From 91b9a9e5e7834c5e26737f029f77b648d6a7af25 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Fri, 26 Jul 2024 07:51:27 +0200 Subject: [PATCH 01/22] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 8f520b6c3..fcebe7a70 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 5edbf57bb..b63dda2b2 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-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index b5c3a3c96..194f6548e 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-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index e2e49b203..1655d6b1a 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-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index d73e02894..d45ad5df8 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-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 282d4c103..61d780844 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-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index af50b8cc1..83ca9b27a 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-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 37893c4cc..c0555e252 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-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 7152afd91..9889d24d9 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-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.1 + 3.1.2-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.1 + 3.1.2-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 299b5d02a..2a6fdd71a 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-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 4daabcfc8..ecb265353 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-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 51f1d0627..37768a064 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-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 5e8c6f957..8bce22c78 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-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 9a3d64760..cb9f80dbe 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-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index ea4e50116..379b9ba3d 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-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 9d1369447..69919c820 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-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 06ba63833..a350d9c72 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-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index d6b6ee1fa..30c55a733 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-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index badebf1ce..3aaaeeb59 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-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 5245abf57..c30eb03a2 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-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index a3d85fcba..eea6d5376 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-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 272b44eec..308d74fc9 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-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 22a1b841b..68d3bdfe9 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-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 4ccb52e5f..fba9a3dd9 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-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 51dace4ed..e3881be63 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-SNAPSHOT diff --git a/pom.xml b/pom.xml index 9ba7bc0b1..d2dbb521c 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.1 + 3.1.2-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 88e5bbca0d15ca5d3c3589a77c6a61ce6de5bec1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:37:18 +0200 Subject: [PATCH 02/22] Added a line on how to compile with Java 8 (e.g. for PathVisio) --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index dbeb70269..847361b70 100644 --- a/README.md +++ b/README.md @@ -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, From 3414c198bbb8c7c394df348c13699487340c31bd Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:51:30 +0200 Subject: [PATCH 03/22] Added some syntax highlighting --- UPGRADE_NOTES.md | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) 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"); +``` From 4bea7ea599363f1336c1d05a68a75c764675f50b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:52:58 +0200 Subject: [PATCH 04/22] BridgeDb Datasources 202407252 --- .../org/bridgedb/bio/datasources.tsv | 34 +++++++++---------- .../resources/org/bridgedb/bio/organisms.tsv | 1 + .../org/bridgedb/bio/datasources.tsv | 32 ++++++++--------- .../resources/org/bridgedb/bio/organisms.tsv | 1 + 4 files changed, 35 insertions(+), 33 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..770e6c833 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 @@ -35,9 +35,9 @@ GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nucco 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 Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$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=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene Gramene Pathway Gp 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=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene @@ -77,7 +77,7 @@ 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=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$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/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$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 @@ -85,7 +85,7 @@ NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 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=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene @@ -110,7 +110,7 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$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=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene @@ -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..bb0f7d8cb 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 @@ -35,9 +35,9 @@ GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nucco 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 Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$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=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene Gramene Pathway Gp 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=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene @@ -77,7 +77,7 @@ 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=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$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/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$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 @@ -110,7 +110,7 @@ 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=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene @@ -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 From f330b5cc4bf27ccff8e1b98ed6b712e8d82278c2 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:09:24 +0200 Subject: [PATCH 05/22] Use https for ChemSpider --- org.bridgedb.rdf/resources/BioDataSource.ttl | 2 +- org.bridgedb.rdf/resources/DataSource.ttl | 10 +++--- .../resources/IdentifiersOrgDataSource.ttl | 32 +++++++++---------- .../resources/IdentifiersOrgDataSource.txt | 4 +-- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 12 +++---- org.bridgedb.rdf/test-data/DataSourceMin.ttl | 8 ++--- .../rdf/DataSourceComparatorTest.java | 2 +- .../src/test/resources/test-data/cs-ops.ttl | 4 +-- .../resources/test-data/cs-ops_lensed.ttl | 4 +-- .../src/test/resources/test-data/cw-cs.ttl | 2 +- .../test/resources/test-data/cw-cs_lensed.ttl | 2 +- .../resources/test-data/ops-ops_lensed.ttl | 2 +- .../org/bridgedb/uri/UriListenerTest.java | 2 +- .../org/bridgedb/uri/UriMapperRdfTest.java | 32 +++++++++---------- .../java/org/bridgedb/IDMapperTestBase.java | 2 +- 15 files changed, 60 insertions(+), 60 deletions(-) diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 33127c1de..52ef12bcb 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -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" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 950b8ac7a..91f9b7d43 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -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" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index e97443446..cb04c8a2a 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -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+$" ; dcterms:alternative "ChemSpider" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -3029,11 +3029,11 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:idExample "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - 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" ; @@ -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/" . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index ac92510e3..917d59c9e 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -94,7 +94,7 @@ LinkedChemistry ChEMBL target linkedchemistry.chembl.target http://l ChemDB chemdb http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id 3966782 unknown 1 urn:miriam:chemdb ^\d+$ Chemical Component Dictionary pdb-ccd http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 unknown 1 urn:miriam:pdb-ccd ^\w{3}$ ChemIDplus chemidplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider Cint C probe 0 CLDB cldb http://bioinformatics.istge.it/hypercldb/$id.html cl3603 unknown 1 urn:miriam:cldb ^cl\d+$ ClinicalTrials.gov clinicaltrials http://clinicaltrials.gov/ct2/show/$id NCT00222573 unknown 1 urn:miriam:clinicaltrials ^NCT\d{8}$ @@ -266,7 +266,7 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 ILMN_\d+ Illumina IMEx imex http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id IM-12080-80 unknown 1 urn:miriam:imex ^IM-\d+(-?)(\d+?)$ IMGT HLA imgt.hla http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$id A*01:01:01:01 unknown 1 urn:miriam:imgt.hla ^[A-Z0-9*:]+$ IMGT LIGM imgt.ligm http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+%5BIMGT%3A%27$id%27%5D M94112 unknown 1 urn:miriam:imgt.ligm ^M\d+$ -InChI inchi http://www.chemspider.com/$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 unknown 1 urn:miriam:inchi ^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$ +InChI inchi https://www.chemspider.com/$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 unknown 1 urn:miriam:inchi ^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$ InChIKey inchikey http://cactus.nci.nih.gov/chemical/structure/$id/names RYYVLZVUVIJVGH-UHFFFAOYSA-N unknown 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-N])? IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct IntAct Molecule intact.molecule http://www.ebi.ac.uk/intact/molecule/$id EBI-366083 unknown 1 urn:miriam:intact.molecule ^EBI\-[0-9]+$ diff --git a/org.bridgedb.rdf/resources/MiriamRegistry.ttl b/org.bridgedb.rdf/resources/MiriamRegistry.ttl index 4bed0d74c..10dc666bf 100644 --- a/org.bridgedb.rdf/resources/MiriamRegistry.ttl +++ b/org.bridgedb.rdf/resources/MiriamRegistry.ttl @@ -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 . @@ -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 ; @@ -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 . @@ -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 ; @@ -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 . diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index 8902f8567..c69676afd 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -3,19 +3,19 @@ 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 . diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index 5e084af37..edfe9769d 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.$id.html"); + UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/Chemical-Structure.$id.html"); assertThat (result, hasItem(pattern)); // pattern = UriPattern.existingOrCreateByPattern("http://identifiers.org/chemspider/$id"); // assertThat (result, hasItem(pattern)); 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/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/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index 7b1c83849..bf17d16b4 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 From eef95263cbf7c2f352b1712631de46dc57e0f318 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:48:16 +0200 Subject: [PATCH 06/22] Only initialize if not done already --- org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index 362e8b4ad..d178a5196 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() == 0) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); From 96bdb86683992bfa0e767a092d075618a4db8d9c Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:48:44 +0200 Subject: [PATCH 07/22] Fixed a minor typo --- .../org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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..85ab7b114 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 @@ -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); From d05ee7f1d27ec72e57022b2452b024824fdfaf46 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:49:18 +0200 Subject: [PATCH 08/22] Mock new datasources, to not cause URL overwrite errors --- .../src/test/java/org/bridgedb/IDMapperTestBase.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index bf17d16b4..2d5a4d312 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java +++ b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java @@ -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#$id").asDataSource(); //Set of Xrefs that are expected to map together. From 194aba640dd4b4a048aa757b291ad35a48d327ae Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:49:40 +0200 Subject: [PATCH 09/22] Updated to match the new BridgeDb Datasources version --- org.bridgedb.rdf/resources/DataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt | 2 +- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 2 +- org.bridgedb.rdf/test-data/DataSourceMin.ttl | 6 +++++- .../test/org/bridgedb/rdf/DataSourceComparatorTest.java | 2 +- 6 files changed, 10 insertions(+), 6 deletions(-) diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 91f9b7d43..231929112 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -290,7 +290,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index cb04c8a2a..f8a350259 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -1059,7 +1059,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index 917d59c9e..924e51b36 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -94,7 +94,7 @@ LinkedChemistry ChEMBL target linkedchemistry.chembl.target http://l ChemDB chemdb http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id 3966782 unknown 1 urn:miriam:chemdb ^\d+$ Chemical Component Dictionary pdb-ccd http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 unknown 1 urn:miriam:pdb-ccd ^\w{3}$ ChemIDplus chemidplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ -Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider Cint C probe 0 CLDB cldb http://bioinformatics.istge.it/hypercldb/$id.html cl3603 unknown 1 urn:miriam:cldb ^cl\d+$ ClinicalTrials.gov clinicaltrials http://clinicaltrials.gov/ct2/show/$id NCT00222573 unknown 1 urn:miriam:clinicaltrials ^NCT\d{8}$ diff --git a/org.bridgedb.rdf/resources/MiriamRegistry.ttl b/org.bridgedb.rdf/resources/MiriamRegistry.ttl index 10dc666bf..711baf3de 100644 --- a/org.bridgedb.rdf/resources/MiriamRegistry.ttl +++ b/org.bridgedb.rdf/resources/MiriamRegistry.ttl @@ -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 . diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index c69676afd..29f328e3c 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -7,7 +7,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . a bridgeDB:uriPattern ; @@ -19,3 +19,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; 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 edfe9769d..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("https://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/$id"); // assertThat (result, hasItem(pattern)); From e876e3d639b627cd4abe89ee01287051336a5fdb Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 15:04:32 +0200 Subject: [PATCH 10/22] Added the missing regexp --- org.bridgedb.rdf/resources/DataSource.ttl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 231929112..2d2bbb9d6 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -366,7 +366,7 @@ bridgeDB:DataSource_drugbankv4Target a bridgeDB:DataSource ; bridgeDB:fullName "Drugbank Target v4" ; bridgeDB:systemCode "drugbankv4.target" ; bridgeDB:idExample "BE0000938" ; - bridgeDB:hasRegexPattern "^BE\\d{7}$" ; + 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 ; From 0c68c3309b50d80977d1db2f8690853b8abcbf3f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:46:15 +0200 Subject: [PATCH 11/22] Added another test --- .../test/java/org/bridgedb/bio/DataSourceTxtTest.java | 9 +++++++++ 1 file changed, 9 insertions(+) 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"); From da202ed9ef772685e67ce43e6ad32ddd571ab212 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:54:06 +0200 Subject: [PATCH 12/22] Tests may have registered things, so do a more realistic check --- org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index d178a5196..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; } - if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); From 5386289a1df7f33462fd3b6011d7adc87d1c3a80 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:54:57 +0200 Subject: [PATCH 13/22] More precise status message --- .../org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 85ab7b114..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); @@ -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(); From c8b657ea30abcc319990c2c9de737946b027299f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:56:58 +0200 Subject: [PATCH 14/22] Support also https --- org.bridgedb/src/main/java/org/bridgedb/DataSource.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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("/")){ From 88194686249154bd93d07fdb177bd6a7a140a48a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:57:16 +0200 Subject: [PATCH 15/22] More testing --- org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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") From b3cdc2a8e976f4ddc8cf8fd64e49e96bab7164e6 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 20:26:58 +0200 Subject: [PATCH 16/22] More updates for the new BridgeDb Datasources release --- .../extract/Ensembl_ETL_Device_v18_local.pl | 12 +- .../org/bridgedb/bio/datasources.tsv | 12 +- .../org/bridgedb/bio/datasources.tsv | 12 +- org.bridgedb.rdf/resources/BioDataSource.ttl | 28 +-- org.bridgedb.rdf/resources/DataSource.ttl | 60 +++--- .../resources/IdentifiersOrgDataSource.ttl | 184 +++++++++--------- .../resources/IdentifiersOrgDataSource.txt | 46 ++--- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 74 +++---- .../resources/graph.properties | 4 +- .../src/org/bridgedb/sql/SQLUriMapper.java | 2 +- .../src/org/bridgedb/pairs/IdSysCodePair.java | 2 +- 11 files changed, 218 insertions(+), 218 deletions(-) diff --git a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl index 42d8576ad..ffbb03311 100755 --- a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl +++ b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl @@ -743,7 +743,7 @@ %{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'], 'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'", "\'ID\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", + "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", "\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'PRIMARY KEY (ID)' @@ -863,7 +863,7 @@ %{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'], 'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", + "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", "\'ftp://rgd.mcw.edu/pub/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', @@ -916,8 +916,8 @@ %{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'], 'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", - "\'http://www.gramene.org\'"], + "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", + "\'https://www.gramene.org\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', @@ -926,8 +926,8 @@ %{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'], 'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'", "\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/pathway\'", "\'\'", - "\'http://www.gramene.org/pathway\'"], + "\'https://www.gramene.org/pathway\'", "\'\'", + "\'https://www.gramene.org/pathway\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', 'PRIMARY KEY (ID)' diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 770e6c833..289fb0957 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -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=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$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=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene 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 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=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$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/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$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 https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase 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 @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz? Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os 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 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 bb0f7d8cb..