Egon Willighagen
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egonw.social.edu.nl.ap.brid.gy
Egon Willighagen
@egonw.social.edu.nl.ap.brid.gy
470 followers 10 following 300 posts
This account is used for tooting conferences and about the Dutch academic system. Sometimes Dutch. Toots are personal and searchable. he/him

🌉 bridged from ⁂ https://social.edu.nl/@egonw, follow @ap.brid.gy to interact
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egonw.social.edu.nl.ap.brid.gy
nice group of 17 people hacking very hard! tons of improvements already live on https://platform.vhp4safety.nl/ :)

#vhp4safety #hackathon
Screenshot of section of the VHP4Safety GitHub Organization page, showing the activity of 5 projects, with the older commits about 4 hours and the most recent commit 11 minutes ago.
December 2, 2025 at 3:12 PM
egonw.social.edu.nl.ap.brid.gy
new blog: "WikiPathways curation reports on profile pages" https://doi.org/10.59350/s7vw2-r7y02 https://chem-bla-ics.linkedchemistry.info/2025/11/30/wikipathways-curation-reports-on-profile-pages.html

#bioinformatics #cheminformatics #curation
Screenshot of the COVID-19 Community page with the pathways curated by this community, showing thumbnails of 21 pathways along with full title and a curation report badge showing the number of curation events. These are colored by the number of events, mostly yellow (1-2 suggestions) and orange (3-4 suggestions) here.
November 30, 2025 at 1:55 PM
egonw.social.edu.nl.ap.brid.gy
for 10 years I have been giving an introduction into protein structure at the Zuyd applied university (two short lectures, two short practicals).

We have been using Proteopedia, because it is Open, it is free, it is interactive, and is powered by Jmol […]

[Original post on social.edu.nl]
Visualization in Jmol of hemoglobin. The four protein strands (cartoon style) are translucent, while the heme groups are solid (spacefilling style). I can rotate it and easily see how the four heme groups are placed in the tertiary structures of the four protein strands.
October 20, 2025 at 4:01 PM
egonw.social.edu.nl.ap.brid.gy
interesting to see that also Journal of Cheminformatics (still not on Bluesky or Mastodon?) articles are also showing up in podcasts :) The most recent related to IP concerns: https://doi.org/10.1186/s13321-025-00982-w

HT @altmetric.com

#publishing #chemistry #cheminformatics
JCheminform. articles are mentioned in three podcast episodes, one from the Arxiv podcast, another from a homeopathy podcast.
October 18, 2025 at 7:52 AM
egonw.social.edu.nl.ap.brid.gy
no, no, and no. Context in narratives matter.
Screenshot of the "Exploring Bioinformatics in the Wild: Insights from Real LLM Conversations" preprint at BioHackrXiv. In the right sidebar we see textmined annotations: GPT -> Gene/Protein LLama -> Organism Mistral -> Chemical
October 12, 2025 at 6:38 AM
egonw.social.edu.nl.ap.brid.gy
the season is nearing... time to get Rudof into the garden https://rudof-project.github.io/

#rdf #shex #openscience
logo of RUDOF, which consists of three 3-member rings, linked in such a way the the blue bottom ring (pointing down) has two further rings, sprouting from the top two blue ring nodes like antlers on the head. If the idea did not land yet, the blue ring's bottom node has a red nose, and two black dots are drawn inside the blue ring, as if they are eyes. The name RUDOF is given below the icon, completing the logo.
October 6, 2025 at 7:19 AM
egonw.social.edu.nl.ap.brid.gy
that doesn't look right... https://doi.org/10.1021/acs.estlett.5c00688
On the left a 2D depiction of 1-octanesulfonic acid group, but it's actually a drawing of octanoic acid
September 27, 2025 at 9:57 AM
egonw.social.edu.nl.ap.brid.gy
I can also do a search in PubMed, which focuses on biomedical literature. Here we see a at least stable, putative rising trend of use of SPARQL.

Yes, I conclude our BioSB course is very timely. So, sign up for our "Knowledge Graphs in the Life Sciences" course […]

[Original post on social.edu.nl]
SPARQL in biomedical literature shows a slightly different picture. Here, with 2018 is outlier with only 10 articles, we see a steady output of 20-30 articles since 2016. We can reasonably assume these are articles that do not study SPARQL itself, but actually use SPARQL. One could argue that the adoption is actually growing, since 2024 had 30 papers (equal to the previous peak in 2017) and 21 in 2025 already.
September 24, 2025 at 7:52 AM
egonw.social.edu.nl.ap.brid.gy
so, we can query two #openscience literature database for #sparql and see how the mentions evolve over time.

First, we say in @OpenAlex that the overall mention of SPARQL has peaked a while back and a stable to slightly declining trend since.

