Mastodon

Charles Tapley Hoytcurrently preparing slides to present at the sixth <a href="https://nfdi.social/@NFDI4Chem" class="u-url mention" rel="nofollow noopener" target="_blank">@NFDI4Chem</a> consortium meeting on using the <a href="https://hachyderm.io/@bioregistry" class="u-url mention" rel="nofollow noopener" target="_blank">@bioregistry</a> for finding ontologies, standardizing cross-references, and supporting RDMalso thinking about how to automate generating slides that summarize the state of the database for future talks and reminded of <a href="https://xkcd.com/1205" rel="nofollow noopener" translate="no" target="_blank">https://xkcd.com/1205</a><a href="https://scholar.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://scholar.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://scholar.social/tags/semanticweb" class="mention hashtag" rel="nofollow noopener" target="_blank">#semanticweb</a> <a href="https://scholar.social/tags/linkeddata" class="mention hashtag" rel="nofollow noopener" target="_blank">#linkeddata</a> <a href="https://scholar.social/tags/FAIR" class="mention hashtag" rel="nofollow noopener" target="_blank">#FAIR</a> <a href="https://scholar.social/tags/rdm" class="mention hashtag" rel="nofollow noopener" target="_blank">#rdm</a> <a href="https://scholar.social/tags/fdm" class="mention hashtag" rel="nofollow noopener" target="_blank">#fdm</a> <a href="https://scholar.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a>

Andrew DalkeAny idea how to get the (<a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>) structures for a <a href="https://toots.nu/tags/ChEBI" class="mention hashtag" rel="nofollow noopener" target="_blank">#ChEBI</a> ontology term? Like, how do I get all the terpenoids, CHEBI:26873?<a href="https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_26873?lang=en" rel="nofollow noopener" target="_blank">https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_26873?lang=en</a> says there are 11,119 terpenoids but I see no way to download them.Trying the web API, <a href="https://www.ebi.ac.uk/chebi/backend/api/public/ontology/all_children_in_path/?relation=has_functional_parent&entity=CHEBI%3A26873&three_star_only=false&page=1&size=15&download=false" rel="nofollow noopener" target="_blank">https://www.ebi.ac.uk/chebi/backend/api/public/ontology/all_children_in_path/?relation=has_functional_parent&entity=CHEBI%3A26873&three_star_only=false&page=1&size=15&download=false</a> says there are 547 (482 if three_star_only=true).With 'download=true' I get the data in full (unpaged) data in tsv format, with the same counts.What am I missing?

Andrew DalkeGiven two <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> count vectors A={aᵢ} and B={bᵢ}, what is Tanimoto(A, B)? Followup with your preferred reference/literature citation if you have one.Also, if you prefer another name for either of the two equations, what is it?

Charles Tapley HoytI used chembl-downloader to create some nice charts on how the number of compounds, assays, activities, and other entities in ChEMBL have grown over time📖 <a href="https://cthoyt.com/2025/08/26/chembl-history.html" rel="nofollow noopener" translate="no" target="_blank">https://cthoyt.com/2025/08/26/chembl-history.html</a><a href="https://scholar.social/tags/chembl" class="mention hashtag" rel="nofollow noopener" target="_blank">#chembl</a> <a href="https://scholar.social/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a> <a href="https://scholar.social/tags/chemometrics" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemometrics</a> <a href="https://scholar.social/tags/chemoinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemoinformatics</a> <a href="https://scholar.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://scholar.social/tags/rdkit" class="mention hashtag" rel="nofollow noopener" target="_blank">#rdkit</a> <a href="https://scholar.social/tags/cdk" class="mention hashtag" rel="nofollow noopener" target="_blank">#cdk</a> <a href="https://scholar.social/tags/proteochemometrics" class="mention hashtag" rel="nofollow noopener" target="_blank">#proteochemometrics</a>

Andrew Dalkechemfp 5.0b2 is out. Get it while it's hot! For Linux:python -m pip install chemfp==5.0b2 -i <a href="https://chemfp.com/packages/" rel="nofollow noopener" target="_blank">https://chemfp.com/packages/</a>I'm still updating the documentation. See 'What's new in 5.0' at <a href="https://chemfp.com/docs/whats_new_in_50.html" rel="nofollow noopener" target="_blank">https://chemfp.com/docs/whats_new_in_50.html</a>* shardsearch - search many target files* simhistogram - histogram all the scores* FPB file now handles 1B+ records* sparse count fingerprints - new FPC format - rdkit2fpc to make them with <a href="https://toots.nu/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#RDKit</a> - fpc2fps to convert to binary fps - fps2fpc for the other way<a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Andrew DalkeIt's official - the upcoming chemfp 5.0 release will have limited support sparse count <a href="https://toots.nu/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> fingerprints, in addition to the normal binary fingerprints.The new format is "FPC", a variant of the FPS format. Details at <a href="https://chemfp.com/fpc_format/" rel="nofollow noopener" target="_blank">https://chemfp.com/fpc_format/</a>.There will also be "rdkit2fpc" for the four <a href="https://toots.nu/tags/RDKit" class="mention hashtag" rel="nofollow noopener" target="_blank">#RDKit</a> count fingerprint generators.Plus "fpc2fps" with several methods to convert sparse count features -> binary.And "fps2fpc" for the reverse (it's just a list of on-bit indices.)

