diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 417ccb74d..0d38b3f7e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -7,8 +7,22 @@ on:
branches: [ series/3.1.0 ]
jobs:
- build:
+ java8:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - name: Set up Java
+ uses: actions/setup-java@v4
+ with:
+ distribution: 'temurin'
+ java-version: 8
+ cache: maven
+ - name: Build with Maven
+ run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql
+
+ build:
+ needs: java8
runs-on: ubuntu-latest
steps:
diff --git a/CITATION.cff b/CITATION.cff
index 716c1c9a7..cdd95bc91 100644
--- 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: 3.1.1
-date-released: '2023-12-18'
+version: 3.1.2
+date-released: '2024-07-30'
authors:
- given-names: Manas
family-names: Awasthi
diff --git a/README.md b/README.md
index dbeb70269..555e3e9a8 100644
--- 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](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 `3.1.1`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`:
For [Maven](https://maven.apache.org/):
@@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/):
org.bridgedb
org.bridgedb.bio
- 3.1.1
+ 3.1.2
```
@@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/):
For [Gradle](https://gradle.org/):
```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.1'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2'
```
For [Ivy](http://ant.apache.org/ivy/):
```xml
-
+
```
For [Buildr](https://buildr.apache.org/):
```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.1.1'
+'org.bridgedb:org.bridgedb.bio:jar:3.1.2'
```
@@ -58,6 +58,8 @@ able to compile with a simple:
mvn clean install -Dgpg.skip
```
+When compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`.
+
You can find the libraries in the folder called "target", in each sublibrary folder (used to be called "dist" in ant).
If you want to ignore failing tests, e.g. because you are not online,
@@ -127,13 +129,13 @@ Making releases
---------------
If it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb),
-this `README.md` and `CITATION.cff` (for Zenodo).
+this `README.md` and `CITATION.cff` (for Zenodo), as well as the `pom-java8.xml`.
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=3.1.2-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.2
mvn clean deploy
```
@@ -143,7 +145,7 @@ and everything.
To make a development (SNAPSHOT) release, use:
```shell
-mvn versions:set -DnewVersion=3.1.1-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.3-SNAPSHOT
mvn clean deploy
```
diff --git a/UPGRADE_NOTES.md b/UPGRADE_NOTES.md
index f6b3f5dab..53aa00618 100644
--- a/UPGRADE_NOTES.md
+++ b/UPGRADE_NOTES.md
@@ -1,35 +1,49 @@
-Upgrade notes to BridgeDb 2.0
+# Upgrade notes to BridgeDb 2.0
-1. Initialing data sources
+## 1. Initialing data sources
Replace
+```java
BioDataSource.init();
+```
with
+```java
DataSourceTxt.init();
+```
-2. Getting DataSource's
+## 2. Getting DataSource's
Replace
+```java
DataSource ds = DataSource.getBySystemCode("Ck");
+```
with
+```java
DataSource ds = DataSource.getExistingBySystemCode("Ck");
+```
Similarly, and more important:
+```java
DataSource ds = DataSource.getByFullName("PubChem-compound");
+```
with
+```java
DataSource ds = DataSource.getExistingByFullName("PubChem-compound");
+```
-The latter two new methods throw an IllegalArgumentException if the DataSource does not exist.
+The latter two new methods throw an `IllegalArgumentException` if the `DataSource` does not exist.
