diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 417ccb74d..0d38b3f7e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,8 +7,22 @@ on: branches: [ series/3.1.0 ] jobs: - build: + java8: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Java + uses: actions/setup-java@v4 + with: + distribution: 'temurin' + java-version: 8 + cache: maven + - name: Build with Maven + run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql + + build: + needs: java8 runs-on: ubuntu-latest steps: diff --git a/CITATION.cff b/CITATION.cff index 716c1c9a7..cdd95bc91 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.1 -date-released: '2023-12-18' +version: 3.1.2 +date-released: '2024-07-30' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index dbeb70269..555e3e9a8 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.1`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.1 + 3.1.2 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.1' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.1' +'org.bridgedb:org.bridgedb.bio:jar:3.1.2' ``` @@ -58,6 +58,8 @@ able to compile with a simple: mvn clean install -Dgpg.skip ``` +When compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`. + You can find the libraries in the folder called "target", in each sublibrary folder (used to be called "dist" in ant). If you want to ignore failing tests, e.g. because you are not online, @@ -127,13 +129,13 @@ Making releases --------------- If it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb), -this `README.md` and `CITATION.cff` (for Zenodo). +this `README.md` and `CITATION.cff` (for Zenodo), as well as the `pom-java8.xml`. To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.2-SNAPSHOT +mvn versions:set -DnewVersion=3.1.2 mvn clean deploy ``` @@ -143,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.1-SNAPSHOT +mvn versions:set -DnewVersion=3.1.3-SNAPSHOT mvn clean deploy ``` diff --git a/UPGRADE_NOTES.md b/UPGRADE_NOTES.md index f6b3f5dab..53aa00618 100644 --- a/UPGRADE_NOTES.md +++ b/UPGRADE_NOTES.md @@ -1,35 +1,49 @@ -Upgrade notes to BridgeDb 2.0 +# Upgrade notes to BridgeDb 2.0 -1. Initialing data sources +## 1. Initialing data sources Replace +```java BioDataSource.init(); +``` with +```java DataSourceTxt.init(); +``` -2. Getting DataSource's +## 2. Getting DataSource's Replace +```java DataSource ds = DataSource.getBySystemCode("Ck"); +``` with +```java DataSource ds = DataSource.getExistingBySystemCode("Ck"); +``` Similarly, and more important: +```java DataSource ds = DataSource.getByFullName("PubChem-compound"); +``` with +```java DataSource ds = DataSource.getExistingByFullName("PubChem-compound"); +``` -The latter two new methods throw an IllegalArgumentException if the DataSource does not exist. +The latter two new methods throw an `IllegalArgumentException` if the `DataSource` does not exist. Use one of the following two methods to check first: +```java DataSource.systemCodeExists("Ck"); DataSource.fullNameExists("PubChem-compound"); +``` diff --git a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl index 42d8576ad..ffbb03311 100755 --- a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl +++ b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl @@ -743,7 +743,7 @@ %{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'], 'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'", "\'ID\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", + "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", "\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'PRIMARY KEY (ID)' @@ -863,7 +863,7 @@ %{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'], 'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", + "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", "\'ftp://rgd.mcw.edu/pub/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', @@ -916,8 +916,8 @@ %{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'], 'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", - "\'http://www.gramene.org\'"], + "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", + "\'https://www.gramene.org\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', @@ -926,8 +926,8 @@ %{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'], 'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'", "\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/pathway\'", "\'\'", - "\'http://www.gramene.org/pathway\'"], + "\'https://www.gramene.org/pathway\'", "\'\'", + "\'https://www.gramene.org/pathway\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', 'PRIMARY KEY (ID)' diff --git a/examples/pom.xml b/examples/pom.xml index 8f520b6c3..0c490e85b 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 5edbf57bb..d92cfc8fe 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..289fb0957 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -77,15 +77,15 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene NCBI Protein Np http://www.ncbi.nlm.nih.gov/protein http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 protein 1 urn:miriam:ncbiprotein ^\w+\d+(\.\d+)?