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egonw.mastodon.social.ap.brid.gy
Egon Willigh☮gen 🟥
@egonw.mastodon.social.ap.brid.gy
820 followers 22 following 980 posts
Chem/Bio/Stats/SemWeb, the CDK, WikiPathways, TGX @ Maastricht University (these posts are personal) (he/him). Here particularly #opensource #openstandards and […]

[bridged from https://mastodon.social/@egonw on the fediverse by https://fed.brid.gy/ ]
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egonw.mastodon.social.ap.brid.gy
@riannefijten mentions the International Network of Open Science & Scholarship Communities (INOSC) which local open science community around the world, see https://osc-international.com/ and the map in the screenshot

#openscience #nosf2025
Screenshot of part of the linked page with the INOSC logo, the full name below that, with 50+ communities in 27 countries and more than 2300 active participants. The maps show them to be located in Europe, Azia, Africa, and Amerca (North and South).
October 24, 2025 at 2:47 PM
egonw.mastodon.social.ap.brid.gy
bringing together a few Dutch #openscience projects at #nosf2025

We see the Dutch VHP4Safety project, @bridgedb, @elixir_europe TeSS, and the @SURF https://taxila.nl/
Screenshot of a local instance of the VHP4Safety platform (logo in the top left) showing information about BridgeDb (an ELIXIR Recommended Interoperability Resource): documentation/training material from the ELIXIR TeSS platform, but also the Dutch SURF taxila.nl. The info is presentated with two faceted search widgets, that allows to search within the BridgeDb documentation.
October 24, 2025 at 1:50 PM
egonw.mastodon.social.ap.brid.gy
Open Science is International!

#nosf2025
Photo of the "Who participated?" slide showing that many countries around the world reported back to the UN about their progress in open science. It shows some statistics and a world map with retiring countries colored blue. The maps shows most continents are covered
October 24, 2025 at 8:37 AM
egonw.mastodon.social.ap.brid.gy
Keynote explaining "Why Open Science?" #nosf2025
Photo of a "Why Open Science" slide and the speaker in front of it. The slides list three main points: UN article 27, development of lagging societies, SDGs.
October 24, 2025 at 8:23 AM
egonw.mastodon.social.ap.brid.gy
Another good year for explicit CiTO annotations! https://scholia.toolforge.org/cito/

Thanks to all Journal of Cheminformatics and BioHackrXiv authors!!!

Looking forward to the #bh25eu and #bh25de preprints with CiTO annotations! Help us set a new record ;) […]

[Original post on mastodon.social]
Screenshot of the "Number of articles with CiTO-annotated citations by year" panel, showing articles with explicit CiTO annotations (so, as part of the articles themselves!), first in 2010 (you should know that by now), and then Journal of Cheminformatics preprints since 2020 (3, 8, 5, 4, 2, 2, yeah, not increasing) and BioHackrXiv since 2022 (2, 11, 13, 10). With BioHackathon Europe and BioHackathon Germany still taking place, we should be able to set a new high.
October 12, 2025 at 6:47 AM
egonw.mastodon.social.ap.brid.gy
@briannosek.bsky.social thanks, it looks good. I just had my first steps around, moderating BioHackrXiv prreprints and that moderation was quite intuitive!

I do run into a glitch: the page to search all BioHackrXiv preprints has unrelated content: https://osf.io/preprints/biohackrxiv/discover
Screenshot of the linked page, showing the right collection logo, but the number of items in the collections is not okay. And the first two results are indeed not BioHackrXiv preprints. Something seems to go wrong with the the filtering.
October 12, 2025 at 5:31 AM
egonw.mastodon.social.ap.brid.gy
@altmetric.com btw, I still very much love your badges and do have them on my personal pages too. It gives me a great way to see how people are using and thinking about my research.
Page for our eLife paper "Science Forum: Wikidata as a knowledge graph for the life sciences" showing the title, the Altmetric badge (showing coverage in blogs, X/FB/Bsky, and Wikipedia. Also 123 bookmarks in Mendeley. The full citations is also given, along with DOI, and two blog posts where I mention this article.
October 9, 2025 at 5:14 AM
egonw.mastodon.social.ap.brid.gy
Ozan Cinar and @Marvin will present tomorrow about the #VHP4Safety solutions for general risk assessment without animal experiments

You can still register: https://us02web.zoom.us/webinar/register/WN_Zp2MIuZMRL-HAehsViIokg#/registration

