use descriptions on how chemists identify chemical structures: https://aionics.io/blog/why-chemical-identifiers-are-the-unsung-heroes-of-innovation/
6.3.2025 08:29use descriptions on how chemists identify chemical structures:...new Ensembl 111-based gene/protein identifier mapping files are available: https://data.bridgedb.org/gene_database/ (thx to Tooba Abbassi-Daloii, https://github.com/tabbassidaloii)
27.2.2025 08:22new Ensembl 111-based gene/protein identifier mapping files are available: https://data.bridgedb.org/gene_database/ (thx to Tooba...the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information when the identifiers was retired (stopped working) and if there is a replacement identifier.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 for who claimed an identifier is retired. Second, the mapping to retired to new identifier are now available as SSSOM. Patches by @cthoyt
Part of @elixir_europe
#RIRs #bioinformatics #cheminformatics
14.1.2025 10:48the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information...a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3: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
15.12.2024 19:44a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3:...@bioconductor 3.20 is out, including BridgeDbR 2.16: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html
No real changes, so everything identifier mapping should just upgrade fine
See https://genomic.social/@bioconductor/113398603927477116 for the general announcement
#interoperability #biology #chemistry
31.10.2024 05:17@bioconductor 3.20 is out, including BridgeDbR 2.16: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.htmlNo real changes, so...Dominik Martinat worked on the @elixir_europe CZ MolMeDB database (https://www.molmedb.upol.cz/detail/intro) and is currently guest in Maastricht at @bigcat_UM for a staff exchange.
He just contributed outdated MolMeDB identifiers to BridgeDb Tiwid: https://github.com/bridgedb/tiwid/pull/27
1.10.2024 07:44Dominik Martinat worked on the @elixir_europe CZ MolMeDB database (https://www.molmedb.upol.cz/detail/intro) and is currently guest in...BridgeDb, the @elixir_europe Recommended Interoperability Resource for (database) identifier mapping, released a new version of the Java library and API: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.28
This update release brings in BridgeDb Datasources 20240925, a new organism (Rosmarinus officinalis), and various dependency updates, including an update of the MySQL driver.
With thanks to ELIXIR-DE for their feature request.
27.9.2024 08:23BridgeDb, the @elixir_europe Recommended Interoperability Resource for (database) identifier mapping, released a new version of the Java...BridgeDb Java 3.1.2 is out too now. This version has similar to 3.0.27 but uses "UniProtKB" instead of "UniProt-TrEMBL", see https://github.com/orgs/bridgedb/projects/2
30.7.2024 14:32BridgeDb Java 3.1.2 is out too now. This version has similar to 3.0.27 but uses "UniProtKB" instead of "UniProt-TrEMBL",...BridgeDb Java 3.0.27 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.27
"This update release brings in BridgeDb Datasources 20240725, a new organism (Solanum tuberosum), and various small stability improvements."
BridgeDb Java is the library that implements a Java API to access identifier mappings (e.g. from #ChEBI to #Wikidata, or from Ensembl to UniProt) from local files (there is API support for online services too, but we need help maintaining this code).
26.7.2024 05:33BridgeDb Java 3.0.27 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.27"This update release brings in...BridgeDb Datasources 20240725 is released: https://github.com/bridgedb/datasources/releases/tag/20240725
"Adds one new species (Solanum tuberosum), fixed a wrong bioregistry.io prefix for one datasource, and updated various datasource URLs."
BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like @wikipathways, PathVisio, and others
25.7.2024 10:41BridgeDb Datasources 20240725 is released: https://github.com/bridgedb/datasources/releases/tag/20240725"Adds one new species (Solanum...it seems ThermoFisher Scientific dropped the Affymetrix probeset ID pages. The @bioregistry and identifiers.org URL patterns no longer work, and the one we have is broken too :(
See e.g. https://bioregistry.io/registry/affy.probeset
25.7.2024 08:59it seems ThermoFisher Scientific dropped the Affymetrix probeset ID pages. The @bioregistry and identifiers.org URL patterns no longer work,...BridgeDb Java 3.0.26 was released yesterday, with a small bug fix: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.26
BridgeDb is a identifier mapping project with a Java library, identifier mapping databases, webservices, an R and Python integration, and more.
4.6.2024 05:08BridgeDb Java 3.0.26 was released yesterday, with a small bug fix: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.26BridgeDb...we're experiencing some server outage. We're on top of it.
You can use this mirror from the VHP4Safety project for the time being: https://bridgedb.cloud.vhp4safety.nl/
8.5.2024 09:25we're experiencing some server outage. We're on top of it.You can use this mirror from the VHP4Safety project for the time being:...@bioconductor 3.19 has been release this week, including BridgeDbR 2.14.0. See https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html and https://genomic.social/@bioconductor/112367926971541500
4.5.2024 11:20@bioconductor 3.19 has been release this week, including BridgeDbR 2.14.0. See...a new metabolite ID mapping database was released today. Smaller in size (2.7GB) but more identifiers and more mappings. Based on the latest HMDB and ChEBI and including Wikidata from this morning. https://doi.org/10.6084/m9.figshare.25610373.v1 #interoperability #chemistry
16.4.2024 10:40a new metabolite ID mapping database was released today. Smaller in size (2.7GB) but more identifiers and more mappings. Based on the latest...BridgeDb was mentioned today at the #DataReuseDay2024 in Leiden as important solution to integration databases with different identifiers for the same things
12.2.2024 19:52BridgeDb was mentioned today at the #DataReuseDay2024 in Leiden as important solution to integration databases with different identifiers...Want to run the BridgeDb Webservice with the default data locally? Just run this:
sudo docker run --restart always -d --name bridgedb -p 8082:8183 -e SERVER_URL='https://webservice.bridgedb.org/' bigcatum/bridgedb:latest
19.12.2023 16:07Want to run the BridgeDb Webservice with the default data locally? Just run this:sudo docker run --restart always -d --name bridgedb -p...the BridgeDb Webservice at https://webservice.bridgedb.org/ is now using the official BridgeDb Webservice Docker! Thanks to @Marvin and others!
19.12.2023 14:52the BridgeDb Webservice at https://webservice.bridgedb.org/ is now using the official BridgeDb Webservice Docker! Thanks to @Marvin and...BridgeDb 3.1.1 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.1.1
"Update release for the BridgeDb 3.1 series. It brings in the changes in the 3.0.24 and 3.0.25 releases."
18.12.2023 12:10BridgeDb 3.1.1 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.1.1"Update release for the BridgeDb 3.1 series....in related news, BridgeDb Datasources 20231202 is out: https://github.com/bridgedb/datasources/releases/tag/20231202
2.12.2023 18:02in related news, BridgeDb Datasources 20231202 is out: https://github.com/bridgedb/datasources/releases/tag/20231202