iiinova — where your digital self keeps evolving

Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026

new blog: "Peer reviewed articles about biological processes in WikiPathways" chem-bla-ics.linkedchemistry.info/2… #openscience #wikipathways #biology #academicchatter "Earlier this year I […] [Original post on social.edu.nl]

Screenshot of the References section of the linked blog post, with the names highlighted of the "Journal of Cell Communication and Signaling" in yellow, which shows that it by far is the most popular journal (7/12 of the references visible in the screenshot) to publish pathways in WikiPathways in.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 03/10/2026

new blog: "New paper: "ToxTempAssistant: using large language models to standardise cell-based toxicological test method descriptions"" […] [Original post on social.edu.nl]

Screenshot of the acceptance note of the article, as archived on Zenodo by the journal. It shows the publisher code of the submission ("TEBT-2025-0014") and below that a colored table with blue, yellow, and green rows, with various bits of information, including the submission title, handling editor, number of reviewers (3), preprint DOI, evaluation stage, and final recommentation ("Accept").

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/10/2026

the Dutch Virtual Human Platform 4 Safety (VHP4Safety) project has a series of webinars upcoming. www.sciencrew.com/c/6594/a/33572695… #toxicology #safety #nederlandseWetenschapsAgenda

"Save the date" infographics for the "VHP4Safety Webinar Series" showing three colored hexagons with the three date/times of the three webinars and next to that the three webinar titles. All on a light blue background. Full details:

Introduction to the VHP
14 October 2026, 13:00 to 14:30 CEST

The first webinar will introduce the VHP4Safety project and the Virtual Human Platform. Participants will see how the platform works, explore its tools and learn how it can support safety assessment workflows. The programme will include a live demonstration of the platform and an example of how it was used to address a regulatory question related to thyroid hormone-mediated brain development.

Deep dive into the Parkinson's case study
28 October 2026, 13:00 to 14:30 CET

The second webinar will focus on VHP4Safety’s Parkinson’s case study. Speakers will explain how the Virtual Human Platform brings together in vitro research, Adverse Outcome Pathways, experimental data and available methods to support risk assessment, as demonstrated through the Parkinson’s case study.

From innovation to implementation
18 November 2026, 13:00 to 14:30 CET

The final webinar of the VHP4Safety webinar series will focus on the social side of building the VHP, including user research supporting the development and implementation of the Virtual Human Platform. It will also examine the public acceptance of computational models and artificial intelligence in risk assessment. The webinar will show how stakeholder needs and perspectives can support the development of tools that are scientifically robust, transparent and fit for purpose.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 24/09/2026

new blog post: "Green Open Access: where is the index?" chem-bla-ics.linkedchemistry.info/2… #openaccess #openalex #wikidata #openscience "Green Open Access is literature that has been made available […] [Original post on social.edu.nl]

Screenshot of a claudevibed application that shows information about a DOI. Here it shows where I could possible get a free version. It shows "full text" links from Europe PMC, OpenAlex, and CrossRef. Here we see that OpenAlex also found the Maastricht University institutional repository. Example of a green open access version.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 20/09/2026

I am also particularly keen on the CiTO/Wikidata integration! Powered by qlever.scholia.wiki/cito and chem-bla-ics.linkedchemistry.info/t…, of course. These two screenshots shows that, in a table and in a d3.js bar-with-tooltip, one for […] [Original post on social.edu.nl]

"CiTO page" for the CDK paper. We see the "Replies" tab with a horizontal bar with various sections of various sizes, mostly in shades of green. The bar section size reflects the number of works with the CiTO intention. Here, for the first CDK paper, "uses method in" with 61 citations is the biggest part. Below the horizontal bar showing the four most abundant CiTO intents.

Same tab page, but now for the Wakefield paper. The table shows the top six intention types, with CiTO "disputes" in a good second with 78 works that dispute the Wakefield paper. the horizontal bar shows a good "red" section for "negative" intents, like "disputes". But also fascinating is the large green area too.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 19/09/2026

it is really sad that the Journal of Cheminformatics did not continue the Citation Typing Ontology Pilot. It has so much potential. When I see how many people are adopting it in @biohackrxiv, I think it is a missed opportunity

While the Journal of Cheminformatics was a second journal to have explicit CiTO citation intent annotation, BioHackrXiv is clearly overtaking it in adoption. Details here: https://qlever.scholia.wiki/cito/

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 13/09/2026

the speaker tonight was Prof. Doris Marko (qlever.scholia.wiki/orcid/0000-0001…) who spoke about the Dark Side (of food additives). The chemotherapy prodrug irinotecan has various routes to got from pro-drug to drug. And causes serious […] [Original post on social.edu.nl]

