ect	^DTXSID(\d{2})?\d{7}\d?$	EPA CompTox Dashboard	P3117	comptox	metabolite
 European Registry of Materials	Nmerm	https://nanocommons.github.io/identifiers/		ERM00000064	material		0		^ERM\d{8}$	European Registry of Materials		erm	material
 FlyBase	F	http://flybase.org/	http://flybase.org/reports/$id.html	FBgn0011293	gene	Drosophila melanogaster	1	urn:miriam:fb	^FB\w{2}\d{7}$	FlyBase	P3852	flybase	gene
 GenBank	G	http://www.ncbi.nlm.nih.gov/genbank/	http://www.ncbi.nlm.nih.gov/nuccore/$id	NW_004190323	gene		0	urn:miriam:insdc	(\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5})	GenBank		insdc	gene
 Gene Wiki	Gw	http://en.wikipedia.org/wiki/Portal:Gene_Wiki	http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id	1017	gene		0	urn:miriam:genewiki	\d+	Gene Wiki	P351	genewiki	gene
 GeneOntology	T	http://www.ebi.ac.uk/QuickGO/	http://www.ebi.ac.uk/QuickGO/GTerm?id=$id	GO:0006915	ontology		0	urn:miriam:go	^GO:\d{7}$	Gene Ontology	P686	go	ontology
-Gramene Arabidopsis	EnAt	https://www.gramene.org/	https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id	ATMG01360	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}	Gramene Arabidopsis			gene
+Gramene Arabidopsis	EnAt	https://www.gramene.org/	https://plants.ensembl.org/id/$id	ATMG01360	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}	Gramene Arabidopsis		ensembl.plant	gene
 Gramene Genes DB	Gg	https://www.gramene.org/	https://archive.gramene.org/db/genes/search_gene?acc=$id	GR:0060184	gene		1	Gg	GR:\d+	Gramene Genes		gramene.gene	gene
 Gramene Literature	Gl	https://www.gramene.org/	https://www.gramene.org/db/literature/pub_search?ref_id=$id	6200	gene		0	Gl		Gramene Literature		gramene.reference	gene
-Gramene Maize	EnZm	https://www.ensembl.org	https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id	GRMZM2G174107	gene		1	EnZm		Gramene Maize			gene
+Gramene Maize	EnZm	https://www.ensembl.org	https://plants.ensembl.org/id/$id	GRMZM2G174107	gene		1	EnZm	^GRMZM2G\d+$	Gramene Maize		ensembl.plant	gene
 Gramene Pathway	Gp	https://www.gramene.org/pathway		AAH72400	pathway		1	Gp		Gramene Pathway			pathway
-Gramene Rice	EnOj	https://www.gramene.org/	http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id	Os05g0113900	gene		1	EnOj		Gramene Rice			gene
+Gramene Rice	EnOj	https://www.gramene.org/	https://plants.ensembl.org/id/$id	Os05g0113900	gene		1	EnOj	^Os\d.*$	Gramene Rice		ensembl.plant	gene
 Guide to Pharmacology	Gpl	http://www.guidetopharmacology.org/	https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id	1627	gene		1		^\d+$	Guide to Pharmacology Targets	P5458	iuphar.receptor	gene
 Guide to Pharmacology Targets	Gpt	http://www.guidetopharmacology.org/	https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id	256	metabolite		1		^\d+$	Guide to Pharmacology	P595	iuphar.ligand	metabolite
 HGNC	H	http://www.genenames.org	https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id	DAPK1	gene	Homo sapiens	1	urn:miriam:hgnc.symbol	^[A-Za-z0-9]+	HGNC Symbol	P353	hgnc.symbol	gene
@@ -70,7 +69,7 @@ LIPID MAPS	Lm	http://www.lipidmaps.org	https://www.lipidmaps.org/data/structure/
 LipidBank	Lb	http://lipidbank.jp/index.html	http://lipidbank.jp/cgi-bin/detail.cgi?id=$id	BBA0001	metabolite		1	urn:miriam:lipidbank	^\w+\d+$	LipidBank		lipidbank	metabolite
 MACiE	Ma	http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html	http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id	M0001	protein		1	urn:miriam:macie	^M\d{4}$	MACiE		macie	protein
