The BridgeDb Project
@bridgedb.fosstodon.org.ap.brid.gy
BridgeDb is a framework to map identifiers between various biological databases and related resources. These mappings are provided for genes, proteins […]
[bridged from https://fosstodon.org/@bridgedb on the fediverse by https://fed.brid.gy/ ]
[bridged from https://fosstodon.org/@bridgedb on the fediverse by https://fed.brid.gy/ ]
BridgeDb Java 3.0.30 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.30 https://doi.org/10.5281/zenodo.18157075
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java […]
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java […]
Original post on fosstodon.org
fosstodon.org
January 5, 2026 at 7:35 PM
BridgeDb Java 3.0.30 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.30 https://doi.org/10.5281/zenodo.18157075
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java […]
"This release updates to BridgeDb Datasources 20260105 adding a few hundred more species and updates various dependencies and Maven plugins."
BridgeDb Java […]
new BridgeDb Datasources release: https://github.com/bridgedb/datasources/releases/tag/20260105 https://doi.org/10.5281/zenodo.18156816
Some @bioregistry alignment improvements, some TAIR updates, and many more plant species.
BridgeDb Datasources is a dataset with metadata about data sources […]
Some @bioregistry alignment improvements, some TAIR updates, and many more plant species.
BridgeDb Datasources is a dataset with metadata about data sources […]
Original post on fosstodon.org
fosstodon.org
January 5, 2026 at 7:34 PM
new BridgeDb Datasources release: https://github.com/bridgedb/datasources/releases/tag/20260105 https://doi.org/10.5281/zenodo.18156816
Some @bioregistry alignment improvements, some TAIR updates, and many more plant species.
BridgeDb Datasources is a dataset with metadata about data sources […]
Some @bioregistry alignment improvements, some TAIR updates, and many more plant species.
BridgeDb Datasources is a dataset with metadata about data sources […]
a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3: https://doi.org/10.6084/m9.figshare.30993322
January 3, 2026 at 8:28 AM
a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3: https://doi.org/10.6084/m9.figshare.30993322
BridgeDb Webservice 2.1.8 has been released: https://github.com/bridgedb/BridgeDbWebservice/releases/tag/2.1.8
This release updates several dependencies: BridgeDb 3.0.29, org.json 20250517, JUnit 5.14.1, and org.restlet 2.4.3. It also adds a new method /${ORG}/xrefs/${COMPACT_IDENTIFIER} that […]
This release updates several dependencies: BridgeDb 3.0.29, org.json 20250517, JUnit 5.14.1, and org.restlet 2.4.3. It also adds a new method /${ORG}/xrefs/${COMPACT_IDENTIFIER} that […]
Original post on fosstodon.org
fosstodon.org
November 9, 2025 at 1:02 PM
BridgeDb Webservice 2.1.8 has been released: https://github.com/bridgedb/BridgeDbWebservice/releases/tag/2.1.8
This release updates several dependencies: BridgeDb 3.0.29, org.json 20250517, JUnit 5.14.1, and org.restlet 2.4.3. It also adds a new method /${ORG}/xrefs/${COMPACT_IDENTIFIER} that […]
This release updates several dependencies: BridgeDb 3.0.29, org.json 20250517, JUnit 5.14.1, and org.restlet 2.4.3. It also adds a new method /${ORG}/xrefs/${COMPACT_IDENTIFIER} that […]
@bioconductor 3.22 is out, including BridgeDbR 2.22: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
This release improves handling of ChEBI compact identifiers from @bioregistry, improves the vignette, and adds a second vignette, and explains more about rJava installation […]
This release improves handling of ChEBI compact identifiers from @bioregistry, improves the vignette, and adds a second vignette, and explains more about rJava installation […]
Original post on fosstodon.org
fosstodon.org
November 9, 2025 at 10:53 AM
@bioconductor 3.22 is out, including BridgeDbR 2.22: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
This release improves handling of ChEBI compact identifiers from @bioregistry, improves the vignette, and adds a second vignette, and explains more about rJava installation […]
This release improves handling of ChEBI compact identifiers from @bioregistry, improves the vignette, and adds a second vignette, and explains more about rJava installation […]
BridgeDb Tiwid 4 is released: https://github.com/bridgedb/tiwid/releases/tag/release-4 https://doi.org/10.5281/zenodo.16628413
This release updates CAS identifiers, adds SSSOM and RDF outputs, adds am optional ORCID provenance column, removes gender-related terms from NCTI because of Executive […]