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 @@ -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=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$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=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene 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 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=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$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/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$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 https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase 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 @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz? Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os 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 diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 52ef12bcb..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" ; @@ -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 2d2bbb9d6..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 . @@ -519,45 +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" . @@ -565,7 +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" ; @@ -807,11 +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 ; @@ -822,7 +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 ; @@ -915,7 +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 ; @@ -1037,24 +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 . @@ -1072,11 +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 f8a350259..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+)?$" ; @@ -921,11 +921,11 @@ bridgeDB:DataSource_CharProt a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CHEBI:\\d+$" ; @@ -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+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_GreenGenes a bridgeDB:DataSource ; bridgeDB:fullName "GreenGenes" ; @@ -3033,7 +3033,7 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:fullName "InChIKey" ; @@ -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/" . @@ -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 924e51b36..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 ; @@ -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 ; @@ -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"^^ ; @@ -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 . @@ -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.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.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 From af89100e846c43d0fcb946b63f71c927185467e2 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Fri, 26 Jul 2024 07:14:14 +0200 Subject: [PATCH 17/22] Different server id, to address a local ID conflict --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index d2dbb521c..89e5e6559 100644 --- a/pom.xml +++ b/pom.xml @@ -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 From f6d831f4764bb1178873d3e9dbeb9617ae3d12a1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 30 Jul 2024 10:37:39 +0200 Subject: [PATCH 18/22] Release 3.1.2 --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- org.bridgedb/src/main/resources/version.props | 2 +- pom.xml | 2 +- 29 files changed, 39 insertions(+), 39 deletions(-) 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 847361b70..833a6e7f8 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' ``` @@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.2-SNAPSHOT +mvn versions:set -DnewVersion=3.1.2 mvn clean deploy ``` @@ -145,7 +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/examples/pom.xml b/examples/pom.xml index fcebe7a70..0c490e85b 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index b63dda2b2..d92cfc8fe 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 194f6548e..2cd2f9413 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 1655d6b1a..a2e97b835 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index d45ad5df8..feb7e76d3 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 61d780844..88c3a389e 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 83ca9b27a..50eec5bc7 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index c0555e252..763f300fe 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 9889d24d9..4d26f9632 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 compile org.bridgedb org.bridgedb.bio - 3.1.2-SNAPSHOT + 3.1.2 compile org.bridgedb org.bridgedb.rdb - 3.1.2-SNAPSHOT + 3.1.2 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 2a6fdd71a..dcd850997 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index ecb265353..9dd9273a2 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 37768a064..32b8fdd5a 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 8bce22c78..7203717ab 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index cb9f80dbe..99572ef6c 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 379b9ba3d..c1ea354c8 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 69919c820..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 - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index a350d9c72..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 - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 30c55a733..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 - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 3aaaeeb59..6d769698e 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index c30eb03a2..eaf9b5248 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index eea6d5376..afb7fe1aa 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 308d74fc9..ccd78fba1 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 68d3bdfe9..9aed75286 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index fba9a3dd9..3ac9a6a9b 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index e3881be63..d641b271f 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 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/pom.xml b/pom.xml index 89e5e6559..e8c9507fc 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.2-SNAPSHOT + 3.1.2 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 64287d2c1e88e39a4ebb90bca5d4c9b49d808675 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:09:38 +0200 Subject: [PATCH 19/22] Added Java8 build step --- .github/workflows/build.yml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 417ccb74d..d97e8d99b 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,8 +7,21 @@ 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: runs-on: ubuntu-latest steps: From 1bab9d743c1e142e7fc2293634426410dd95dca8 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:11:15 +0200 Subject: [PATCH 20/22] Only do the second step if compiling with Java8 worked --- .github/workflows/build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d97e8d99b..0d38b3f7e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -22,6 +22,7 @@ jobs: 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: From 4f36020147b58e8196a2354831afc37da585e70b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:29:49 +0200 Subject: [PATCH 21/22] Do not run when not having Java 11 or higher --- org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java | 8 ++++++++ 1 file changed, 8 insertions(+) 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(); From f83387458d16c0d5e9f657f96394e97ad1f12366 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 30 Jul 2024 11:04:06 +0200 Subject: [PATCH 22/22] Bumped the PathVisio bundle too --- README.md | 2 +- pom-java8.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 833a6e7f8..555e3e9a8 100644 --- a/README.md +++ b/README.md @@ -129,7 +129,7 @@ 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: 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