Depiction of the various biological pathways in which the pro-drug can convert into the drug. This can happen already in the intestine, in the liver, and in the blood system.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 09/09/2026

new blog post: "WikiPathways: biological pathways across the species" chem-bla-ics.linkedchemistry.info/2… "So, when this week the article Xenbase: A Guide to the Xenopus Genetics and […] [Original post on social.edu.nl]

Thumbnail of part of a screenshot of a Wikidata Query Service bar chart from the linked blog post showing the number of pathways per species, for the six species with the most pathways. Humas is off the scale (>400 pathways), Cow around 240, Mouse around 210, Rat 125, yeast just over 100, and worm around 55.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 04/09/2026

"Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool" doi.org/10.1039/d3dd00069a #health #aging #biomarker #wikipathways this paper is not getting the attention is deserves: network biology to […] [Original post on social.edu.nl]

Part if Figure 12A: "Network visualization of aging biomarkers found in blood. (A) Overview of directed shortest path calculations for one of the analyzed datasets (MTBLS265) in this study, where relevant metabolites considered to be biomarkers for aging (high CV30 values) have a diamond shape; round nodes depict metabolites needed for connectivity, and hexagons visualize proteins. The thickness of the arrows between the nodes indicates the occurrence of this reaction in different pathways."

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 31/08/2026

but you can find work that I contributed to at #eccb2026. Elena del Pup is presenting her PlantMetWiki work with a poster. She loves to meet up and discuss biological plant pathways! And the matching @biorxivpreprint preprint is here […] [Original post on social.edu.nl]

Photo of Elena del Pup next to and presenting the poster about PlantMetWiki. The poster is very general in design. It doesn't have anything not covered in more detail in the preprint.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 07/08/2026

I listened to a @scientias podcast with @blog and @JonaLendering: "Scientias, oudheidkunde, en wetenschap, hoe dan" chem-bla-ics.linkedchemistry.info/2… doi.org/10.59350/jtx6g-4d547 "I […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 03/08/2026

this was one of the key papers from my PhD thesis: "Supervised Self-Organizing Maps in Crystal Property and Structure Prediction" doi.org/10.1021/cg060872y Cited only 8 times, and noting much changed since this 2010 blog: "My worst cited paper […] [Original post on social.edu.nl]

Image for the table of contents showing three connected panels: left a Kohonen map, in de middle a 2D scatterplot with multiple computer generated crystal structure (colored by structural cluster), and right a panel with two crystal structures depictions, each with two or three structures almost the same, but with quite different unit cell definition.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 26/07/2026

new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" doi.org/10.59350/yhf27-fp921 "Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and […] [Original post on social.edu.nl]

2d depiction of cisplatin: it has four ligands around a platinum atom, all in a single plane. In this image, in red, is actually an annotation of how the ligands are oriented around the platinum. This is also reflected in the isomeric SMILES in Wikidata: Cl[Pt@SP1]([NH3])([NH3])Cl.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 23/07/2026

I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: w.wiki/SgFB What is your favorite organometalic compound in Wikipedia? […] [Original post on social.edu.nl]

Table of research from the linked query. It shows a table with 117 results, of which some 11 are visible. The first column shows the Wikidata identifier, the second the name of the organometalic, the third one a SMILES (showing some of where their chemistry is wonderfully more interesting than simple organic compounds), and the fourth column the link to the matching Wikipedia page.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 13/07/2026

new blog post: "Carbon beats gold: Diamond Open Access is the future #2" doi.org/10.59350/gfrxs-bxn43 "So, let’s assume you are interested in the idea, and want to know what diamond open access journals exist in your research field, before you can even […] [Original post on social.edu.nl]

Screenshot from the blog post showing QLever SPARQL results as a table, with a list of the first ten diamond open access journals, their QID, names, ISSNs, language, and main subjects.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 06/06/2026

new blog post: "The launch of the Virtual Human Platform" doi.org/10.59350/s784p-s1y68 "Nine days ago, the VHP4Safety project (see these posts) held a launch event in Utrecht for the Virtual Human Platform (VHP), a key result of the Dutch Research […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 30/05/2026

Fwd: "New paper: pyBiodatafuse: Extending interoperability of data using modular queries across biomedical resources" doi.org/10.59350/7n2bs-zsm80 "In a recent paper, Yojana Gadiya, Javier Millán Acosta, and Tooba Abbassi-Daloii led a project called […] [Original post on social.edu.nl]

Schematic diagram showing many entities, like Gene, Key Event, Drug, Pathway, function, etc, along with ontology IDs for those types, and in colored arrows lines between them. The diagram is the result of data from multiple databases aggregated with the Python pyBiodatafuse package into a question-specific knowledge graph.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 06/05/2026

okay, we're again a step closer :) doi.org/10.5281/zenodo.20058112 500079 IUPAC names, 437358 unique names, reflecting 308603 unique InChIKeys Thank you, Europe PMC and all those Open Access authors! As well as the authors of OPSIN (Daniel!) and OSCAR […] [Original post on social.edu.nl]

