diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 772e88a35..96ad9a4d2 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,9 +2,7 @@ name: build on: push: - branches: [ series/4.0 ] pull_request: - branches: [ series/4.0 ] jobs: build: @@ -12,9 +10,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Java - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: distribution: 'temurin' java-version: 17 @@ -22,6 +20,6 @@ jobs: - name: Build with Maven run: mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql - name: push JaCoCo stats to codecov.io - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 env: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/README.md b/README.md index 5fced022b..e38b83006 100644 --- a/README.md +++ b/README.md @@ -7,15 +7,15 @@ BridgeDb [![codecov](https://codecov.io/gh/bridgedb/BridgeDb/branch/master/graph/badge.svg?token=F0kJdoEt0x)](https://codecov.io/gh/bridgedb/BridgeDb) [![NWO](https://img.shields.io/badge/NWO%20Open%20Science-203.001.121-orange)](https://www.nwo.nl/en/projects/203001121) -BridgeDb is currently tested with Java 11 and higher (3.0.x releases and master branch). +BridgeDb is currently tested with Java 17 and higher (4.0.x releases). 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. +[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 `3.1.0`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `4.0.0`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.0 + 4.0.0 ``` @@ -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: '3.1.0' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '4.0.0' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.0' +'org.bridgedb:org.bridgedb.bio:jar:4.0.0' ``` @@ -133,7 +133,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.0 +mvn versions:set -DnewVersion=4.0.0 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/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 141b04c09..bbda15198 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..289fb0957 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$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/java/org/bridgedb/bio/Organism.java b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java index 2b0791061..ff8bf2377 100644 --- a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java +++ b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java @@ -92,6 +92,7 @@ public enum Organism { RattusNorvegicus("Rattus norvegicus", "Rn", "Rat", 10116), SaccharomycesCerevisiae("Saccharomyces cerevisiae", "Sc", "Yeast", 4932), SolanumLycopersicum("Solanum lycopersicum", "Sl", "Tomato", 4081), + SolanumTuberosum("Solanum tuberosum", "St", "Potato", 4113), SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567), SorexAraneus ("Sorex araneus", "Sa", "Shrew", 42254), 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..289fb0957 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/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -77,15 +77,15 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$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/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..5bd53714f 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 @@ -31,8 +31,14 @@ import java.lang.reflect.Method; import java.util.HashSet; import java.util.Set; +import java.util.regex.Pattern; import org.bridgedb.DataSource; +import org.bridgedb.DataSourcePatterns; +import org.junit.BeforeClass; +import org.junit.jupiter.api.BeforeAll; + +import static org.junit.jupiter.api.Assertions.*; /** @@ -41,6 +47,11 @@ */ public class DataSourceTxtTest { + @BeforeAll + public static void setUpSources() { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + } + @org.junit.jupiter.api.Test public void testUniqueSystemCodes() { Set codes = new HashSet(); @@ -127,6 +138,15 @@ 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.bio/src/test/java/org/bridgedb/bio/XrefTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/XrefTest.java new file mode 100644 index 000000000..7aafef028 --- /dev/null +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/XrefTest.java @@ -0,0 +1,25 @@ +package org.bridgedb.bio; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.bridgedb.DataSource; +import org.bridgedb.Xref; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class XrefTest { + + @BeforeAll + public static void setUpSources() { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + } + + @Test + public void testCheckCorrectBioregistryIdentifier() { + Xref xref = Xref.fromBioregistryIdentifier("ensembl:ENSGALG00000007562"); + assertNotNull(xref); + assertEquals("En:ENSGALG00000007562:T", xref.toString()); + } + +} diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index c83304d1e..7eed83328 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index f7dac777d..42f464c7f 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -80,8 +80,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 6755aec47..6a7d2b878 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -79,8 +79,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime 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/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=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arxiv.org/abs/" . @@ -7007,8 +7007,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bio2rdf.org/uniprot:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://biocyc.org/getid?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://biocyc.org/getid?