Use one of the following two methods to check first:
+```java
DataSource.systemCodeExists("Ck");
DataSource.fullNameExists("PubChem-compound");
+```
diff --git a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl
index 42d8576ad..ffbb03311 100755
--- a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl
+++ b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl
@@ -743,7 +743,7 @@
%{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'],
'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'",
"\'ID\|\'", "\'\|$species\|\'", "\'\'",
- "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
+ "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
"\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'PRIMARY KEY (ID)'
@@ -863,7 +863,7 @@
%{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'],
'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'",
"\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
- "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
+ "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
"\'ftp://rgd.mcw.edu/pub/\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
@@ -916,8 +916,8 @@
%{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'],
'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'",
"\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
- "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
- "\'http://www.gramene.org\'"],
+ "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
+ "\'https://www.gramene.org\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
'Description VARCHAR(255) DEFAULT NULL',
@@ -926,8 +926,8 @@
%{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'],
'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'",
"\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
- "\'http://www.gramene.org/pathway\'", "\'\'",
- "\'http://www.gramene.org/pathway\'"],
+ "\'https://www.gramene.org/pathway\'", "\'\'",
+ "\'https://www.gramene.org/pathway\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Description VARCHAR(255) DEFAULT NULL',
'PRIMARY KEY (ID)'
diff --git a/examples/pom.xml b/examples/pom.xml
index 8f520b6c3..0c490e85b 100644
--- a/examples/pom.xml
+++ b/examples/pom.xml
@@ -3,7 +3,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
4.0.0
org.bridgedb.examples
diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml
index 5edbf57bb..d92cfc8fe 100644
--- a/org.bridgedb.bio/pom.xml
+++ b/org.bridgedb.bio/pom.xml
@@ -8,7 +8,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
index 1c4891254..289fb0957 100644
--- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
+++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
@@ -1,21 +1,21 @@
-Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe
-Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe
+Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe
+Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe
AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event
AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway
AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction
AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite
BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction
-BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene
-BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction
-BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway
-BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway
-BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein
-BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite
+BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene
+BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction
+BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway
+BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway
+BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein
+BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite
CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite
-CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene
+CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene
ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite
-ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite
-Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite
+ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite
+Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite
CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe
Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex
Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction
@@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$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 http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
-Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
-Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
-Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
-Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
-Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
+Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
+Gramene 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=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
+Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
+Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
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/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -77,15 +77,15 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction
-miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
-miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
+miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
+miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
NCBI Protein Np http://www.ncbi.nlm.nih.gov/protein http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 protein 1 urn:miriam:ncbiprotein ^\w+\d+(\.\d+)?$ NCBI Protein ncbiprotein protein
NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway pathway 1 urn:miriam:pid.pathway ^\w+$ NCI Pathway Interaction Database pid.pathway pathway
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/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ ensembl gene
+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
Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene
@@ -110,9 +110,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H
RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene
RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
-RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd 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 http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
+Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene 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
@@ -125,7 +125,7 @@ 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 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
+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
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
diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
index f20b733ea..560d65f42 100644
--- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
+++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
@@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116
Saccharomyces cerevisiae Yeast Sc 4932
Skeletonema marinoi Sm 267567
Solanum lycopersicum Tomato Sl 4081
+Solanum tuberosum St 4113
Sorex araneus Shrew Sa 42254
Sorghum bicolor Sorghum Sb 4558
Sus scrofa Pig Ss 9823
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
index 1c4891254..66cb63176 100644
--- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
+++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
@@ -1,21 +1,21 @@
-Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe
-Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe
+Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe
+Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe
AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event
AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway
AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction
AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite
BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction
-BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene
-BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction
-BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway
-BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway
-BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein
-BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite
+BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene
+BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction
+BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway
+BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway
+BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein
+BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite
CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite
-CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene
+CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene
ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite
-ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite
-Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite
+ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite
+Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite
CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe
Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex
Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction
@@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$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 http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
-Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
-Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
-Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
-Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
-Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
+Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
+Gramene 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=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
+Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
+Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
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/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -77,8 +77,8 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u
MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction
-miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
-miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
+miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
+miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
@@ -110,9 +110,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H
RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene
RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
-RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd 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 http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
+Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene 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
@@ -125,7 +125,7 @@ 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 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
+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
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
diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
index f20b733ea..560d65f42 100644
--- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
+++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
@@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116
Saccharomyces cerevisiae Yeast Sc 4932
Skeletonema marinoi Sm 267567
Solanum lycopersicum Tomato Sl 4081
+Solanum tuberosum St 4113
Sorex araneus Shrew Sa 42254
Sorghum bicolor Sorghum Sb 4558
Sus scrofa Pig Ss 9823
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
index df989ca7a..67f06fba0 100644
--- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java
+++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java
@@ -127,6 +127,15 @@ 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");
diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml
index b5c3a3c96..2cd2f9413 100644
--- a/org.bridgedb.file.orthoxml/pom.xml
+++ b/org.bridgedb.file.orthoxml/pom.xml
@@ -6,7 +6,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml
index e2e49b203..a2e97b835 100644
--- a/org.bridgedb.gui/pom.xml
+++ b/org.bridgedb.gui/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml
index d73e02894..feb7e76d3 100644
--- a/org.bridgedb.rdb.construct/pom.xml
+++ b/org.bridgedb.rdb.construct/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml
index 282d4c103..88c3a389e 100644
--- a/org.bridgedb.rdb/pom.xml
+++ b/org.bridgedb.rdb/pom.xml
@@ -7,7 +7,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java
index f9cf6b643..59ae298e6 100644
--- a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java
+++ b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java
@@ -61,6 +61,14 @@ public static void setup() {
@org.junit.jupiter.api.Test
public void testGdbProvider() throws ClassNotFoundException, IDMapperException, IOException{
+ // only for Java 11 and higher
+ String specVersion = System.getProperty("java.specification.version");
+ if (specVersion.contains(".")) specVersion = specVersion.substring(0, specVersion.indexOf('.'));
+ if (Integer.valueOf(specVersion) < 11) {
+ System.out.print("Only running testGdbProvider() for Java 11 or higher");
+ return;
+ }
+
Class.forName("org.bridgedb.file.IDMapperText");
ClassLoader classLoader = this.getClass().getClassLoader();
diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml
index af50b8cc1..50eec5bc7 100644
--- a/org.bridgedb.rdf/pom.xml
+++ b/org.bridgedb.rdf/pom.xml
@@ -6,7 +6,7 @@
bridgedb-bundle
org.bridgedb
- 3.1.1
+ 3.1.2
diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl
index 33127c1de..5b3bc8747 100644
--- a/org.bridgedb.rdf/resources/BioDataSource.ttl
+++ b/org.bridgedb.rdf/resources/BioDataSource.ttl
@@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ;
bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:fullName "BioCyc" ;
bridgeDB:systemCode "Bc" ;
- bridgeDB:mainUrl "http://biocyc.org" ;
+ bridgeDB:mainUrl "https://biocyc.org" ;
bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:fullName "BioGrid" ;
bridgeDB:systemCode "Bg" ;
- bridgeDB:mainUrl "http://thebiogrid.org/" ;
+ bridgeDB:mainUrl "https://thebiogrid.org/" ;
bridgeDB:idExample "31623" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "interaction" ;
@@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ;
bridgeDB:fullName "BioModels Database" ;
bridgeDB:systemCode "Bm" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ;
bridgeDB:idExample "BIOMD0000000048" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "pathway" ;
@@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ;
bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
bridgeDB:fullName "ChEBI" ;
bridgeDB:systemCode "Ce" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ;
bridgeDB:idExample "CHEBI:36927" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
@@ -115,7 +115,7 @@ bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ;
bridgeDB:fullName "Chemspider" ;
bridgeDB:systemCode "Cs" ;
- bridgeDB:mainUrl "http://www.chemspider.com/" ;
+ bridgeDB:mainUrl "https://www.chemspider.com/" ;
bridgeDB:idExample "56586" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
@@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Arabidopsis" ;
bridgeDB:systemCode "EnAt" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "ATMG01360-TAIR-G" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Genes DB" ;
bridgeDB:systemCode "Gg" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "GR:0060184" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Literature" ;
bridgeDB:systemCode "Gl" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "6200" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "gene" ;
@@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Maize" ;
bridgeDB:systemCode "EnZm" ;
- bridgeDB:mainUrl "http://www.ensembl.org" ;
+ bridgeDB:mainUrl "https://www.ensembl.org" ;
bridgeDB:idExample "GRMZM2G174107" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Pathway" ;
bridgeDB:systemCode "Gp" ;
- bridgeDB:mainUrl "http://www.gramene.org/pathway" ;
+ bridgeDB:mainUrl "https://www.gramene.org/pathway" ;
bridgeDB:idExample "AAH72400" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "pathway" ;
@@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Rice" ;
bridgeDB:systemCode "EnOj" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "osa-MIR171a" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ;
bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ;
bridgeDB:fullName "miRBase mature sequence" ;
bridgeDB:systemCode "Mbm" ;
- bridgeDB:mainUrl "http://www.mirbase.org/" ;
+ bridgeDB:mainUrl "https://www.mirbase.org/" ;
bridgeDB:idExample "MIMAT0000001" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ;
bridgeDB:DataSource_RGD a bridgeDB:DataSource ;
bridgeDB:fullName "RGD" ;
bridgeDB:systemCode "R" ;
- bridgeDB:mainUrl "http://rgd.mcw.edu/" ;
+ bridgeDB:mainUrl "https://rgd.mcw.edu/" ;
bridgeDB:idExample "2018" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ;
bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
bridgeDB:fullName "Rice Ensembl Gene" ;
bridgeDB:systemCode "Os" ;
- bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ;
+ bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ;
bridgeDB:idExample "LOC_Os04g54800" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ;
bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:fullName "TAIR" ;
bridgeDB:systemCode "A" ;
- bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ;
+ bridgeDB:mainUrl "https://www.arabidopsis.org/" ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl
index 950b8ac7a..cd15ae023 100644
--- a/org.bridgedb.rdf/resources/DataSource.ttl
+++ b/org.bridgedb.rdf/resources/DataSource.ttl
@@ -38,32 +38,32 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ;
bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:fullName "BioCyc" ;
bridgeDB:systemCode "Bc" ;
- bridgeDB:mainUrl "http://biocyc.org" ;
+ bridgeDB:mainUrl "https://biocyc.org" ;
bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasUriPattern .
bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:fullName "BioGrid" ;
bridgeDB:systemCode "Bg" ;
- bridgeDB:mainUrl "http://thebiogrid.org/" ;
+ bridgeDB:mainUrl "https://thebiogrid.org/" ;
bridgeDB:idExample "31623" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "interaction" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ;
bridgeDB:fullName "BioModels Database" ;
bridgeDB:systemCode "Bm" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ;
bridgeDB:idExample "BIOMD0000000048" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "pathway" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasUriPattern .
@@ -134,16 +134,16 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ;
bridgeDB:idExample "CCDS43989" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern .
+ bridgeDB:hasPrimaryUriPattern .
bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
bridgeDB:fullName "ChEBI" ;
bridgeDB:systemCode "Ce" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ;
bridgeDB:idExample "CHEBI:36927" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasUriPattern ; #Deprecated
bridgeDB:hasIdentifiersOrgPattern .
@@ -286,16 +286,16 @@ bridgeDB:DataSource_ChEMBL_target_component a bridgeDB:DataSource ;
bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ;
bridgeDB:fullName "Chemspider" ;
bridgeDB:systemCode "Cs" ;
- bridgeDB:mainUrl "http://www.chemspider.com/" ;
+ bridgeDB:mainUrl "https://www.chemspider.com/" ;
bridgeDB:idExample "56586" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasUriPattern ;
- bridgeDB:hasUriPattern ;
- bridgeDB:hasUriPattern ;
- bridgeDB:hasUriPattern .
+ bridgeDB:hasUriPattern ;
+ bridgeDB:hasUriPattern ;
+ bridgeDB:hasUriPattern .
bridgeDB:DataSource_Cint a bridgeDB:DataSource ;
bridgeDB:fullName "Cint" ;
@@ -366,7 +366,7 @@ bridgeDB:DataSource_drugbankv4Target a bridgeDB:DataSource ;
bridgeDB:fullName "Drugbank Target v4" ;
bridgeDB:systemCode "drugbankv4.target" ;
bridgeDB:idExample "BE0000938" ;
- bridgeDB:hasRegexPattern "^BE\\d{7}$" ;
+ bridgeDB:hasRegexPattern "^BE\\d{7}$" ;
bridgeDB:mainUrl "http://www.drugbank.ca/" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
@@ -379,6 +379,7 @@ bridgeDB:DataSource_drugbankDrugs a bridgeDB:DataSource ;
bridgeDB:systemCode "Dr" ;
bridgeDB:mainUrl "http://www.drugbank.ca/" ;
bridgeDB:idExample "DB00001" ;
+ bridgeDB:hasRegexPattern "^DB\\d{5,7}$" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
bridgeDB:hasPrimaryUriPattern ;
@@ -518,45 +519,45 @@ bridgeDB:DataSource_GOA a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Arabidopsis" ;
bridgeDB:systemCode "EnAt" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "ATMG01360-TAIR-G" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:Organism bridgeDB:Organism_At .