Screenshot of section of the linked Zenodo page with the project data releases. It shows the "Versions" panel, here with 5 releases: Version milestone-10k, 50k, 100k, 200k, and 500k. The last was is just now, and the others all between March 4 (10k) and May 20 (200k). The second link in the post, to a blog post, explains.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/05/2026

new blog post: "One Million IUPAC names #5: a new approach and 400k names" doi.org/10.59350/gqtbx-jta57 #openaccess #iupac #cheminformatics #blueObelisk "Europe PMC, however, also provides the JATS XML files as download on their FTP site. Already that […] [Original post on social.edu.nl]

Screenshot of a (KDE) konsole with 8 streams of scientific literature, consisting of a long series of x, ., and o. In each stream, an x means a new article to be processed. Each . and o that follows is a single <p> element and the difference is that an o means at least one IUPAC name was detected in the paragraph.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 28/04/2026

for example, it found this IUPAC name in the past hour: tert-butyl (tert-butoxycarbonyl)(9-((2R,3R,4R,5R)-4-((tert-butyldimethylsilyl)oxy)-5-(((tert-butyldimethylsilyl)oxy)methyl)-3-(((E)-4-(diisopropoxyphosphoryl)-4 […] [Original post on social.edu.nl]

2D depiction of the chemical structure represented by the IUPAC name in the main post. it's a beast with 42 carbons, 74 hydrogens, 2 fluors, 5 nitrogens, eleven oxygens, a phosphorus, and two silicon atoms. It looks like an intermediate of some synthesis with various protection groups.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 26/04/2026

do you remember we have been collecting IUPAC names from literature (using Europe PMC) with the 1M names goal? Last August we reached 275 thousand (doi.org/10.59350/krw9n-dv417) and since then it really slowed down. I have been continued analyzing […] [Original post on social.edu.nl]

Four parallel processes analyzing a single xml.gz file. The screenshot shows four white-on-black panels. When extracting IUPAC names, it writes an 'x' for each new article (up to 10 thousand in a single .xml.gz), and a '.' or 'o' for each paragraph (<p> element in the XML). A '.' for a paragraph without an IUPAC name, and a 'o' for one with at least one IUPAC name. It's mesmerizing to watch the progress of the analyses pass by (an animating would show it adds at least one line per second), tho I rather had it as matrix animations.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 20/04/2026

our university has a nice new tool that searches the internet for FAIR and/or Open Data *and* Software and helps me getting this added in our "UM's Current Research Information System (CRIS)" This help is most welcome, as metadata for these research output […] [Original post on social.edu.nl]

Screenshot of the new helper tool. It shows the search parameters on the left, and a table with results in the main panel. In this long list, for each, I can indicate if that is correct, has an error in the metadata, and if I want to ignore it. I can also mark it for inclusion in the UM CRIS (other screenshot).

Screenshot of the Datasets/Software section of the UM CRIS system. It shows some general metadata for me, and the first two datasets currently in CRIS.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 25/03/2026

JH shows recent work where they use LLMs together with chemical similarity knowledge to do ChEBI ontology classification, the chebifier: chebifier.hastingslab.org and doi.org/10.1039/D3DD00238A #swat4hcls #cheminformatics

Screenshot of the Chebifier website in action in the SMILES CCCCCCO, recognizing it as a primary alcohol (and organooxygen compound).

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 15/03/2026

Registered the @elixir_europe Toxicology Community Hybrid Meeting 2026 meeting (25/26 June) in Taxila and TeSS: elixir-europe.org/events/toxicology… Local organizers: @Marvin, Danyel Jennen, and me Registration is open! #toxicology #learning #FAIRdata #safety #ELIXIREurope

Since Taxila and ELIXIR TeSS use the same software, the left (Taxila) and right (TeSS) pages for the same linked meeting, the pages look more or less the same (Taxila uses OpenStreetMap, where TeSS uses Google Maps). Otherwise, they both show the meeting title, dates, location, some more metadata (see the linked page), and a description:

"The ELIXIR Toxicology Community hybrid meeting will bring together Community members and partners for two days of presentations, workshops and collaborative discussion. The programme will review lessons learned from the INTOXICOM workshops, reflect on progress since the first Toxicology Community white paper, and outline priorities for the second white paper. Participants will also align Community needs with the new ELIXIR Roadmap and identify next goals and strategic directions. The meeting aims to strengthen collaboration across the Community and ensure continued alignment with ELIXIR strategic priorities."