This release updates CAS identifiers, adds SSSOM and RDF outputs, adds am optional ORCID provenance column, removes gender-related terms from NCTI because of Executive […]
Original post on fosstodon.org
fosstodon.org
July 31, 2025 at 7:43 AM
BridgeDb Tiwid 4 is released: https://github.com/bridgedb/tiwid/releases/tag/release-4 https://doi.org/10.5281/zenodo.16628413
This release updates CAS identifiers, adds SSSOM and RDF outputs, adds am optional ORCID provenance column, removes gender-related terms from NCTI because of Executive […]
This release updates CAS identifiers, adds SSSOM and RDF outputs, adds am optional ORCID provenance column, removes gender-related terms from NCTI because of Executive […]
BridgeDb Java 3.0.29 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.29
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various […]
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various […]
Original post on fosstodon.org
fosstodon.org
July 29, 2025 at 7:59 AM
BridgeDb Java 3.0.29 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.29
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various […]
"This update release brings in BridgeDb Datasources 20270728, improves the backwards compatibility with old Apache Derby versions, adds a BridgeDb.getVersion() method, and updates various […]
new BridgeDb Datasources release: https://github.com/bridgedb/datasources/releases/tag/20270728
"Uses UniProtKB as name, removes EcoGene, and multiple small updates"
BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like […]
"Uses UniProtKB as name, removes EcoGene, and multiple small updates"
BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like […]
Original post on fosstodon.org
fosstodon.org
July 28, 2025 at 7:26 PM
new BridgeDb Datasources release: https://github.com/bridgedb/datasources/releases/tag/20270728
"Uses UniProtKB as name, removes EcoGene, and multiple small updates"
BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like […]
"Uses UniProtKB as name, removes EcoGene, and multiple small updates"
BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like […]
Reposted by The BridgeDb Project
ha! that's a new record for me. Closing a bug report, using the proposal from the report: https://github.com/bridgedb/datasources/issues/4
AFTER 10 YEARS!
#bioinformatics
AFTER 10 YEARS!
#bioinformatics
Miriam identifiers for Gramene sources in datasources.txt · Issue #4 · bridgedb/datasources
In datasources.txt, Gramene Genes should have the Miriam identifier urn:miriam:gramene.gene. Should we create new Miriam identifiers also for the following rows? Gramene Arabidopsis Gramene Rice Gr...
github.com
July 28, 2025 at 4:55 PM
ha! that's a new record for me. Closing a bug report, using the proposal from the report: https://github.com/bridgedb/datasources/issues/4
AFTER 10 YEARS!
#bioinformatics
AFTER 10 YEARS!
#bioinformatics
"BridgeDB & Wikidata. Una poderosa combinación que genera investigación abierta interoperable" (2022) https://www.youtube.com/watch?v=cgQ6LidwFIs
June 7, 2025 at 7:48 AM
"BridgeDB & Wikidata. Una poderosa combinación que genera investigación abierta interoperable" (2022) https://www.youtube.com/watch?v=cgQ6LidwFIs
@bioconductor 3.21 is out, including BridgeDbR 2.18: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
Includes BridgeDb 3.0.28, and session info and CiTO annotation in the vignette.
See https://genomic.social/@bioconductor/114349555185162646 for the general announcement
Includes BridgeDb 3.0.28, and session info and CiTO annotation in the vignette.
See https://genomic.social/@bioconductor/114349555185162646 for the general announcement
BridgeDbR
Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.
bioconductor.org
April 18, 2025 at 12:37 PM
@bioconductor 3.21 is out, including BridgeDbR 2.18: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
Includes BridgeDb 3.0.28, and session info and CiTO annotation in the vignette.
See https://genomic.social/@bioconductor/114349555185162646 for the general announcement
Includes BridgeDb 3.0.28, and session info and CiTO annotation in the vignette.
See https://genomic.social/@bioconductor/114349555185162646 for the general announcement
use descriptions on how we identify chemical structures: https://aionics.io/blog/why-chemical-identifiers-are-the-unsung-heroes-of-innovation/
#chemistry #identifier
#chemistry #identifier
Why Chemical Identifiers are the Unsung Heroes of Innovation - Aionics, Inc.