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Genes DB" ;
bridgeDB:systemCode "Gg" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "GR:0060184" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Literature" ;
bridgeDB:systemCode "Gl" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "6200" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern .
+ bridgeDB:hasPrimaryUriPattern .
bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Maize" ;
bridgeDB:systemCode "EnZm" ;
- bridgeDB:mainUrl "http://www.ensembl.org" ;
+ bridgeDB:mainUrl "https://www.ensembl.org" ;
bridgeDB:idExample "GRMZM2G174107" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern .
+ bridgeDB:hasPrimaryUriPattern .
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Pathway" ;
bridgeDB:systemCode "Gp" ;
- bridgeDB:mainUrl "http://www.gramene.org/pathway" ;
+ bridgeDB:mainUrl "https://www.gramene.org/pathway" ;
bridgeDB:idExample "AAH72400" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "pathway" .
@@ -564,7 +565,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Rice" ;
bridgeDB:systemCode "EnOj" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "osa-MIR171a" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
@@ -806,11 +807,11 @@ bridgeDB:CodeMapper_MGI a bridgeDB:CodeMapper ;
bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ;
bridgeDB:fullName "miRBase mature sequence" ;
bridgeDB:systemCode "Mbm" ;
- bridgeDB:mainUrl "http://www.mirbase.org/" ;
+ bridgeDB:mainUrl "https://www.mirbase.org/" ;
bridgeDB:idExample "MIMAT0000001" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ;
@@ -821,7 +822,7 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ;
bridgeDB:idExample "MI0000001" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_NASC_Gene a bridgeDB:DataSource ;
@@ -914,7 +915,7 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ;
bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ;
bridgeDB:systemCode "PW" ;
bridgeDB:xrefPrefix "PW:";
- bridgeDB:hasUriPattern ;
+ bridgeDB:hasUriPattern ;
bridgeDB:hasUriPattern ;
bridgeDB:hasUriPattern ;
bridgeDB:hasUriPattern ;
@@ -1036,24 +1037,24 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ;
bridgeDB:DataSource_RGD a bridgeDB:DataSource ;
bridgeDB:fullName "RGD" ;
bridgeDB:systemCode "R" ;
- bridgeDB:mainUrl "http://rgd.mcw.edu/" ;
+ bridgeDB:mainUrl "https://rgd.mcw.edu/" ;
bridgeDB:idExample "2018" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
- bridgeDB:hasUriPattern ;
+ bridgeDB:hasUriPattern ;
bridgeDB:hasUriPattern ;
bridgeDB:Organism bridgeDB:Organism_Rn .
bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
bridgeDB:fullName "Rice Ensembl Gene" ;
bridgeDB:systemCode "Os" ;
- bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ;
+ bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ;
bridgeDB:idExample "LOC_Os04g54800" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:Organism bridgeDB:Organism_Os ;
bridgeDB:hasRegexUriPattern .
@@ -1071,11 +1072,11 @@ bridgeDB:DataSource_SGD a bridgeDB:DataSource ;
bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:fullName "TAIR" ;
bridgeDB:systemCode "A" ;
- bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ;
+ bridgeDB:mainUrl "https://www.arabidopsis.org/" ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern .
bridgeDB:DataSource_TIGR a bridgeDB:DataSource ;
diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
index e97443446..0b72ed5d4 100644
--- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
+++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
@@ -504,11 +504,11 @@ bridgeDB:DataSource_BioCatalogue a bridgeDB:DataSource ;
bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:fullName "BioCyc" ;
bridgeDB:systemCode "Bc" ;
- bridgeDB:mainUrl "http://biocyc.org" ;
+ bridgeDB:mainUrl "https://biocyc.org" ;
bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^[A-Z-0-9]+(? ;
bridgeDB:type "interaction" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\d+$" ;
@@ -531,11 +531,11 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ;
bridgeDB:fullName "BioModels Database" ;
bridgeDB:systemCode "Bm" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ;
bridgeDB:idExample "BIOMD0000000048" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "pathway" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$" ;
@@ -832,7 +832,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ;
bridgeDB:idExample "CCDS43989" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^CCDS\\d+(\\.\\d+)?$" ;
@@ -921,11 +921,11 @@ bridgeDB:DataSource_CharProt a bridgeDB:DataSource ;
bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
bridgeDB:fullName "ChEBI" ;
bridgeDB:systemCode "Ce" ;
- bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ;
+ bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ;
bridgeDB:idExample "CHEBI:36927" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^CHEBI:\\d+$" ;
@@ -1055,16 +1055,16 @@ bridgeDB:DataSource_ChemIDplus a bridgeDB:DataSource ;
bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ;
bridgeDB:fullName "Chemspider" ;
bridgeDB:systemCode "Cs" ;
- bridgeDB:mainUrl "http://www.chemspider.com/" ;
+ bridgeDB:mainUrl "https://www.chemspider.com/" ;
bridgeDB:idExample "56586" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "metabolite" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\d+$" ;
dcterms:alternative "ChemSpider" ;
- bridgeDB:hasUriPattern , , , .