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=" . @@ -10557,8 +10557,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://mi.caspur.it/PMDB/user/search.php?idsearch=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=" . @@ -10953,23 +10953,23 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rfam.sanger.ac.uk/family/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=" . @@ -11076,8 +11076,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tgr.pharma.openphacts.com/target/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://thebiogrid.org/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://thebiogrid.org/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tolweb.org/" . @@ -11292,22 +11292,22 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; bridgeDB:hasPrefix "http://www.cellsignal.com/reference/pathway/" ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".rdf" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.conceptwiki.org/concept/" . @@ -11347,8 +11347,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/arrayexpress/experiments/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/biomodels-main/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/biomodels/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/biosamples/browse.html?keywords=" . @@ -11363,11 +11363,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "https://www.ebi.ac.uk/chembl/target/inspect/" . @@ -11610,29 +11610,29 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.gpcr.org/7tm/proteins/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/genes/search_gene?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/genes/search_gene?acc=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/literature/pub_search?ref_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/literature/pub_search?ref_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/ontology/search?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/ontology/search?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/protein/protein_search?protein_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/protein/protein_search?protein_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/geneview?gene=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/geneview?gene=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" . @@ -11722,7 +11722,7 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=" . - a bridgeDB:UriPattern ; + a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizesequence.org/Zea_mays/Gene/Summary?g=" . a bridgeDB:UriPattern ; @@ -11734,11 +11734,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://mirbase.org/mature/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=" . @@ -11764,8 +11764,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/biosystems/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&%3BDATA=" . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index ac92510e3..6b85d16d7 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -47,9 +47,9 @@ BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch BindingDB bindingDB http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id 22360 unknown 1 urn:miriam:bindingDB ^\d+$ BioCarta Pathway biocarta.pathway http://www.biocarta.com/pathfiles/$id.asp h_aktPathway unknown 1 urn:miriam:biocarta.pathway ^([hm]\_)?\w+Pathway$ BioCatalogue biocatalogue.service https://www.biocatalogue.org/services/$id 614 unknown 1 urn:miriam:biocatalogue.service ^\d+$ -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^[A-Z-0-9]+(? ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1003,7 +1003,7 @@ Each page contains information about a particular group, with pages linked one t "USA"^^ ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1313,7 +1313,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -1329,7 +1329,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -2236,7 +2236,7 @@ The interactions include direct (physical) and indirect (functional) association a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -3203,7 +3203,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3368,7 +3368,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3781,7 +3781,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3904,7 +3904,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4134,7 +4134,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -4274,7 +4274,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4461,7 +4461,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4551,7 +4551,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4945,7 +4945,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Medical College of Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -5126,7 +5126,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -5431,7 +5431,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Bioinformatics Research Group, SRI International, California"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -5451,7 +5451,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5510,7 +5510,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5875,7 +5875,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6485,7 +6485,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6555,7 +6555,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7041,7 +7041,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7093,7 +7093,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7265,7 +7265,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -8447,7 +8447,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -8545,7 +8545,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -9346,7 +9346,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "Canada"^^ ; "Ontario Cancer Institute"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -9518,7 +9518,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -9925,7 +9925,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -10534,7 +10534,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "98"^^ ; @@ -12015,7 +12015,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -12342,7 +12342,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "European Bioinformatics Institute, Hinxton, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -12408,7 +12408,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "USA"^^ ; "Medical College of