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 22/02/2026

new blog post: "Where do the WikiPathways come from?" chem-bla-ics.linkedchemistry.info/2… doi.org/10.59350/6smn2-ah530 "We can see who the 8 people are who contributed to this pathway ..], and […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 12/02/2026

new blog: "Open Infrastructures #2: the SURF Fediverse" doi.org/10.59350/1ja9h-jem83 chem-bla-ics.linkedchemistry.info/2… "But SURF operates a second fediverse server, one using the PeerTube software, also […] [Original post on social.edu.nl]

Screenshot of the FAIR4ChemNL page on SURF's video.surf.nl showing a project description and a first video at the bottom, which is one describing the aims and work packages of the project.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 27/01/2026

while everyone seems to be taking a PISS as some journals (see the PISS preprint), did people notice the significant growth of the stock sentence: "No datasets were generated or analysed during the current study." It seems to be a new publisher thing […] [Original post on social.edu.nl]

Screenshot of the first page of Europe PMC search results showing 13 thousand finds in 2024 and 26 thousand in 2025 of the exact phrase. The screenshot also shows the search bar, those numbers as histogram, and a few papers with that stock phrase (and it doesn't matter so much which ones those are).

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 10/01/2026

new blog post: "Where does the WikiPathways Cited In information come from?" doi.org/10.59350/0xxqw-90533 chem-bla-ics.linkedchemistry.info/2… "with so many articles […] [Original post on social.edu.nl]

Screenshot of a GitHub 'git blame' page showing who added what in the citedin_lookup.yml page: https://github.com/wikipathways/wikipathways-database/commits/main/downstream/citedin_lookup.yml

We see on the right-hand side the yaml file, and on the left, for each line, which git commit last added or changed that line, and who was author of that commit, and when that commit was made.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 05/01/2026

new blog post: "" chem-bla-ics.linkedchemistry.info/2… doi.org/10.59350/wyz5v-vts33 "I am happy that Elena and Denise pulled me into a collaboration to create an RDF-based knowledge graph about plant pathways." tl;dr: […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 01/01/2026

new (review/position) paper: "Challenges and Future Directions in Assessing the Quality and Completeness of Advanced Materials Safety Data for Re‐Usability: A Position Paper From the Nanosafety Community" doi.org/10.1002/adsu.202500567 "While the FAIR […] [Original post on social.edu.nl]

Figure 1: "a) The quality and completeness of (curated) material-specific data are viewed as overlapping, yet distinct, concepts that together determine the transferability (or re-usability) of data: the data re-use context determines the (meta)data required for completeness. Whilst quality is not dependent upon the transferability (i.e., intended use/re-use) of the data, the specific (meta)data required for quality assessment may be dependent upon the experimental scenario (e.g., its reproducibility, underlying up-to-date science). Adapted from Marchese Robinson et al., (2016).[9] b) Iterative and interconnected increase of (meta)data completeness, transferability, and quality (indicated by the gradually enlarging hexagons for overlapping data concepts with re-use)."

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 29/12/2025

new blog post: "Open Infrastructures #1: Research Software Directory" chem-bla-ics.linkedchemistry.info/2… doi.org/10.59350/g30ef-gxm10 "RSD gives rich context to the research software. It can track the […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 22/12/2025

but focus on the things that make me happy. And that concludes a long intro which went in a different direction than intended... So, you haven't heard me much about CiTO citation intentions much in the past months. It has not stopped at all. 2025 will be […] [Original post on social.edu.nl]

Scholia barchart showing the number of articles with CiTO-annotated citations by year. The original Shotton 2010 paper is there, in green the Journal of Cheminformatics CiTO Pilot (2025 had 1 article with CiTO annotation), a large upcoming BioHackrXiv peak 16 preprints with intent annotations, and a growing number of intention annotation backed by nanopublications. Right now, 2024 still has the max, with 24 articles with CiTO-intent annotations, and 2025 just behind that with 22 (but there are a few more on the way...)

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/12/2025

nice group of 17 people hacking very hard! tons of improvements already live on 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.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 20/10/2025

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.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 18/10/2025

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: 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.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 12/10/2025

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

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 24/09/2025

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.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 24/09/2025

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).

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 09/09/2025

new preprint: "Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities" doi.org/10.12688/f1000research.1682… "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)."

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 31/08/2025

flash talk #2: "Retracted articles in Wikidata and how to use them" meta.wikimedia.org/wiki/File:WikiCi… (with huge thanks to Retraction Watch and @crossref !) #WikiCite2025

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 31/08/2025

flash talk #1: "Update on the Citation Typing Ontology citation intention annotations" meta.wikimedia.org/wiki/File:WikiCi… #WikiCite2025

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 14/08/2025

porting more content of the old Groovy #Cheminformatics with the #Chemistry Development Kit book to Markdown, here about substructure searching: cdk.github.io/cdkbook/substructure.…

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

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 13/08/2025

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 fosstodon.org/@wikipathways/1149254…). 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.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 13/08/2025

new blog post: "Integrating comments via the Fediverse" chem-bla-ics.linkedchemistry.info/2… 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.

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