bridgedb - Network

use descriptions on how chemists identify chemical structures:...

use descriptions on how chemists identify chemical structures: https://aionics.io/blog/why-chemical-identifiers-are-the-unsung-heroes-of-innovation/

#chemistry #identifier

new Ensembl 111-based gene/protein identifier mapping files are available: https://data.bridgedb.org/gene_database/ (thx to Tooba...

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)

the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information...

the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information when the identifiers was retired (stopped working) and if there is a replacement identifier.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

a new BridgeDb metabolite ID mapping database has been released, compatible with PathVisio 3.3:...

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

@bioconductor 3.20 is out, including BridgeDbR 2.16: https://bioconductor.org/packages/release/bioc/html/BridgeDbR.htmlNo real changes, so...

@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

Dominik Martinat worked on the @elixir_europe CZ MolMeDB database (https://www.molmedb.upol.cz/detail/intro) and is currently guest in...

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He just contributed outdated MolMeDB identifiers to BridgeDb Tiwid: https://github.com/bridgedb/tiwid/pull/27

BridgeDb, the @elixir_europe Recommended Interoperability Resource for (database) identifier mapping, released a new version of the Java...

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.

BridgeDb 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 3.1.2 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

BridgeDb Java 3.0.27 is released: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.27"This update release brings in...

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).

BridgeDb Datasources 20240725 is released: https://github.com/bridgedb/datasources/releases/tag/20240725"Adds one new species (Solanum...

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

it seems ThermoFisher Scientific dropped the Affymetrix probeset ID pages. The @bioregistry and identifiers.org URL patterns no longer work,...

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

#bioinformatics

BridgeDb Java 3.0.26 was released yesterday, with a small bug fix: https://github.com/bridgedb/BridgeDb/releases/tag/release_3.0.26BridgeDb...

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.

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:...

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/

@bioconductor 3.19 has been release this week, including BridgeDbR 2.14.0. See...

@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

a new metabolite ID mapping database was released today. Smaller in size (2.7GB) but more identifiers and more mappings. Based on the latest...

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

BridgeDb was mentioned today at the #DataReuseDay2024 in Leiden as important solution to integration databases with different identifiers...

BridgeDb was mentioned today at the #DataReuseDay2024 in Leiden as important solution to integration databases with different identifiers for the same things

Want to run the BridgeDb Webservice with the default data locally? Just run this:sudo docker run --restart always -d --name bridgedb -p...

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

the BridgeDb Webservice at https://webservice.bridgedb.org/ is now using the official BridgeDb Webservice Docker! Thanks to @Marvin and...

the BridgeDb Webservice at https://webservice.bridgedb.org/ is now using the official BridgeDb Webservice Docker! Thanks to @Marvin and others!

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....

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."

in related news, BridgeDb Datasources 20231202 is out: https://github.com/bridgedb/datasources/releases/tag/20231202

in related news, BridgeDb Datasources 20231202 is out: https://github.com/bridgedb/datasources/releases/tag/20231202