This matches the […]

[Original post on social.edu.nl]
Results of a search for "SPARQL" in OpenAlex, showing 5 highly cited papers. Eric's publication has been cited over three thousand times. The peak was 520 publications in 2014. SPARQL as been merged into production solutions and the research into SPARQL itself has just slowed down (I think).
September 24, 2025 at 7:46 AM
egonw.social.edu.nl.ap.brid.gy
new preprint: "Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities" https://doi.org/10.12688/f1000research.168288.1

"The ELIXIR Communities framework is made up of a suite of tools and processes that ensure […]

[Original post on social.edu.nl]
"Figure 1. Stages in the development of ELIXIR Communities. Timeline to show the progression of each ELIXIR Community through the stages of Community maturity, following the processes outlined along the top row. Once a community has reached the phase of Heads of Nodes approval (i.e. approval by the country-level bioinformatics leads), it becomes an official ELIXIR Community and can begin work on an internal project funded through ELIXIR’s core funds. The most mature Communities are shown in the top right (these were the four ELIXIR-EXCELERATE Use Cases), with the newest Communities shown in the bottom left (Communities portfolio as of December 2023)."
September 9, 2025 at 11:56 AM
egonw.social.edu.nl.ap.brid.gy
flash talk #2: "Retracted articles in Wikidata and how to use them" https://meta.wikimedia.org/wiki/File:WikiCite_2025_Retractions_-_Egon_Willighagen.pdf

(with huge thanks to Retraction Watch and @crossref !)

#wikicite2025
Screenshot of the title slide in the WikiCite 2025 "Bern" style. The style has the meeting logo on the left ("wikicite BERN '25") on the left with below that an drawing of a man in an landscape with a white piece of paper in his hand with some writing, possibly a "citation". Custom part is the title of my talk, my name followed with matching ORCID and ROR logos, my department name "Translational Genomics", and the name of my university. At the very bottom a template notice to the audience to stay muted during the recording.
August 31, 2025 at 3:44 PM
egonw.social.edu.nl.ap.brid.gy
flash talk #1: "Update on the Citation Typing Ontology citation intention annotations" https://meta.wikimedia.org/wiki/File:WikiCite_2025_CiTO_Update_-_Egon_Willighagen.pdf

#wikicite2025
Screenshot of the title slide in the WikiCite 2025 "Bern" style. The style has the meeting logo on the left ("wikicite BERN '25") on the left with below that an drawing of a man in an landscape with a white piece of paper in his hand with some writing, possibly a "citation". Custom part is the title of my talk, my name followed with matching ORCID and ROR logos, my department name "Translational Genomics", and the name of my university. At the very bottom a template notice to the audience to stay muted during the recording.
August 31, 2025 at 3:42 PM
egonw.social.edu.nl.ap.brid.gy
porting more content of the old Groovy #cheminformatics with the #chemistry Development Kit book to Markdown, here about substructure searching: https://cdk.github.io/cdkbook/substructure.html
Screenshot of the book and the section "Exact Search" showing two scripts about exact structure matching. There is general text, but also two snippets of Groovy code, with links to show the full code example. At the bottom we see the 2D depictions of two chemical structures, isobutane and cycloproane
August 14, 2025 at 12:51 PM
egonw.social.edu.nl.ap.brid.gy
the new @wikipathways RDF is loaded in the SPARQL endpoint and this includes triples we did not have before, based on the "Cited In" functionality of WikiPathways (see https://fosstodon.org/@wikipathways/114925438577051352).

So, you can now list all pathways […]

[Original post on social.edu.nl]
Screenshot of a table with SPARQL query results of the first linked SPARQL query, with 13 COVID-19 community portal pathways, of which the most cited pathway ("COVID-19 adverse outcome pathway") is cited 13 times, three more cited 10, and a long tail.
August 13, 2025 at 3:22 PM
egonw.social.edu.nl.ap.brid.gy
new blog post: "Integrating comments via the Fediverse" https://chem-bla-ics.linkedchemistry.info/2025/08/13/integrating-comments-via-the-fediverse.html https://doi.org/10.59350/r4mbg-yyb06

"Almost half a year ago I read this post by Bastian about, well […]

[Original post on social.edu.nl]
Screenshot from the "comments section" from https://chem-bla-ics.linkedchemistry.info/2025/08/11/the-internet-journal-of-chemistry.html showing my test reply message and a follow up comment by Bastian.
August 13, 2025 at 10:30 AM
egonw.social.edu.nl.ap.brid.gy
I wrote up my notes and results of my effort to collect information about the Internet Journal of Chemistry: https://chem-bla-ics.linkedchemistry.info/2025/08/11/the-internet-journal-of-chemistry.html

Feedback, curation, ideas, etc are all most welcome!

