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 […]

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 […]

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 […]

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

"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

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

the BridgeDb Tiwid project ("this is where identifiers die") collects outdated identifiers, and when known, provides information when the identifiers was retired (stopped working) and if there is a replacement identifier.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

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

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 -> […]

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

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