#safety #toxicology #nam
Meeting infographic for the webinar with project logos on the left (ASPIS, ONTOX, VHP4Safety), the title of the webinar ("Exploring the ONTOX and VHP4Safety IT platforms"), and the name of the speakers. Third speaker is Joerg Marusczyk of ONTOX.
October 7, 2025 at 3:37 PM
egonw.mastodon.social.ap.brid.gy
ERM identifiers as keywords on Zenodo, thanks Irini! It makes it easy to find research output from the ASINA project about a specific nanomaterial it studied. Cool! https://zenodo.org/communities/asina/records?q=&f=resource_type%3Adataset&l=list&p=1&s=10&sort=newest
"Subjects" section of the Zenodo's faceted searching showing six ERM identifiers.
September 26, 2025 at 2:12 PM
egonw.mastodon.social.ap.brid.gy
September 20, 2025 at 10:36 AM
egonw.mastodon.social.ap.brid.gy
#airborne #Ginkelseheide
September 20, 2025 at 9:29 AM
egonw.mastodon.social.ap.brid.gy
ah, nice to see the new @Codeberg and @bioconductor features in action! https://research-software-directory.org/software/rwikipathways

#openscience #bioinformatics #wikipathways
Screenshot of a section of the linked page, the metadata column on the right hand side, showing the Keywords panel (with Bioinformatics and WikiPathways), the Programming languages as horizontal bar plot (mostly HTML (95%) despite it being an R (5%) package), License (MIT), Source code (Codeberg), and Packages (BioConductor). The last two are with their logos.
September 7, 2025 at 10:57 AM
egonw.mastodon.social.ap.brid.gy
very interesting use of @nanopub at #wikicite2025 with a template where people can claim (authenticated with @ORCID_Org!) they are participant. And that can then be used in @wikidata s reference (links in the alt texts)
Screenshot of https://nanodash.knowledgepixels.com/query?36&runquery=RAgmOo0brWLCIrEXd4uQblVGipB34XMOy7TixmOW6hz4s/get-wikicite2025-participants showing the resutls of a query that lists all instances nanopublications about being participant in WikiCite 2025. It shows 7 of them, four of which show a participant name, two just an ORCID, and one a Wikidata identifier. Other columns are the name (basically same info as the participant column), the nanopub ID (linked), and the date when the nanopub was created. Screenshot of the Wikidata page for WikiCite 2025: https://www.wikidata.org/wiki/Q133846580#P710 It shows the "particpant" (P710) section with four participant statements, each with a separate nanopub (from the list of the first screenshot) as reference. This screenshot of https://nanodash.knowledgepixels.com/explore?48&id=RAN2sKflou4vxB8yWeHWkgqJXrJcc1Mw29ky2cMwIzPfs shows one of the 7 nanopubs and we see a webpage listing the full identifier just below a hash-based title (uninformative), and then the status of the nanopublication (can be updates, retracted, etc), and the nanopublication itself, with facts shown in the three colors of the nanopub system: yellow for the statement (assertions), purple for the provenance, and blue for info about the nanopub. Yellow here states (asserts) "I (0000-0001-6122-0777) participated in WikiCite 2025." Purple lists that the assertion is made by 0000-0001-6122-0777. (mind you, this is authenticated with ORCID.org, so by whomever can use that ORCID account) Blue says who created the nanopub (again 0000-0001-6122-0777) and when.
August 31, 2025 at 4:18 PM
egonw.mastodon.social.ap.brid.gy
is there a name for this? just trying to wrap up https://doi.org/10.3897/rio.10.e124884

#cdk2024
Really hard trying to convince myself the project results are really okay and I should not be afraid to just write it up. Right now: empty page with the title "CDK2024 Report" and my name and ORCID.
August 31, 2025 at 10:19 AM
egonw.mastodon.social.ap.brid.gy
is there a name for this? #cdk2024
Really hard trying to convince myself the project results are really okay and I should not be afraid to just write it up. Right now: empty page with the title "CDK2024 Report" and my name and ORCID.
August 31, 2025 at 10:18 AM
egonw.mastodon.social.ap.brid.gy
hi @opencitations, are you at the #wikicite2025 too? I am online, but in parallel to the meeting, I was exploring the #wikicite content and found an "author correction" of one of my articles in #wikidata (not sure if a correction is really notable, but that's […]

[Original post on mastodon.social]
Screenshot of a OpenCitations JSON snippet: { "oci": "06301347470-06260695958", "citing": "10.1093/nar/gkaa1024", "cited": "10.1038/s41597-020-00589-w 10.1038/s41597-020-0477-8", "creation": "2020-11-19", "timespan": "P0Y6M14D", "journal_sc": "no", "author_sc": "yes" },
August 30, 2025 at 11:31 AM
egonw.mastodon.social.ap.brid.gy
I am attending #wikicite2025 this weekend, from home, with two flash talks tomorrow about retractions in Wikidata and citation intent typing annotations (partly in Wikidata)

Right now, catching up with what happened yesterday: https://egonw.github.io/WikiCite2025/
Screenshot of the linke fediwall, showing apage with 6 column with fediverse posts with the hashtag #WikiCite2025 We see some text posts, links to meeting info, and some photos, e.g. about a bear cookie, a power connector, and some weird small device on the cealing where the posts asks what it is.
August 30, 2025 at 8:38 AM
egonw.mastodon.social.ap.brid.gy
@rupdecat we can add some more semantics here, e.g. using @bioregistry and schema.org's mainEntity. My suggestions in red