Wisconsin, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -13094,7 +13094,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -13327,7 +13327,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14443,7 +14443,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14554,7 +14554,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14576,7 +14576,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -14618,7 +14618,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -16492,7 +16492,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -17403,7 +17403,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -18125,7 +18125,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index 362e8b4ad..f7a62083e 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java @@ -95,7 +95,7 @@ public static void refreshUriPatterns() throws BridgeDBException{ if (initialized){ return; } - DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java index 32bd0d745..5b7182e60 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java @@ -92,7 +92,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException // for (String multiple:multiples){ // checkMultiple(repositoryConnection, multiple); // } - Reporter.println("Registry read in. Now loading DataSources"); + Reporter.println("Registry read in. Now loading DataSources from the in memory store"); loadData(repositoryConnection); } catch (Exception ex) { throw new BridgeDBException ("Error parsing RDF inputStream: " + ex.getMessage(), ex); @@ -134,7 +134,7 @@ public static void init() throws BridgeDBException{ public static void saveRegister() throws BridgeDBException { try { URL url = new URL(MIRAM_REGISTRY_URI); - Reporter.println("Readng " + url); + Reporter.println("Reading " + url); InputStream inputStream = url.openStream(); InputStreamReader inputReader = new InputStreamReader(inputStream); BufferedReader inputBuffer = new BufferedReader(inputReader); @@ -204,7 +204,7 @@ private DataSource readDataSource(RepositoryConnection repositoryConnection, Res UriPattern.register(identiferOrgBase + "$id", sysCode, UriPatternType.identifiersOrgPatternSimple); String identifersOrgInfoBase = identiferOrgBase.replace("identifiers.org","info.identifiers.org"); UriPattern.register(identifersOrgInfoBase + "$id", sysCode, UriPatternType.identifiersOrgPatternInfo); - + DataSource ds = DataSource.register(sysCode, fullName) .identifiersOrgBase(identiferOrgBase) .asDataSource(); diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index 8902f8567..29f328e3c 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -3,19 +3,23 @@ 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 . a bridgeDB:uriPattern ; bridgeDB:hasPrefix "http://identifiers.org/chemspider/" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . - a bridgeDB:uriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" ; + bridgeDB:hasPostfix "" ; + bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index 5e084af37..2b4e8fa58 100644 --- a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java +++ b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java @@ -100,7 +100,7 @@ public void testGetUriPatterns() throws BridgeDBException{ BridgeDBRdfHandler.parseRdfInputStream(dataSourceStream); Set result = UriPattern.byCodeAndType("Cs", UriPatternType.mainUrlPattern); assertFalse("Could not find main URL pattern for Cs", result.isEmpty()); - UriPattern pattern = UriPattern.existingByPattern("http://www.chemspider.com/Chemical-Structure.$id.html"); + UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/$id"); assertThat (result, hasItem(pattern)); // pattern = UriPattern.existingOrCreateByPattern("http://identifiers.org/chemspider/$id"); // assertThat (result, hasItem(pattern)); diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index fd6d87d62..acbfccdad 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -47,8 +47,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 184fb625d..e3d344a16 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 3133c7344..9f4ddfe0a 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl index 8b7f06aa8..b83034c73 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl @@ -30,11 +30,11 @@ pav:createdOn "2014-11-03"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl index 43a8723fe..402a2dbae 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl @@ -25,11 +25,11 @@ dcterms:created "2014-11-21"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl index 6b66cd9e9..09c540d2a 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl index c5e22fc58..47e9e5701 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl index 8fde9b3ba..57e7f7dfa 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl @@ -25,7 +25,7 @@ dcterms:created "2014-11-21"^^xsd:date . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 8aa65e39a..ed58dc561 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -64,8 +64,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.uri.sql/resources/graph.properties b/org.bridgedb.uri.sql/resources/graph.properties index c77029660..ab351ded6 100644 --- a/org.bridgedb.uri.sql/resources/graph.properties +++ b/org.bridgedb.uri.sql/resources/graph.properties @@ -80,10 +80,10 @@ context.chebi1.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id context.chebi1.graph http://www.ebi.ac.uk/chebi context.chebi2.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi2.graph http://www.ebi.ac.uk/chebi/direct +context.chebi2.graph https://www.ebi.ac.uk/chebi/direct context.chebi3.