+ bridgeDB:hasUriPattern , , , .
bridgeDB:DataSource_Cint a bridgeDB:DataSource ;
bridgeDB:fullName "Cint" ;
@@ -2515,11 +2515,11 @@ bridgeDB:DataSource_GPCRDB a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Arabidopsis" ;
bridgeDB:systemCode "EnAt" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "ATMG01360-TAIR-G" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:Organism bridgeDB:Organism_At ;
bridgeDB:hasRegexPattern "AT[\\dCM]G\\d{5}\\-TAIR\\-G" ;
dcterms:alternative "Grameen Arabidopsis" .
@@ -2527,11 +2527,11 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Genes DB" ;
bridgeDB:systemCode "Gg" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "GR:0060184" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^GR\\:\\d+$" ;
@@ -2543,36 +2543,36 @@ bridgeDB:DataSource_Gramene_Growth_Stage_Ontology a bridgeDB:DataSource ;
bridgeDB:idExample "GRO:0007133" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^GRO\\:\\d+$" ;
- bridgeDB:hasUriPattern .
+ bridgeDB:hasUriPattern .
bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Literature" ;
bridgeDB:systemCode "Gl" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "6200" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
dcterms:alternative "Gramene Literature" .
bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Maize" ;
bridgeDB:systemCode "EnZm" ;
- bridgeDB:mainUrl "http://www.ensembl.org" ;
+ bridgeDB:mainUrl "https://www.ensembl.org" ;
bridgeDB:idExample "GRMZM2G174107" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
dcterms:alternative "Gramene Maize" .
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Pathway" ;
bridgeDB:systemCode "Gp" ;
- bridgeDB:mainUrl "http://www.gramene.org/pathway" ;
+ bridgeDB:mainUrl "https://www.gramene.org/pathway" ;
bridgeDB:idExample "AAH72400" ;
bridgeDB:primary "false"^^ ;
bridgeDB:type "pathway" ;
@@ -2584,7 +2584,7 @@ bridgeDB:DataSource_Gramene_protein a bridgeDB:DataSource ;
bridgeDB:idExample "78073" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\d+$" .
@@ -2595,7 +2595,7 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ;
bridgeDB:idExample "CQG5" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\w+$" .
@@ -2603,11 +2603,11 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Rice" ;
bridgeDB:systemCode "EnOj" ;
- bridgeDB:mainUrl "http://www.gramene.org/" ;
+ bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "osa-MIR171a" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
dcterms:alternative "Gramene Rice" .
bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ;
@@ -2616,11 +2616,11 @@ bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ;
bridgeDB:idExample "GR_tax:013681" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^GR\\_tax\\:\\d+$" ;
- bridgeDB:hasUriPattern .
+ bridgeDB:hasUriPattern .
bridgeDB:DataSource_GreenGenes a bridgeDB:DataSource ;
bridgeDB:fullName "GreenGenes" ;
@@ -3029,11 +3029,11 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ;
bridgeDB:idExample "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ;
- bridgeDB:hasUriPattern , , , .
+ bridgeDB:hasUriPattern , , , .
bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ;
bridgeDB:fullName "InChIKey" ;
@@ -3045,7 +3045,7 @@ bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-N])?" ;
- bridgeDB:hasUriPattern .
