Egon Willighagen<p>chemical compound identifiers in <span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span>: <a href="https://edu.nl/xb8y7" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">edu.nl/xb8y7</span><span class="invisible"></span></a></p><p><a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>wikidata</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
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#Cheminformatics
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Egon Willighagen<p>did you notice I started <span class="h-card" translate="no"><a href="https://social.anoxinon.de/@Codeberg" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>Codeberg</span></a></span> ?</p><p><a href="https://social.edu.nl/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opensource</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Egon Willighagen<p>new blog post: "PFAS in the blood of the Dutch population" <a href="https://chem-bla-ics.linkedchemistry.info/2025/07/06/pfas-in-the-blood-of-the-dutch-population.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2025/07/06/pfas-in-the-blood-of-the-dutch-population.html</span></a></p><p>About the recent <span class="h-card" translate="no"><a href="https://social.overheid.nl/@rivm" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rivm</span></a></span> report.</p><p>"So, what can I do to make this report more FAIR?"</p><p><a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://social.edu.nl/tags/pfas" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pfas</span></a> <a href="https://social.edu.nl/tags/netherlands" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>netherlands</span></a> <a href="https://social.edu.nl/tags/health" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>health</span></a> <a href="https://social.edu.nl/tags/chemours" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemours</span></a> <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>wikidata</span></a></p>
Blue Obelisk<p>and follows by CMLXOM 4.12: <a href="https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.12" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/BlueObelisk/cmlxom/</span><span class="invisible">releases/tag/cmlxom-4.12</span></a></p><p>CMLXOM is a Java library for processing CML, implementing the XML object model (XOM) for the Chemical Markup Language (CML).</p><p><a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Blue Obelisk<p>Euclid 2.11 is released: <a href="https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.11" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/BlueObelisk/euclid/</span><span class="invisible">releases/tag/euclid-2.11</span></a></p><p>Euclid is a library of numeric, geometric and XML routines.</p><p><a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Egon Willighagen<p>Ammar's PhD thesis can be found online at <a href="https://cris.maastrichtuniversity.nl/en/publications/enhancing-the-interoperability-and-reusability-of-nanosafety-data" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">cris.maastrichtuniversity.nl/e</span><span class="invisible">n/publications/enhancing-the-interoperability-and-reusability-of-nanosafety-data</span></a> and his defense is live streamed, see the link at <a href="https://www.maastrichtuniversity.nl/events/phd-defence-ammar-ammar" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">maastrichtuniversity.nl/events</span><span class="invisible">/phd-defence-ammar-ammar</span></a></p><p>It contains a lot of <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a>: <a href="https://social.edu.nl/@egonw/114766897696096032" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">social.edu.nl/@egonw/114766897</span><span class="invisible">696096032</span></a></p><p>And in the afternoon there is a minisymposium on the thesis topic: <a href="https://social.edu.nl/@egonw/114705860626722108" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">social.edu.nl/@egonw/114705860</span><span class="invisible">626722108</span></a></p><p><a href="https://social.edu.nl/tags/semanticWeb" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>semanticWeb</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/maastricht" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>maastricht</span></a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
UK<p><a href="https://www.europesays.com/uk/210189/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">europesays.com/uk/210189/</span><span class="invisible"></span></a> A framework to evaluate machine learning crystal stability predictions <a href="https://pubeurope.com/tags/AI" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AI</span></a> <a href="https://pubeurope.com/tags/ArtificialIntelligence" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ArtificialIntelligence</span></a> <a href="https://pubeurope.com/tags/AtomisticModels" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AtomisticModels</span></a> <a href="https://pubeurope.com/tags/Cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cheminformatics</span></a> <a href="https://pubeurope.com/tags/CombinatorialLibraries" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CombinatorialLibraries</span></a> <a href="https://pubeurope.com/tags/ComputationalMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ComputationalMethods</span></a> <a href="https://pubeurope.com/tags/engineering" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>engineering</span></a> <a href="https://pubeurope.com/tags/general" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>general</span></a> <a href="https://pubeurope.com/tags/Technology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Technology</span></a> <a href="https://pubeurope.com/tags/UK" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UK</span></a> <a href="https://pubeurope.com/tags/UnitedKingdom" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UnitedKingdom</span></a></p>