#chemistry #wikidata
One of the screenshots from the linked blog post, showing an abstract of the Internet Journal of Chemistry, archived in the Internet Archive. The page shows the title, author list, publication data, abstract, and a bit more.
August 11, 2025 at 8:25 AM
egonw.social.edu.nl.ap.brid.gy
as Marshall College Professor Jones could have said: "This belongs in a database!" https://doi.org/10.1021/acsomega.4c10413

Well, the first pKa column and all arsonic acids are now in @wikidata :)

#openscience #chemistry #cheminformatics
Top part of Table 1 from the linked paper, showing 6 columns, an index, an IUPAC name (of a series of arsonic acids), and in the last two columns pKa values (first and second, of the arsonic acid).
July 31, 2025 at 7:55 PM
egonw.social.edu.nl.ap.brid.gy
yeah, that's cool

"Now, researchers have found a way to image the sugars at a resolution of just 9 Ångström — 0.9 nanometres — using an off-the-shelf light microscope." https://doi.org/10.1038/d41586-025-02376-2 and https://doi.org/10.1038/s41565-025-01966-5

#bioinformatics #sugar
July 30, 2025 at 9:47 AM
egonw.social.edu.nl.ap.brid.gy
chemical compound identifiers in @wikidata: https://edu.nl/xb8y7

#chemistry #wikidata #cheminformatics
Bar plot behind the link in the post, showing some 60 databases identifiers on the x-axes and the number of identifiers in Wikidata on they y-axis. There are only 5 identifiers with more then 900k identifiers, with three around 1.4M. The rest of the databases have at most 200k identifiers.
July 26, 2025 at 9:05 AM
egonw.social.edu.nl.ap.brid.gy
fwd: 'Wikidata for botanists: benefits of collaborating and sharing Linked Open Data" https://doi.org/10.1093/aob/mcaf062

#wikidata #linkeddata #botany
Screenshot of the linked page, showing the title of the paper, the authors (Sabine von Mering, Siobhan Leachman, Joaquim Santos, and Heidi M Meudt), and the Background and Scope sections of the abstract (see linked page). In the last, the Scholia (@wdscholia@wikis.world) tool (highlighted with a hand drawn red annotation).
July 25, 2025 at 9:26 AM
egonw.social.edu.nl.ap.brid.gy
ha, I managed to convert a CXSMILES in @wikidata via the MDL V2000 molfile and the #inchi webtool into an #InChI (!B) and InChIKey :) https://www.wikidata.org/wiki/Q66421202#P117

#cheminformatics #polymers
Screenshot of the linked Wikidata page showing the statements for 'chemical structure' showing a man-made image with a 2D depiction of the polymer (with the big square brackets notation), followed by the CXSMILES (with a autogenerated 2D depiction by CDK Depict), and then the InChI and InChIKey!
July 23, 2025 at 1:09 PM
egonw.social.edu.nl.ap.brid.gy
it would be so useful if every chemistry drawing tool (think JChemPaint, Sketcher, JME, MarvinSomething, etc) would always show the matching 3D structure alongside the 2D depiction

#chemistry
July 22, 2025 at 12:26 PM
egonw.social.edu.nl.ap.brid.gy
* nanoJava update: check
* ERM database update: check (no nano InChI yet)
* #inchi fediwall: check -> https://egonw.github.io/INOSC/?tags=inchi&accounts=
Screenshot of the linked #fediwall showing posts by me, @dalia@nfdi.social, @wendympatterson@mas.to, @BeilsteinInstitut@hessen.social, @cdk@fosstodon.org, @NFDI4Chem@nfdi.social, and @ChemistryViews@mstdn.social
July 20, 2025 at 8:45 PM
egonw.social.edu.nl.ap.brid.gy
curation reports for the @wikipathways Lipids portal on the portal itself. Using the curation tests defined in the @elixir_europe curation grant with LIPID MAPS https://lipids.wikipathways.org/ (click the Gallery tab)

#lipidomics #bioinformatics
Screenshot of the "Gallery" tab in the page linked in the post. It shows a gallery of thumbnails of 14 pathways, their titles just below the thumbnail depicting of the pathway, and below that the curation status bar. Some are green (no curation reports), yellow (some reports), or orange (several attention points).
July 20, 2025 at 6:17 PM
egonw.social.edu.nl.ap.brid.gy
oh boy... finally getting there... so close to finalizing and release a new SMARTCyp?

See for context https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html and https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html #cdk2024

#opensource #cheminformatics
Finally a working code example, based on CDK 2.9, for rendering a molecule with an highlighted atom.
July 16, 2025 at 10:21 PM