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi3.graph http://www.ebi.ac.uk/chebi/inference +context.chebi3.graph https://www.ebi.ac.uk/chebi/inference context.enzyme1.pattern.1 http://purl.uniprot.org/enzyme/$id context.enzyme1.graph http://purl.uniprot.org/enzyme diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java index f3c442a60..76065ee22 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java @@ -449,7 +449,7 @@ public IdSysCodePair toIdSysCodePair(String uri) throws BridgeDBException { //Know dulicate prefixes of this type include //http://www.kegg.jp/entry/ //http://www.ebi.ac.uk/ontology-lookup/?termId= - //http://www.gramene.org/db/ontology/search?id= + //https://www.gramene.org/db/ontology/search?id= //http://stke.sciencemag.org/cgi/cm/stkecm; //http://purl.uniprot.org/uniprot/ //http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name= diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java index 8d12943bd..38040182b 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java @@ -192,7 +192,7 @@ public static void setupUriPatterns() throws BridgeDBException{ DataSourcePatterns.registerPattern(DataSource2, Pattern.compile("^\\d+$")); uriPattern1 = UriPattern.register(uriSpace1, dataSource1Code, UriPatternType.dataSourceUriPattern); uriPattern2 = UriPattern.register(uriSpace2, dataSource2Code, UriPatternType.dataSourceUriPattern); - uriPattern2 = UriPattern.register("http://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); + uriPattern2 = UriPattern.register("https://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace2a + "$id", dataSource2Code, UriPatternType.dataSourceUriPattern); uriPattern3 = UriPattern.register(uriSpace3, dataSource3Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace3a + "$id", dataSource3Code, UriPatternType.dataSourceUriPattern); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java index d7662147a..e1cca43a5 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java @@ -129,10 +129,10 @@ public void testMappingNoLink() throws Exception { assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @@ -156,10 +156,10 @@ public void testMappingNoLinkFixedPredicate() throws Exception { assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); IRI mapSet1Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); IRI mapSet1_3Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); @@ -196,10 +196,10 @@ public void testMappingWithLink() throws Exception { assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @Test @@ -220,10 +220,10 @@ public void testMappingWithLinkOverride() throws Exception { assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } } diff --git a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java index 45d680a78..9646affe0 100644 --- a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java +++ b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java @@ -28,7 +28,7 @@ * This is required for xrefs like "ChEBI" * These refs contain "CHEBI:" as part of the id. Such as CHEBI:36927 * Which is fine for URIs like: - * http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or + * https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or * http://identifiers.org/obo.chebi/CHEBI:36927 * but does not work for others like: * http://purl.org/obo/owl/CHEBI#CHEBI_36927 or diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 30715e164..6a3028145 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -16,24 +16,24 @@ target/classes ${project.artifactId}-${project.version} target/test-classes - src + src/main/java scripts - test + src/test/java - resources + src/main/resources - test-resources + src/test/resources org.apache.felix maven-bundle-plugin - 5.1.1 + ${felix.version} true @@ -57,7 +57,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF @@ -80,5 +80,35 @@ ${project.parent.version} compile + + org.bridgedb + org.bridgedb.bio + ${project.parent.version} + test + + + org.junit.platform + junit-platform-surefire-provider + 1.3.2 + test + + + org.junit.jupiter + junit-jupiter-engine + ${junit5.jupiter.version} + test + + + org.junit.vintage + junit-vintage-engine + ${junit5.jupiter.version} + test + + + org.junit.jupiter + junit-jupiter-api + ${junit5.jupiter.version} + test + diff --git a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java b/org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java similarity index 100% rename from org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java rename to org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java new file mode 100644 index 000000000..645f2e75d --- /dev/null +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -0,0 +1,49 @@ +// Copyright 2024 Egon Willighagen +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +package org.bridgedb.webservice.bridgerest; + +import static org.junit.Assert.assertNotSame; +import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.util.Set; + +import org.bridgedb.DataSource; +import org.bridgedb.IDMapperException; +import org.bridgedb.Xref; +import org.bridgedb.bio.DataSourceTxt; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class BridgeRestTest { + + private static BridgeRest service; + + @BeforeAll + public static void init() throws IDMapperException { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + BridgeRestTest.service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + assertTrue(service.isConnected()); + } + + @Test + public void testMap() throws IDMapperException { + assertNotNull(service); + assertTrue(service.isConnected()); + Set mappings = service.mapID(new Xref("CHEBI:123", DataSource.getExistingBySystemCode("Ce"))); + assertNotSame(0, mappings.size()); + } +} diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 637ac7145..1bf0e7ef3 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -23,12 +23,17 @@ ${junit5.jupiter.version} test - + org.junit.jupiter junit-jupiter-api ${junit5.jupiter.version} test + + org.mockito + mockito-core + 1.10.19 + bridgedb-bundle @@ -57,7 +62,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -81,7 +86,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 2c8712d5a..1487399ae 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -973,10 +973,10 @@ public static DataSource getByMiriamBase(String base) * @return the DataSource for a given base, or null if the base is invalid or unknown. */ public static