Chemical identifiers ensure accuracy in finding chemicals, thus driving innovation in science and industry. Learn how to use them.
aionics.io
March 6, 2025 at 8:29 AM
use descriptions on how we identify chemical structures: https://aionics.io/blog/why-chemical-identifiers-are-the-unsung-heroes-of-innovation/
#chemistry #identifier
#chemistry #identifier
new Enxembl 111-based gene/protein identifier mapping files are available: https://data.bridgedb.org/gene_database/ (thx to Tooba Abbassi-Daloii, https://github.com/tabbassidaloii)
data
Repository to mimic the old data/gene_database/ API
data.bridgedb.org
February 27, 2025 at 8:33 AM
new Enxembl 111-based gene/protein identifier mapping files are available: https://data.bridgedb.org/gene_database/ (thx to Tooba Abbassi-Daloii, https://github.com/tabbassidaloii)
the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information when the identifiers was retired (stopped working) and if there is a replacement identifier.
In the past week two new features got added. ORCIDs can now be provided […]
In the past week two new features got added. ORCIDs can now be provided […]
Original post on fosstodon.org
fosstodon.org
January 14, 2025 at 10:48 AM
the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information when the identifiers was retired (stopped working) and if there is a replacement identifier.
In the past week two new features got added. ORCIDs can now be provided […]
In the past week two new features got added. ORCIDs can now be provided […]
Reposted by The BridgeDb Project
new conference proceedings: "BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction" https://ceur-ws.org/Vol-3890/ https://ceur-ws.org/Vol-3890/paper-23.pdf
#rdf #sparql #bioinformatics #python
#rdf #sparql #bioinformatics #python
CEUR-WS.org/Vol-3890 - 15th International Conference on Semantic Web Applications and Tools for Health Care
and Life Sciences 2024
ceur-ws.org
January 7, 2025 at 3:51 AM
new conference proceedings: "BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction" https://ceur-ws.org/Vol-3890/ https://ceur-ws.org/Vol-3890/paper-23.pdf
#rdf #sparql #bioinformatics #python
#rdf #sparql #bioinformatics #python
Reposted by The BridgeDb Project
Did you know #wikidata can be used to translate IDs of one website to IDs of another website?
https://wikidata-todo.toolforge.org/beacon.php
For example, Twitter usernames to Mastodon addresses -> https://wikidata-todo.toolforge.org/beacon.php?prop=4033&source=2002&site=
Or ORCiD to IMDB -> […]
https://wikidata-todo.toolforge.org/beacon.php
For example, Twitter usernames to Mastodon addresses -> https://wikidata-todo.toolforge.org/beacon.php?prop=4033&source=2002&site=
Or ORCiD to IMDB -> […]
Original post on mastodon.social
mastodon.social
December 29, 2024 at 5:37 PM
Did you know #wikidata can be used to translate IDs of one website to IDs of another website?
https://wikidata-todo.toolforge.org/beacon.php
For example, Twitter usernames to Mastodon addresses -> https://wikidata-todo.toolforge.org/beacon.php?prop=4033&source=2002&site=
Or ORCiD to IMDB -> […]
https://wikidata-todo.toolforge.org/beacon.php
For example, Twitter usernames to Mastodon addresses -> https://wikidata-todo.toolforge.org/beacon.php?prop=4033&source=2002&site=
Or ORCiD to IMDB -> […]
Reposted by The BridgeDb Project
meanwhile, one @bridgedb feature request implemented: the website now also lists the species common names (if giving on the JSON config files)
#sr24 #metakids #elixireurope
#sr24 #metakids #elixireurope
December 19, 2024 at 9:31 AM
meanwhile, one @bridgedb feature request implemented: the website now also lists the species common names (if giving on the JSON config files)
#sr24 #metakids #elixireurope
#sr24 #metakids #elixireurope
a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3: https://doi.org/10.6084/m9.figshare.28030427.v1
To support #sr24 #metakids pathway curation, see https://social.edu.nl/@egonw/113599062833652441
To support #sr24 #metakids pathway curation, see https://social.edu.nl/@egonw/113599062833652441
Metabolite BridgeDb ID Mapping Database (20241215)
BridgeDb ID mapping database for metabolites, using HMDB 5.0 (Release of April 2024), ChEBI (Release of December 2024), and Wikidata (15 December 2024) as data sources.
figshare.com
December 15, 2024 at 7:48 PM
a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3: https://doi.org/10.6084/m9.figshare.28030427.v1
To support #sr24 #metakids pathway curation, see https://social.edu.nl/@egonw/113599062833652441
To support #sr24 #metakids pathway curation, see https://social.edu.nl/@egonw/113599062833652441