+ bridgeDB:hasUriPattern .
bridgeDB:DataSource_IntAct a bridgeDB:DataSource ;
bridgeDB:fullName "IntAct" ;
@@ -3799,11 +3799,11 @@ bridgeDB:DataSource_MIPModDB a bridgeDB:DataSource ;
bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ;
bridgeDB:fullName "miRBase mature sequence" ;
bridgeDB:systemCode "Mbm" ;
- bridgeDB:mainUrl "http://www.mirbase.org/" ;
+ bridgeDB:mainUrl "https://www.mirbase.org/" ;
bridgeDB:idExample "MIMAT0000001" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "MIMAT\\d{7}" ;
@@ -3816,12 +3816,12 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ;
bridgeDB:idExample "MI0000001" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "MI\\d{7}" ;
dcterms:alternative "miRBase Sequence" ;
- bridgeDB:hasUriPattern .
+ bridgeDB:hasUriPattern .
bridgeDB:DataSource_mirEX a bridgeDB:DataSource ;
bridgeDB:fullName "mirEX" ;
@@ -4608,7 +4608,7 @@ bridgeDB:DataSource_Pathway_Commons a bridgeDB:DataSource ;
bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ;
bridgeDB:fullName "Pathway Ontology" ;
bridgeDB:systemCode "PW" ;
- bridgeDB:mainUrl "http://rgd.mcw.edu/rgdweb/ontology/search.html" ;
+ bridgeDB:mainUrl "https://rgd.mcw.edu/rgdweb/ontology/search.html" ;
bridgeDB:idExample "PW:0000208" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
@@ -4616,12 +4616,12 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^PW:\\d{7}$" ;
- bridgeDB:hasUriPattern , .
+ bridgeDB:hasUriPattern , .
bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ;
bridgeDB:systemCode "PW" ;
bridgeDB:xrefPrefix "PW:" ;
- bridgeDB:hasUriPattern , , , , .
+ bridgeDB:hasUriPattern , , , , .
bridgeDB:DataSource_PATO a bridgeDB:DataSource ;
bridgeDB:fullName "PATO" ;
@@ -5195,7 +5195,7 @@ bridgeDB:DataSource_Rat_Genome_Database_qTL a bridgeDB:DataSource ;
bridgeDB:idExample "1354581" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\d+$" .
@@ -5206,7 +5206,7 @@ bridgeDB:DataSource_Rat_Genome_Database_strain a bridgeDB:DataSource ;
bridgeDB:idExample "5688061" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "unknown" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^\\d+$" .
@@ -5290,17 +5290,17 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ;
bridgeDB:DataSource_RGD a bridgeDB:DataSource ;
bridgeDB:fullName "RGD" ;
bridgeDB:systemCode "R" ;
- bridgeDB:mainUrl "http://rgd.mcw.edu/" ;
+ bridgeDB:mainUrl "https://rgd.mcw.edu/" ;
bridgeDB:idExample "2018" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:Organism bridgeDB:Organism_Rn ;
bridgeDB:hasRegexPattern "^\\d{4,7}$" ;
dcterms:alternative "Rat Genome Database" ;
- bridgeDB:hasUriPattern , .
+ bridgeDB:hasUriPattern , .
bridgeDB:DataSource_Rhea a bridgeDB:DataSource ;
bridgeDB:fullName "Rhea" ;
@@ -5318,11 +5318,11 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ;
bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
bridgeDB:fullName "Rice Ensembl Gene" ;
bridgeDB:systemCode "Os" ;
- bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ;
+ bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ;
bridgeDB:idExample "LOC_Os04g54800" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:Organism bridgeDB:Organism_Os ;
dcterms:alternative "Rice Ensembl Gene" .
@@ -5770,11 +5770,11 @@ bridgeDB:DataSource_T3DB a bridgeDB:DataSource ;
bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:fullName "TAIR" ;
bridgeDB:systemCode "A" ;
- bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ;
+ bridgeDB:mainUrl "https://www.arabidopsis.org/" ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^ ;
bridgeDB:type "gene" ;
- bridgeDB:hasPrimaryUriPattern ;
+ bridgeDB:hasPrimaryUriPattern ;
bridgeDB:hasIdentifiersOrgPattern ;
bridgeDB:hasIdentifiersOrgInfoPattern ;
bridgeDB:hasRegexPattern "^AT[1-5]G\\d{5}$" ;
@@ -6875,8 +6875,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ;
a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?accession=" .
- a bridgeDB:UriPattern ;
- bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?type=locus&name=" .
+