DataSource getByIdentiferOrgBase(String base) { - if (base == null || !base.startsWith (IDENTIFIERS_ORG_PREFIX)) - { - return null; - } + if (base == null) return null; + // support the HTTPS variant too + base = base.replace("https://identifiers.org", "http://identifiers.org"); + if (!base.startsWith (IDENTIFIERS_ORG_PREFIX)) return null; String key = base.substring(IDENTIFIERS_ORG_PREFIX.length()); if (key.endsWith("/")){ diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourcePatternsTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourcePatternsTest.java new file mode 100644 index 000000000..cfa44b427 --- /dev/null +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourcePatternsTest.java @@ -0,0 +1,44 @@ +/*Copyright (c) 2024 Youp Hendriks + * + *Licensed under the Apache License, Version 2.0 (the "License"); + *you may not use this file except in compliance with the License. + *You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 + * + *Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, + *WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + *See the License for the specific language governing permissions and limitations under the License. + */ +package org.bridgedb; + +import static org.junit.jupiter.api.Assertions.*; +import org.junit.jupiter.api.DisplayName; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Assertions; + +/** + * Tests the {@link org.bridgedb.DataSourcePatterns} class. + * + * @author youphendriks + */ +public class DataSourcePatternsTest { + + protected static DataSource key; + + @Test + @DisplayName("Test getDataSourceMatches class, valid input") + public void testgetDataSourceMatchesValid() { + assertNotNull(DataSourcePatterns.getDataSourceMatches("F")); + } + + @Disabled + @Test + @DisplayName("Test getDataSourceMatches class, invalid input") + public void testgetDataSourceMatchesInvalid() { + Assertions.assertThrows(IllegalArgumentException.class, + () -> { + DataSourcePatterns.getDataSourceMatches(""); + }); + } + +} diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java index 4eab3aa5c..c782b6a30 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java @@ -375,7 +375,9 @@ public void testBuilders() { .alternative("MetaboLoci Alternative") .asDataSource(); assertEquals("Ecogene",DataSource.getByMiriamBase("urn:miriam:ecogene").toString()); - assertEquals("urn:miriam:ecogene:urn%3Amiriam%3Aecogene",source3.getMiriamURN("urn:miriam:ecogene").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/").toString()); + assertEquals("urn:miriam:ecogene:EG10173",source3.getMiriamURN("EG10173").toString()); DataSource source4 = DataSource.register("Ect", "EPA CompTox") .urnBase("urn:miriam:Ect") diff --git a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index 7b1c83849..2d5a4d312 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java +++ b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java @@ -71,7 +71,7 @@ public abstract class IDMapperTestBase { protected static String badKey; protected static final String uriSpace1 = "http://www.conceptwiki.org/concept/$id"; - protected static final String uriSpace2 = "http://www.chemspider.com/Chemical-Structure.$id.html"; + protected static final String uriSpace2 = "https://www.chemspider.com/Chemical-Structure.$id.html"; protected static final String uriSpace3 = "http://chemistry.openphacts.org/OPS$id"; @BeforeAll @@ -87,16 +87,16 @@ public abstract class IDMapperTestBase { public static void setupXref() throws IDMapperException{ //If the actual source to be tested does not contain these please overwrite with ones that do exist. dataSource1Code = "ConceptWiki"; - DataSource1 = DataSource.register(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) + DataSource1 = DataSource.mock(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) .idExample("33a28bb2-35ed-4d94-adfd-3c96053cbaaf").asDataSource(); dataSource2Code = "Cs"; - DataSource2 = DataSource.register(dataSource2Code, "Chemspider").urlPattern(uriSpace2) + DataSource2 = DataSource.mock(dataSource2Code, "Chemspider").urlPattern(uriSpace2) .idExample("56586").asDataSource(); dataSource3Code = "OPS-CRS"; - DataSource3 = DataSource.register(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) + DataSource3 = DataSource.mock(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) .idExample("8").asDataSource(); //This DataSource MUST not be supported - DataSourceBad = DataSource.register("TestDSBad", "TestDSBad") + DataSourceBad = DataSource.mock("TestDSBad", "TestDSBad") .urlPattern("http://www.NotInTheURlMapper.com#$id").asDataSource(); //Set of Xrefs that are expected to map together. diff --git a/org.bridgedb/src/test/java/org/bridgedb/XrefTest.java b/org.bridgedb/src/test/java/org/bridgedb/XrefTest.java index 238e434db..fc9af7381 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/XrefTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/XrefTest.java @@ -19,8 +19,6 @@ import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotSame; import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; @@ -196,4 +194,5 @@ public void testToString() { public void testGetKnownUrl() { System.out.println(new Xref("CHEBI:17855", CHEBI, true).getKnownUrl()); } + } diff --git a/pom.xml b/pom.xml index 33e41aa09..3d20ddfd3 100644 --- a/pom.xml +++ b/pom.xml @@ -44,11 +44,12 @@ UTF-8 UTF-8 1.2 - 3.2.14 + 3.6.4 + 5.1.9 2.2 1.10 2.22.0 - 8.0.33 + 9.0.0 Tomcat 3.4 4.3.8 @@ -149,7 +150,7 @@ 1.6.8 true - ossrh + sso https://oss.sonatype.org/ true @@ -188,7 +189,7 @@ org.apache.maven.plugins maven-enforcer-plugin - 3.3.0 + 3.5.0 enforce-maven @@ -198,7 +199,7 @@ - 3.2.5 + 3.6.3 17 @@ -215,11 +216,11 @@ - ossrh + sso https://oss.sonatype.org/service/local/staging/deploy/maven2/ - ossrh + sso https://oss.sonatype.org/content/repositories/snapshots @@ -340,4 +341,11 @@ https://github.com/bridgedb/BridgeDb/issues + + + mvnrepository + https://mvnrepository.com/artifact/ + + +