Andrew Dalke<p>Huh. Was using my new <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> fingerprint generator code generator on the PubChem fingerprints which can be defined by a single match.</p><p>It told me bits 472 and 506 are the same.</p><p>I pulled up the primary documentation, at <a href="https://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">ftp.ncbi.nlm.nih.gov/pubchem/s</span><span class="invisible">pecifications/pubchem_fingerprints.txt</span></a> and .. indeed they are, with the same patterns in reverse order!</p><p>472 C:N:C-C<br>506 C-C:N:C</p><p>The full list of such pairs is:</p><p>472/506, 585/657, 589/626, 620/632, 462/537, 581/642, 594/666, 470/520, 584/677, 595/608, 634/668, 490/556, 660/678</p>
Egon Willighagen<p>scientific discussion moved from "letters to the editor" to PubPeer. There is a lot to be said about that, but one thing that must be said is that PubPeer can disappear.</p><p>But Letters to the Editor are preserved, for better or worse. if not mistaken, it was <span class="h-card" translate="no"><a href="https://toots.nu/@dalke" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>dalke</span></a></span> that pointed me at <a href="https://social.edu.nl/tags/ICCS2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ICCS2025</span></a> to a 1977-1978 discussion via such letters. I looked them up, and annotated some of the citations with the Citation Typing Ontology, made <span class="h-card" translate="no"><a href="https://mas.to/@nanopub" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>nanopub</span></a></span> and put them in <span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span> </p><p><a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Blue Obelisk<p>new preprint with <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> by <span class="h-card" translate="no"><a href="https://mastodon.social/@Kohulan" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>Kohulan</span></a></span> et al.: "Cheminformatics Microservice V-3: A Web Portal for Chemical Structure Manipulation and Analysis" <a href="https://doi.org/10.26434/chemrxiv-2025-xjkxl" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.26434/chemrxiv-2025</span><span class="invisible">-xjkxl</span></a></p><p>"Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that provides unified programmatic access to cheminformatics libraries, including RDKit, Chemistry Development Kit (CDK), and Open Babel through a RESTful API framework."</p>
Egon Willighagen<p>so, maybe you are wondering how we're doing with the 1 million IUPAC names? <a href="https://chem-bla-ics.linkedchemistry.info/2025/03/08/iupac-names.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2025/03/08/iupac-names.html</span></a> <a href="https://chem-bla-ics.linkedchemistry.info/2025/04/27/one-million-iupac-names-2-the-100-thousand-milestone.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2025/04/27/one-million-iupac-names-2-the-100-thousand-milestone.html</span></a></p><p>Well, last week the 200k milestone was passed. But we're also running out of <a href="https://social.edu.nl/tags/openaccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openaccess</span></a> articles from Europe PMC.</p><p>By doing some simple string replacements (e.g. methyl/ethyl/propyl) we can grow the size easily to beyond 1 million! That is not bad, with three months of running scripts in the background.</p><p>But first <a href="https://social.edu.nl/tags/ICCS2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ICCS2025</span></a> and teaching grading first.</p><p><a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Andrew Dalke<p>Did my first timings of chemfp's "shardsearch" for searching ~1 billion <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> fingerprints by aggregate search of smaller shards.</p><p>Was annoyed that k=3 NN search of 1024-bit Morgan fingerprints took 10 minutes on my desktop. It should have been much faster, like less than a minute.</p><p>Then realized "wc shard*.fpb" takes *23 minutes*.</p><p>I'm gonna need a faster disk. Have spinning rust for 7 TB of space, not speed.</p><p>Zstd should help. It uses 1/4 the space. I'll need smaller shards to test.</p>
