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Egon Willighagenha, I managed to convert a CXSMILES in @wikidata via the MDL V2000 molfile and the <a href="https://social.edu.nl/tags/inchi" class="mention hashtag" rel="nofollow noopener" target="_blank">#inchi</a> webtool into an <a href="https://social.edu.nl/tags/InChI" class="mention hashtag" rel="nofollow noopener" target="_blank">#InChI</a> (!B) and InChIKey :) <a href="https://www.wikidata.org/wiki/Q66421202#P117" rel="nofollow noopener" translate="no" target="_blank">https://www.wikidata.org/wiki/Q66421202#P117</a><a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://social.edu.nl/tags/polymers" class="mention hashtag" rel="nofollow noopener" target="_blank">#polymers</a>

Egon Willighagenheading to the 2nd day of the Technical InChI Meeting in Aachen/Germany<a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://social.edu.nl/tags/inchi" class="mention hashtag" rel="nofollow noopener" target="_blank">#inchi</a>

Egon Willighagenheading tomorrow to the InChI Technical Exchange Meeting Summer 2025 in Aachen/DELooking forward to it, and particularly talking about the InChI for inorganics and trying that in <a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@wikidata</a> :) See <a href="https://doi.org/10.26434/chemrxiv-2025-53n0w" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.26434/chemrxiv-2025-53n0w</a>And also the nano InChI, see <a href="https://doi.org/10.3390/nano10122493" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.3390/nano10122493</a><a href="https://social.edu.nl/tags/nanoinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#nanoinformatics</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://social.edu.nl/tags/inchi" class="mention hashtag" rel="nofollow noopener" target="_blank">#inchi</a> <a href="https://social.edu.nl/tags/wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#wikidata</a> <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a>

Egon Willighagenupdating some java <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> libraries... Euclid and CMLXOM, and possibly making a Bacting release... but need to continue working on the CDK Depiction book chapter too...

Egon Willighagenoh boy... finally getting there... so close to finalizing and release a new SMARTCyp?See for context <a href="https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html" rel="nofollow noopener" translate="no" target="_blank">https://chem-bla-ics.linkedchemistry.info/2024/04/07/cdk2024.html</a> and <a href="https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html" rel="nofollow noopener" translate="no" target="_blank">https://chem-bla-ics.linkedchemistry.info/2024/06/16/cdk2024-3.html</a> <a href="https://social.edu.nl/tags/cdk2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#cdk2024</a> <a href="https://social.edu.nl/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#opensource</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Egon Willighagendid you notice I started <a href="https://social.anoxinon.de/@Codeberg" class="u-url mention" rel="nofollow noopener" target="_blank">@Codeberg</a> ?<a href="https://social.edu.nl/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#opensource</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Egon Willighagen# Qleverfile for PubChem, use with the # QLever CLI (`pip install qlever`) # # qlever get-data # ~2 hours, ~120 GB, ~19 billion triples # qlever index # ~6 hours, ~20 GB RAM, ~350 GB disk space (for the index) # qlever start # a few secondsSource: <a href="https://github.com/ad-freiburg/qlever-control/blob/main/src/qlever/Qleverfiles/Qleverfile.pubchem" rel="nofollow noopener" translate="no" target="_blank">https://github.com/ad-freiburg/qlever-control/blob/main/src/qlever/Qleverfiles/Qleverfile.pubchem</a><a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Egon WillighagenI think I am going to try to recover a bit of <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> / <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a> <a href="https://social.edu.nl/tags/history" class="mention hashtag" rel="nofollow noopener" target="_blank">#history</a>, and make the index of the Internet Journal of Chemistry (IJC) FAIR in <a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@wikidata</a> While the journal no longer exists, many articles are cited quite a few times.I did some exploration some time ago, and for some I found full text "self-archiving" versions online.And, TIL that Web of Science has entries for the articles too, which I just added for the 9 articles already in <a href="https://social.edu.nl/tags/Wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#Wikidata</a>: <a href="https://w.wiki/Eide" rel="nofollow noopener" translate="no" target="_blank">https://w.wiki/Eide</a>

Andrew DalkeAnyone have views or references on the effectiveness of count/sparse <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> fingerprints compared to binary/dense fingerprints?What about comparing methods to turn count/sparse fingerprints into binary ones? I know of several approaches, but nothing methodical or published.I'm trying to understand how I might add sparse/count fingerprints to chemfp.

Egon Willighagennew 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">https://chem-bla-ics.linkedchemistry.info/2025/07/06/pfas-in-the-blood-of-the-dutch-population.html</a>About the recent <a href="https://social.overheid.nl/@rivm" class="u-url mention" rel="nofollow noopener" target="_blank">@rivm</a> report."So, what can I do to make this report more FAIR?"<a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://social.edu.nl/tags/pfas" class="mention hashtag" rel="nofollow noopener" target="_blank">#pfas</a> <a href="https://social.edu.nl/tags/netherlands" class="mention hashtag" rel="nofollow noopener" target="_blank">#netherlands</a> <a href="https://social.edu.nl/tags/health" class="mention hashtag" rel="nofollow noopener" target="_blank">#health</a> <a href="https://social.edu.nl/tags/chemours" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemours</a> <a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://social.edu.nl/tags/wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#wikidata</a>

