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BridgeDb is @bridgedb@fosstodon.org @BridgeDbProject

Identifier mapping project. More about us in bmcbioinformatics.biomedcent……

Joined August 2018
  • Tweets 145
  • Following 10
  • Followers 103
29 Photos and videos
BridgeDb 3.0.23 was released, with improvements for the quality control tool: doi.org/10.5281/zenodo.82213… Full release notes here: github.com/bridgedb/BridgeDb…
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BridgeDb is @bridgedb@fosstodon.org retweeted
BiGCaT Maastricht@bigcat_UM
19 May 2023
new paper: "The FAIR Cookbook - the essential resource for and by FAIR doers" doi.org/10.1038/s41597-023-0…
Screenshot of how a FAIR CookBook recipe credits authors, by ORCID, using the CreDIT attribtution ontology, and how it has itself a global, unique identifier.

ALT Screenshot of how a FAIR CookBook recipe credits authors, by ORCID, using the CreDIT attribtution ontology, and how it has itself a global, unique identifier.
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BridgeDb Java 3.0.20 is released, a minor update: github.com/bridgedb/BridgeDb…

Release BridgeDb 3.0.20 · bridgedb/BridgeDb

Minor release that fixes a typo in the VoID tool, adds OSGI support for the org.bridgedb.webservice.bridgerest module, and ensures the version.props is shipped with the jars. The below examples ass...

github.com
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RT @egonw@scholar.social Fwd: "BridgeDb NWO grant update #6: second hackathon" chem-bla-ics.blogspot.com/20… bridgedb #hackathon #bridgeDbNWO scholar.social/@egonw/109845…
Screenshot of the GitHub Action history showing the history of Docker generation processes.

ALT Screenshot of the GitHub Action history showing the history of Docker generation processes.
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during the #bridgedbnwo hackathon today we release a new BridgeDb DataSources release, new BridgeDb Docker images, and a new BridgeDb Java release :)
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today the 2nd NWO Open Science grant hackathon starts (until tomorrow lunchtime): github.com/bridgedb/nwo-hack… #bridgedbnwo

GitHub - bridgedb/nwo-hackathon-2023

Contribute to bridgedb/nwo-hackathon-2023 development by creating an account on GitHub.

github.com
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today the 2nd NWO Open Science grant hackathon starts (until tomorrow lunchtime): github.com/bridgedb/nwo-hack… (ping @egonw@akademienl.social if you want to participate)

GitHub - bridgedb/nwo-hackathon-2023

Contribute to bridgedb/nwo-hackathon-2023 development by creating an account on GitHub.

github.com
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Our webserver was down yesterday, for unclear reasons. Apologies for the inconvenience. We took the opportunity to load the latest Gene/Protein identifier mapping databases released earlier this month, see bridgedb.github.io/data/gene…

data

Repository to mimic the old data/gene_database/ API

data.bridgedb.org
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RT @egonw@scholar.social Blog: "BridgeDb NWO grant update #5: BioHackathon, Webservice, Bioregistry " chem-bla-ics.blogspot.com/20… scholar.social/@egonw/109493…
Image from the linked blog post showing the new Mastodon account at https://fosstodon.org/@bridgedb

ALT Image from the linked blog post showing the new Mastodon account at https://fosstodon.org/@bridgedb
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BridgeDb 3.0.18 is released, with updates the versions of several dependencies, including Apache Derby 10.15.2.0, handling ChEBI identifiers with Bioregistry better, and a much cleaner BridgeDb QC tool github.com/bridgedb/BridgeDb…

Release BridgeDb 3.0.18 · bridgedb/BridgeDb

Minor release that updates the versions of several dependencies, including Apache Derby 10.15.2.0, handling ChEBI identifiers with Bioregistry better, and a much cleaner BridgeDb QC tool. The below...

github.com
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RT @egonw@akademienl.social I just added the first article (partly) funded with our NWO ISAAC browser plugin, one with 19 authors, in about 2 minutes. The browser plugin is a real time saver! chrome.google.com/webstore/d… Just give it a DOI and off it goes. akademienl.social/@egonw/109…
Screenshot of the NWO ISAAC database "Producten" page with the newly added research article ("Wetenschappelijk artikel") add with the plugin. About Bioregistry.org, btw.

ALT Screenshot of the NWO ISAAC database "Producten" page with the newly added research article ("Wetenschappelijk artikel") add with the plugin. About Bioregistry.org, btw.
RT @egonw@scholar.social it's been a bit silent on the bridgedb NWO Open Science grant front. Holiday, and a lot of teaching in Sept/Oct. But our team continued working on upgrading the BridgeDb Webservice code. Today I saw some really nice new results, basically (1/2)
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reflecting the hard part is done. We see here the new JSON response to an API call! scholar.social/@egonw/109349… (2/2)
Screenshot of part of a postman.co website with a API call to a locally running BridgeDb webservice, doing a batch identifier mapping and returning JSON!

ALT Screenshot of part of a postman.co website with a API call to a locally running BridgeDb webservice, doing a batch identifier mapping and returning JSON!
RT @egonw@scholar.social we are getting better at tracking outdated identifiers. I just added a bunch of no-longer existing #wikidata identifiers to bridgedb Tiwid, huge thanks to Tooba and Denise (and cthoyt for setting up the GitHub Action to make the plot automatically (1/2)
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:) scholar.social/@egonw/109338… (2/2)
Barplot for the now ten data sources, with Wikidata now leading with 13.4 thousand outdatad identifiers, beating the now runner up LIPID MAPS with 3.4 thousand identifiers.

ALT Barplot for the now ten data sources, with Wikidata now leading with 13.4 thousand outdatad identifiers, beating the now runner up LIPID MAPS with 3.4 thousand identifiers.
BridgeDb is cited. Check this paper what their story is about identifier mapping
JOSS@JOSS_TheOJ
2 Nov 2022
Just published in JOSS: 'MSMetaEnhancer: A Python package for mass spectra metadata annotation' doi.org/10.21105/joss.04494
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We've been journalclubbed: "BridgeDB & Wikidata. Una poderosa combinación que genera investigación abierta interoperable" youtube.com/watch?v=cgQ6Lidw…

BridgeDB & Wikidata. Una poderosa combinación que genera investigac...

Journal Club del 22 de septiembre del 2022 👩🏻‍🏫Expositor: Yessica ...

youtube.com
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BridgeDb is @bridgedb@fosstodon.org retweeted
Maria J. Cruz @mariacruz@akademienl.social@gravana
23 Sep 2022
Did you miss the @NWONieuws #OpenScience in Practice webinar on interoperable #openresearch with @egonwillighagen, @jambelien and Sander de Ridder? The recording is now available: nwo.nl/en/open-science-pract…

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it looks like we have DNS problems with our website. Likely solve tomorrow. Ping @egonwillighagen if you need specific info from the website, and he'll try to help
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we received some reports that suggested that the BridgeDb Webservice was slow in responding. We just rebooted the service. Plz let us know if you continue to experience issues.
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