$ NCBI Protein ncbiprotein protein NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway pathway 1 urn:miriam:pid.pathway ^\w+$ NCI Pathway Interaction Database pid.pathway pathway OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease -OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ ensembl gene +OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ gene ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene @@ -110,9 +110,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein @@ -125,7 +125,7 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..560d65f42 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv @@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..66cb63176 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -77,8 +77,8 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene @@ -110,9 +110,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein @@ -125,7 +125,7 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..560d65f42 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv @@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index df989ca7a..67f06fba0 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -127,6 +127,15 @@ public void testMIRIAMFeatures() throws Exception { assertEquals("chebi", chebi.getCompactIdentifierPrefix()); } + @org.junit.jupiter.api.Test + public void testEcoGene() throws Exception { + DataSource ecogene = DataSource.getExistingByFullName("EcoGene"); + assertNotNull(ecogene); + assertEquals("urn:miriam:ecogene:EG10173", ecogene.getMiriamURN("EG10173")); + assertNotNull(DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/")); + assertNotNull(DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/")); + } + @org.junit.jupiter.api.Test public void testPrefix() throws Exception { DataSource ds = DataSource.getExistingBySystemCode("L"); diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index b5c3a3c96..2cd2f9413 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index e2e49b203..a2e97b835 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index d73e02894..feb7e76d3 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 282d4c103..88c3a389e 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java index f9cf6b643..59ae298e6 100644 --- a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java +++ b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java @@ -61,6 +61,14 @@ public static void setup() { @org.junit.jupiter.api.Test public void testGdbProvider() throws ClassNotFoundException, IDMapperException, IOException{ + // only for Java 11 and higher + String specVersion = System.getProperty("java.specification.version"); + if (specVersion.contains(".")) specVersion = specVersion.substring(0, specVersion.indexOf('.')); + if (Integer.valueOf(specVersion) < 11) { + System.out.print("Only running testGdbProvider() for Java 11 or higher"); + return; + } + Class.forName("org.bridgedb.file.IDMapperText"); ClassLoader classLoader = this.getClass().getClassLoader(); diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index af50b8cc1..50eec5bc7 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 33127c1de..5b3bc8747 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; @@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; @@ -115,7 +115,7 @@ bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; @@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; @@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 950b8ac7a..cd15ae023 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -38,32 +38,32 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . @@ -134,16 +134,16 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasUriPattern ; #Deprecated bridgeDB:hasIdentifiersOrgPattern . @@ -286,16 +286,16 @@ bridgeDB:DataSource_ChEMBL_target_component a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -366,7 +366,7 @@ bridgeDB:DataSource_drugbankv4Target a bridgeDB:DataSource ; bridgeDB:fullName "Drugbank Target v4" ; bridgeDB:systemCode "drugbankv4.target" ; bridgeDB:idExample "BE0000938" ; - bridgeDB:hasRegexPattern "^BE\\d{7}$" ; + bridgeDB:hasRegexPattern "^BE\\d{7}$" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -379,6 +379,7 @@ bridgeDB:DataSource_drugbankDrugs a bridgeDB:DataSource ; bridgeDB:systemCode "Dr" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:idExample "DB00001" ; + bridgeDB:hasRegexPattern "^DB\\d{5,7}$" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; bridgeDB:hasPrimaryUriPattern ; @@ -518,45 +519,45 @@ bridgeDB:DataSource_GOA a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At . bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" . @@ -564,7 +565,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -806,11 +807,11 @@ bridgeDB:CodeMapper_MGI a bridgeDB:CodeMapper ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; @@ -821,7 +822,7 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_NASC_Gene a bridgeDB:DataSource ; @@ -914,7 +915,7 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:"; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; @@ -1036,24 +1037,24 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:Organism bridgeDB:Organism_Rn . bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; bridgeDB:hasRegexUriPattern . @@ -1071,11 +1072,11 @@ bridgeDB:DataSource_SGD a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_TIGR a bridgeDB:DataSource ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index e97443446..0b72ed5d4 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -504,11 +504,11 @@ bridgeDB:DataSource_BioCatalogue a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z-0-9]+(? ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; @@ -531,11 +531,11 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$" ; @@ -832,7 +832,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CCDS\\d+(\\.\\d+)?$" ; @@ -921,11 +921,11 @@ bridgeDB:DataSource_CharProt a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CHEBI:\\d+$" ; @@ -1055,16 +1055,16 @@ bridgeDB:DataSource_ChemIDplus a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; dcterms:alternative "ChemSpider" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -2515,11 +2515,11 @@ bridgeDB:DataSource_GPCRDB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At ; bridgeDB:hasRegexPattern "AT[\\dCM]G\\d{5}\\-TAIR\\-G" ; dcterms:alternative "Grameen Arabidopsis" . @@ -2527,11 +2527,11 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\:\\d+$" ; @@ -2543,36 +2543,36 @@ bridgeDB:DataSource_Gramene_Growth_Stage_Ontology a bridgeDB:DataSource ; bridgeDB:idExample "GRO:0007133" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GRO\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Literature" . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Maize" . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" ; @@ -2584,7 +2584,7 @@ bridgeDB:DataSource_Gramene_protein a bridgeDB:DataSource ; bridgeDB:idExample "78073" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -2595,7 +2595,7 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:idExample "CQG5" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\w+$" . @@ -2603,11 +2603,11 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Rice" . bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; @@ -2616,11 +2616,11 @@ bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; bridgeDB:idExample "GR_tax:013681" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\_tax\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_GreenGenes a bridgeDB:DataSource ; bridgeDB:fullName "GreenGenes" ; @@ -3029,11 +3029,11 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:idExample "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:fullName "InChIKey" ; @@ -3045,7 +3045,7 @@ bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-N])?" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_IntAct a bridgeDB:DataSource ; bridgeDB:fullName "IntAct" ; @@ -3799,11 +3799,11 @@ bridgeDB:DataSource_MIPModDB a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MIMAT\\d{7}" ; @@ -3816,12 +3816,12 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MI\\d{7}" ; dcterms:alternative "miRBase Sequence" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_mirEX a bridgeDB:DataSource ; bridgeDB:fullName "mirEX" ; @@ -4608,7 +4608,7 @@ bridgeDB:DataSource_Pathway_Commons a bridgeDB:DataSource ; bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:fullName "Pathway Ontology" ; bridgeDB:systemCode "PW" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/rgdweb/ontology/search.html" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/rgdweb/ontology/search.html" ; bridgeDB:idExample "PW:0000208" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -4616,12 +4616,12 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^PW:\\d{7}$" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:" ; - bridgeDB:hasUriPattern , , , , . + bridgeDB:hasUriPattern , , , , . bridgeDB:DataSource_PATO a bridgeDB:DataSource ; bridgeDB:fullName "PATO" ; @@ -5195,7 +5195,7 @@ bridgeDB:DataSource_Rat_Genome_Database_qTL a bridgeDB:DataSource ; bridgeDB:idExample "1354581" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5206,7 +5206,7 @@ bridgeDB:DataSource_Rat_Genome_Database_strain a bridgeDB:DataSource ; bridgeDB:idExample "5688061" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5290,17 +5290,17 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:Organism bridgeDB:Organism_Rn ; bridgeDB:hasRegexPattern "^\\d{4,7}$" ; dcterms:alternative "Rat Genome Database" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:fullName "Rhea" ; @@ -5318,11 +5318,11 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; dcterms:alternative "Rice Ensembl Gene" . @@ -5770,11 +5770,11 @@ bridgeDB:DataSource_T3DB a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^AT[1-5]G\\d{5}$" ; @@ -6875,8 +6875,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?accession=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?type=locus&name=" . + 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 37893c4cc..763f300fe 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 7152afd91..4d26f9632 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.1 + 3.1.2 compile org.bridgedb org.bridgedb.bio - 3.1.1 + 3.1.2 compile org.bridgedb org.bridgedb.rdb - 3.1.1 + 3.1.2 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 299b5d02a..dcd850997 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 4daabcfc8..9dd9273a2 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 51f1d0627..32b8fdd5a 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 5e8c6f957..7203717ab 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 9a3d64760..99572ef6c 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 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 ea4e50116..c1ea354c8 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 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.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 9d1369447..dc097d6e5 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 06ba63833..6b615cf78 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index d6b6ee1fa..4638f2530 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index badebf1ce..6d769698e 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 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.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 5245abf57..eaf9b5248 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index a3d85fcba..afb7fe1aa 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 272b44eec..ccd78fba1 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 22a1b841b..9aed75286 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 4ccb52e5f..3ac9a6a9b 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 51dace4ed..d641b271f 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2 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/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 3d10b72ab..6cc9da92d 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.1 +bridgedb.version=3.1.2 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/pom-java8.xml b/pom-java8.xml index 107aa4116..4b568673d 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.0.22 + 3.1.2 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database diff --git a/pom.xml b/pom.xml index 9ba7bc0b1..e8c9507fc 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.1 + 3.1.2 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database @@ -150,7 +150,7 @@ 1.6.8 true - ossrh + sso https://oss.sonatype.org/ true @@ -192,11 +192,11 @@ - ossrh + sso https://oss.sonatype.org/service/local/staging/deploy/maven2/ - ossrh + sso https://oss.sonatype.org/content/repositories/snapshots