Blue Obeliskand follows by CMLXOM 4.12: <a href="https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.12" rel="nofollow noopener" translate="no" target="_blank">https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.12</a>CMLXOM is a Java library for processing CML, implementing the XML object model (XOM) for the Chemical Markup Language (CML).<a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Blue ObeliskEuclid 2.11 is released: <a href="https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.11" rel="nofollow noopener" translate="no" target="_blank">https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.11</a>Euclid is a library of numeric, geometric and XML routines.<a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Andrew DalkeVersion 5.0b1 of chemfp - the comprehensive package for binary <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> fingerprints - is out and ready for curious beta testers.Here's are highlights. For more info and Linux install info see <a href="https://chemfp.com/chemfp-50b1-available-for-beta-testing.html" rel="nofollow noopener" target="_blank">https://chemfp.com/chemfp-50b1-available-for-beta-testing.html</a>- shardsearch to search multiple files- simhistogram for a histogram of pairwise Tanimoto comparisons- the FPB file size limit increased from ~250M fingerprints to well over a billion- new Klekota-Roth fingerprint type for RDKit and OpenEye<a href="https://chemfp.com/" rel="nofollow noopener" target="_blank">https://chemfp.com/</a>

Egon WillighagenAmmar'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">https://cris.maastrichtuniversity.nl/en/publications/enhancing-the-interoperability-and-reusability-of-nanosafety-data</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">https://www.maastrichtuniversity.nl/events/phd-defence-ammar-ammar</a>It contains a lot of <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a>: <a href="https://social.edu.nl/@egonw/114766897696096032" rel="nofollow noopener" translate="no" target="_blank">https://social.edu.nl/@egonw/114766897696096032</a>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">https://social.edu.nl/@egonw/114705860626722108</a><a href="https://social.edu.nl/tags/semanticWeb" class="mention hashtag" rel="nofollow noopener" target="_blank">#semanticWeb</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://social.edu.nl/tags/maastricht" class="mention hashtag" rel="nofollow noopener" target="_blank">#maastricht</a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a>

UK<a href="https://www.europesays.com/uk/210189/" rel="nofollow noopener" translate="no" target="_blank">https://www.europesays.com/uk/210189/</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">#AI</a> <a href="https://pubeurope.com/tags/ArtificialIntelligence" class="mention hashtag" rel="nofollow noopener" target="_blank">#ArtificialIntelligence</a> <a href="https://pubeurope.com/tags/AtomisticModels" class="mention hashtag" rel="nofollow noopener" target="_blank">#AtomisticModels</a> <a href="https://pubeurope.com/tags/Cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Cheminformatics</a> <a href="https://pubeurope.com/tags/CombinatorialLibraries" class="mention hashtag" rel="nofollow noopener" target="_blank">#CombinatorialLibraries</a> <a href="https://pubeurope.com/tags/ComputationalMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalMethods</a> <a href="https://pubeurope.com/tags/engineering" class="mention hashtag" rel="nofollow noopener" target="_blank">#engineering</a> <a href="https://pubeurope.com/tags/general" class="mention hashtag" rel="nofollow noopener" target="_blank">#general</a> <a href="https://pubeurope.com/tags/Technology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Technology</a> <a href="https://pubeurope.com/tags/UK" class="mention hashtag" rel="nofollow noopener" target="_blank">#UK</a> <a href="https://pubeurope.com/tags/UnitedKingdom" class="mention hashtag" rel="nofollow noopener" target="_blank">#UnitedKingdom</a>

Andrew DalkeHuh. Was using my new <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> fingerprint generator code generator on the PubChem fingerprints which can be defined by a single match.It told me bits 472 and 506 are the same.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">https://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt</a> and .. indeed they are, with the same patterns in reverse order!472 C:N:C-C 506 C-C:N:CThe full list of such pairs is: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

Egon Willighagenscientific 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.But Letters to the Editor are preserved, for better or worse. if not mistaken, it was <a href="https://toots.nu/@dalke" class="u-url mention" rel="nofollow noopener" target="_blank">@dalke</a> that pointed me at <a href="https://social.edu.nl/tags/ICCS2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#ICCS2025</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 <a href="https://mas.to/@nanopub" class="u-url mention" rel="nofollow noopener" target="_blank">@nanopub</a> and put them in <a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@wikidata</a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Egon Willighagenthe average number of citations to articles in the Journal of Cheminformatics dropped for the second year in a row. Still leading the <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> field, but no longer significantly.Meanwhile, I can publish in RSC's Digital Discovery for free (NL big deal) and J.Cheminform. not (excluded from the NL big deal).Both are CC-BY, similar review standards, similar average citation count, similar open data standards, publisher support by RSC better than BMC.You see my problem?

Egon Willighagen"How many of the compounds that appear in the chemical literature are mentioned just once?" <a href="https://doi.org/10.59350/rzepa.28802" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.59350/rzepa.28802</a>"I am actually impressed that as many as 61.5% are mentioned more than once, since before learning the answer, I had intuitively guessed that percentage as being much lower."(me too)<a href="https://social.edu.nl/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Blue Obelisknew preprint with <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#opensource</a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> by <a href="https://mastodon.social/@Kohulan" class="u-url mention" rel="nofollow noopener" target="_blank">@Kohulan</a> 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">https://doi.org/10.26434/chemrxiv-2025-xjkxl</a>"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."

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