 MaizeGDB	Mg	https://maizegdb.org/	https://maizegdb.org/gene_center/gene/$id	acc1	gene	Zea mays	1	Mg		MaizeGDB		maizegdb.locus	gene
-MatrixDB	Md	http://matrixdb.ibcp.fr/	http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$id&class=Association	P00747_P07355	interaction		1	urn:miriam:matrixdb.association	^([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]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$	MatrixDB		matrixdb.association	interaction
+MatrixDB	Md	http://matrixdb.univ-lyon1.fr/	http://matrixdb.univ-lyon1.fr/association/$id	P00747_P07355	interaction		1	urn:miriam:matrixdb.association	^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$	MatrixDB		matrixdb.association	interaction
 MeSH	Me	http://id.nlm.nih.gov/mesh/	http://id.nlm.nih.gov/mesh/$id	C000100	other		1	urn:miriam:mesh	^(C|D)\d{6}$	Medical Subject Headings		mesh	disease,metabolite,gene,other
 MetaboLights Compounds	Ml	http://www.ebi.ac.uk/metabolights/	http://www.ebi.ac.uk/metabolights/$id	MTBLC17170	metabolite		1	Ml	^MTBLC\d{1,6}$	MetaboLights Compounds	P3890	metabolights	metabolite
 MetaCyc	Mc	http://www.metacyc.org/	http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id	D-GLUTAMATE-OXIDASE-RXN	interaction		1	Mc		MetaCyc		metacyc.reaction	interaction
@@ -111,7 +110,7 @@ RESID	Res	http://www.ebi.ac.uk/RESID/	http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
 Rfam	Rf		https://rfam.org/family/$id	RF00066	gene		1	Rf	RF\d+	RFAM		rfam	gene
 RGD	R	https://rgd.mcw.edu/	https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id	2018	gene	Rattus norvegicus	1	urn:miriam:rgd	^\d{4,7}$	Rat Genome Database	P3853	rgd	gene
 Rhea	Rh	http://www.ebi.ac.uk/rhea/	http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id	12345	interaction		1	urn:miriam:rhea	^\d{5}$	Rhea		rhea	interaction
-Rice Ensembl Gene	Os	https://www.gramene.org/Oryza_sativa	https://www.gramene.org/Oryza_sativa/geneview?gene=$id	Os04g54800	gene	Oryza sativa	1	Os		Rice Ensembl Gene			gene
+Rice Ensembl Gene	Os	https://www.gramene.org/Oryza_sativa	https://plants.ensembl.org/id/$id	Os04g54800	gene	Oryza sativa	1	Os	^Os.*$	Rice Ensembl Gene		ensembl.plant	gene
 SGD	D	http://www.yeastgenome.org/	http://www.yeastgenome.org/locus/$id	S000028457	gene	Saccharomyces cerevisiae	1	urn:miriam:sgd	^S\d+$	SGD	P3406	sgd	gene
 Small Molecule Pathway Database	Sm	http://www.smpdb.ca/pathways	https://smpdb.ca/view/$id	SMP00001	pathway		1	urn:miriam:smpdb	^SMP\d{5}$	Small Molecule Pathway Database		smpdb	pathway
 SMART	Sma	http://smart.embl-heidelberg.de/	http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id	SM00015	protein		1	urn:miriam:smart	^SM\d{5}$	SMART	P3524	smart	protein

diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java
@@ -131,15 +131,6 @@ public void testMIRIAMFeatures() throws Exception {
 		assertEquals("chebi", chebi.getCompactIdentifierPrefix());
 	}
 
-	@org.junit.jupiter.api.Test
-	public void testEcoGene() throws Exception {
-		DataSource ecogene = DataSource.getExistingByFullName("EcoGene");
-		assertNotNull(ecogene);
-		assertEquals("urn:miriam:ecogene:EG10173", ecogene.getMiriamURN("EG10173"));
-		assertNotNull(DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/"));
-		assertNotNull(DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/"));
-	}
-
 	@org.junit.jupiter.api.Test
 	public void testPrefix() throws Exception {
 		DataSource ds = DataSource.getExistingBySystemCode("L");