#nescollab
Schema.org JSON-LD snippet showing a schema:Dataset with @id, name, etc, and in red suggestions, e.g. the use of schema:mainEntity with a list of schema:Things (one protein structure and one (bio)schemas:MolecularEntity with @id, name, and identifier, but omitting the relevant "conformsTo". Also suggestions for citing a related publication and how to add the ORCID as id for a creator.
August 29, 2025 at 10:49 AM
egonw.mastodon.social.ap.brid.gy
I wonder if someone is keeping @wikidata's coordinate location uptodate today: https://www.svtplay.se/video/KnDgQ9G/den-stora-kyrkflytten/forsta-dagen?video=visa

#kyrka #kiruna #wikidata #svt
Screenshot of the linked SVTplay website showing a live stream of a church begin moved by a big (well, Mamoet) truck across Kiruna in Sweden. Left the map with the route, and right the live stream showing the church-on-wheels.
August 19, 2025 at 11:38 AM
egonw.mastodon.social.ap.brid.gy
Another nice feature that is new to me is the packages section, which shows where binary packages of the software can be downloaded (see screenshot). Meanwhile, Team Maastricht University ( […]

[Original post on mastodon.social]
Screenshot of the "Packages" section of an example RSD entry, showing this software has packages in various platforms, visualized by their logo: R logo (CRAN), Debian logo (Debian pkg), Sonatype (for Maven pkgs), and Python logo (Python Index, pypi).
August 16, 2025 at 10:36 AM
egonw.mastodon.social.ap.brid.gy
@openstreetmap is an awesome project, running for 21 years now. See https://en.wikipedia.org/wiki/OpenStreetMap

I have contributed small updates it over the years, but one aspect that I only started using this year, is the coverage and accurateness of their […]

[Original post on mastodon.social]
OpenStreetMap of the region south-east, south, and south-west of the Dutch city Roermond. It shows a basic OSM but with bike routes on top of that red and purple lines showing the bicycle routes and the numbers of their crossing points. IRL each crossing point has a similar map (also OSM? did not think of checking that) and signs to the next crossing point (number).
August 13, 2025 at 7:22 AM
egonw.mastodon.social.ap.brid.gy
in welk seizoen is deze foto gemaakt? hoogwater, maar wel heel selectief. En elders hele meren drooggelegd.

#volkskrant
Vreemde kaart van Nederland, zeker als je bedenkt dat dat het eigenlijk om Borculo gaat. Eigenaardigheden omvatten een deels een droogelegde Veluwemeer en een schijnbare grote dam bij Eijsden, zodat de Maas bijna helemaal vie het Belgische kanaal richting Antwerpen gaat, maar net daarvoor stopt. Waarschijnlijk ivm met de werkzaamheden aan de rondweg.
August 10, 2025 at 9:28 PM
egonw.mastodon.social.ap.brid.gy
things I am doing this morning:

1. check up on the impact of retracted articles (with @wikidata)
2. curation of @wikipathways pathways

The second follows up from work yesterday, going through a long list of pathways on the old website but not on the new […]

[Original post on mastodon.social]
2D diagram of the CYP metabolism pathway, with an outdated list of CYP enzymes. The metabolism is drawn as a circular process, involving oxygen, iron ions, and CYP enzymes. It is "homology converted" and can be updated with knowledge from the two references I added today (see the two reply posts).
August 8, 2025 at 9:05 AM
egonw.mastodon.social.ap.brid.gy
oh, sigh... @academicchatter, when are we actually improving our knowledge dissemination?

Are we going to be like "Linux on the desktop" here?

#addedvalue #publishing #fail
Screenshot of the "Supplementary data" section of a journal article, with six files, all "Multimedia component" (they're Excel spreadsheets, looking at the file extension), and nothing else. Surely, we can do better than that :(
August 7, 2025 at 9:02 AM
egonw.mastodon.social.ap.brid.gy
@molly0xfff @mfenner @rogue_scholar this is what it looks like in the JSON Feed, along with a second Rogue Scholar-supported extension for grants:
Screenshot of this JSON Feed snippet: "_references": [ { "url": "https://doi.org/10.26434/CHEMRXIV-2025-53N0W", "doi": "10.26434/CHEMRXIV-2025-53N0W" }, { "url": "https://doi.org/10.1021/acs.est.3c04855", "doi": "10.1021/acs.est.3c04855", "cito": [ "citesAsRecommendedReading" ] } ], "_funding": [ { "award": { "title": "The Virtual Human Platform for Safety Assessment", "acronym": "VHP4Safety", "uri": "drc.filenumber:nwa129219272" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } } ],
August 7, 2025 at 8:19 AM