Blue Obelisk<p>thanks to the <span class="h-card" translate="no"><a href="https://fosstodon.org/@fosstodon" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>fosstodon</span></a></span> admins for giving statements. Not all our <a href="https://fosstodon.org/tags/fosstodon" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>fosstodon</span></a> answers have been answered.</p><p>We live in difficult times where tensions run high and where independent justice on social media is absent. <span class="h-card" translate="no"><a href="https://fosstodon.org/@fosstodon" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>fosstodon</span></a></span> welcomed our project, with hesitance, not knowing who is behind this account or who is behind the Blue Obelisk movement. This brings risks, courage, and misuse.</p><p>We like to thank <span class="h-card" translate="no"><a href="https://fosstodon.org/@fosstodon" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>fosstodon</span></a></span> for allowing us to share our <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> news here for 2.5 years</p>
Blue Obelisk<p><a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> dates back to the late nineties with the emerging collaborative development of JChemPaint, Jmol, and the Chemical Markup Language. Sketch of the history by Chris Steinbeck: "The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation" <a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-025-00990-w" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jcheminf.biomedcentral.com/art</span><span class="invisible">icles/10.1186/s13321-025-00990-w</span></a></p>
The Chemistry Development Kit<p>Jonas Schaub: "Last week, I presented my work on algorithmic substructure extraction (scaffolds, functional groups, and aglycones) at the Chemistry Development Kit User Group Meeting (<a href="https://fosstodon.org/tags/CDK25UGM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CDK25UGM</span></a>) in Maastricht.</p><p>You can now find my slides on Zenodo: <a href="https://doi.org/10.5281/zenodo.15058008" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.5281/zenodo.1505800</span><span class="invisible">8</span></a>"</p><p><a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
The Chemistry Development Kit<p>new paper: "Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK-Based Force Field Library" <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.70071" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">onlinelibrary.wiley.com/doi/fu</span><span class="invisible">ll/10.1002/jcc.70071</span></a> or <a href="https://doi.org/10.1002/jcc.70071" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.1002/jcc.70071</span><span class="invisible"></span></a></p><p>" This paper introduces JMolecular Energy (JME), a novel, open-source Java library designed to implement MMFF94 with a robust and extendable API (Application Programming Interface) that allows for access to individual energy components."</p><p><a href="https://fosstodon.org/tags/Chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Chemistry</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
The Chemistry Development Kit<p>right in time for the upcoming User Group Meeting?</p><p>CDK code running in your webbrowser, with JavaScript... how cool is that?</p><p><a href="https://github.com/BobHanson/cdk-SwingJS?tab=readme-ov-file" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/BobHanson/cdk-Swing</span><span class="invisible">JS?tab=readme-ov-file</span></a></p><p><a href="https://fosstodon.org/tags/javascript" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>javascript</span></a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a></p>
Egon Willighagen<p>the archives of the CHMINF-L mailing list go back to 1991 and is an absolute treasure trove of history of <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> tho perhaps a bit ACS biased: <a href="https://list.iu.edu/sympa/arc/chminf-l/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">list.iu.edu/sympa/arc/chminf-l</span><span class="invisible">/</span></a></p><p><a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/history" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>history</span></a></p>
ICCS<p>we now have an infographics for the JCheminform. Collection for accepted abstracts.</p><p>Abstract submission: <a href="https://iccs-nl.org/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">iccs-nl.org/</span><span class="invisible"></span></a><br>Collection info: <a href="https://www.biomedcentral.com/collections/ICCS25" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biomedcentral.com/collections/</span><span class="invisible">ICCS25</span></a></p><p><a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/ai" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ai</span></a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://social.edu.nl/tags/chemsky" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemsky</span></a></p>
ICCS<p>the abstract deadlines is two weeks away (for both orals and posters): <a href="https://social.edu.nl/@intconfchemstr/113871380288328159" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">social.edu.nl/@intconfchemstr/</span><span class="invisible">113871380288328159</span></a></p><p>Accepted abstracts presented at the ICCS in June will get invited for submitting the work to a special collection in the Journal of Cheminformatics. The collection page is now online! <a href="https://www.biomedcentral.com/collections/ICCS25" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biomedcentral.com/collections/</span><span class="invisible">ICCS25</span></a></p><p><a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://social.edu.nl/tags/openaccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openaccess</span></a></p>
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