Egon Willighagenporting more content of the old Groovy <a href="https://social.edu.nl/tags/Cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Cheminformatics</a> with the <a href="https://social.edu.nl/tags/Chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#Chemistry</a> Development Kit book to Markdown, here about substructure searching: <a href="https://cdk.github.io/cdkbook/substructure.html" rel="nofollow noopener" translate="no" target="_blank">https://cdk.github.io/cdkbook/substructure.html</a>

Egon WillighagenFwd: "Unleashing 4 million IUPAC names into the wild" <a href="https://chembl.blogspot.com/2025/08/unleashing-4-million-iupac-names-into.html" rel="nofollow noopener" translate="no" target="_blank">https://chembl.blogspot.com/2025/08/unleashing-4-million-iupac-names-into.html</a>"In support of Egon Willighagen's 'One Million IUPAC Names' project, we have just released more than 4 million IUPAC names text-mined from patents. Here are the details as listed on Zenodo:"<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/iupac" class="mention hashtag" rel="nofollow noopener" target="_blank">#iupac</a> <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a>

Blue ObeliskOscar4 5.3.0 has been released: <a href="https://github.com/BlueObelisk/oscar4/releases/tag/5.3.0" rel="nofollow noopener" translate="no" target="_blank">https://github.com/BlueObelisk/oscar4/releases/tag/5.3.0</a>"OSCAR (Open Source Chemistry Analysis Routines) is an open source extensible system for the automated annotation of chemistry in scientific articles. It can be used to identify chemical names, reaction names, ontology terms, enzymes and chemical prefixes and adjectives, and chemical data such as state, yield, IR, NMR and mass spectra and elemental analyses."<a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://fosstodon.org/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a>

Noel O'BoyleBlog post on "A new job, a postdoc opportunity, an open biological curator role, and a user group meeting " <a href="https://baoilleach.blogspot.com/2025/07/a-new-job-postdoc-opportunity-open.html" rel="nofollow noopener" translate="no" target="_blank">https://baoilleach.blogspot.com/2025/07/a-new-job-postdoc-opportunity-open.html</a><a href="https://mstdn.science/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://mstdn.science/tags/chemjobs" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemjobs</a> <a href="https://mstdn.science/tags/chempostdocs" class="mention hashtag" rel="nofollow noopener" target="_blank">#chempostdocs</a>

Egon Willigh☮gen 🟥the preprint argues that a flood of mediocre articles is (partly) caused by open data making it easy to do all sorts of analyses of these.It seems to me that the observation is correct. I have had this impression in <a href="https://mastodon.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> too, and, indeed, running an analysis on a data set like Tox21, ChEMBL, etc, had been getting increasingly easy.But I do not think that <a href="https://mastodon.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> and <a href="https://mastodon.social/tags/FAIR" class="mention hashtag" rel="nofollow noopener" target="_blank">#FAIR</a> are the problem, nor restricting access the solution.I have some ideas about the underlying problem:

Egon Willighagenas Marshall College Professor Jones could have said: "This belongs in a database!" <a href="https://doi.org/10.1021/acsomega.4c10413" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1021/acsomega.4c10413</a>Well, the first pKa column and all arsonic acids are now 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/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>

The BridgeDb Projectnew BridgeDb Datasources release: <a href="https://github.com/bridgedb/datasources/releases/tag/20270728" rel="nofollow noopener" translate="no" target="_blank">https://github.com/bridgedb/datasources/releases/tag/20270728</a>"Uses UniProtKB as name, removes EcoGene, and multiple small updates"BridgeDb Datasources is a dataset with metadata about data sources and organisms used by BridgeDb Java and downstream tools like <a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@wikipathways</a>, PathVisio, and others<a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Egon Willighagenchemical compound identifiers in <a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@wikidata</a>: <a href="https://edu.nl/xb8y7" rel="nofollow noopener" translate="no" target="_blank">https://edu.nl/xb8y7</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/wikidata" class="mention hashtag" rel="nofollow noopener" target="_blank">#wikidata</a> <a href="https://social.edu.nl/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a>

Charles Tapley HoytMost cheminformatics code that queries ChEMBL struggles with reproducibility.chembl-downloader can help:>>> import chembl_downloader as cd >>> df = cd.query(""" SELECT chembl_id, pref_name FROM molecule_dictionary WHERE pref_name IS NOT NULL """)It's even sneaking its way into <a href="https://masto.ai/@wpwalters" class="u-url mention" rel="nofollow noopener" target="_blank">@wpwalters</a> and <a href="https://mastodon.social/@dr_greg_landrum" class="u-url mention" rel="nofollow noopener" target="_blank">@dr_greg_landrum</a> blogs :)Code/Docs: <a href="https://github.com/cthoyt/chembl-downloader" rel="nofollow noopener" translate="no" target="_blank">https://github.com/cthoyt/chembl-downloader</a>Preprint: <a href="https://arxiv.org/pdf/2507.17783" rel="nofollow noopener" translate="no" target="_blank">https://arxiv.org/pdf/2507.17783</a><a href="https://scholar.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#cheminformatics</a> <a href="https://scholar.social/tags/chemoinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemoinformatics</a> <a href="https://scholar.social/tags/chembl" class="mention hashtag" rel="nofollow noopener" target="_blank">#chembl</a> <a href="https://scholar.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#reproducibility</a> <a href="https://scholar.social/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#chemistry</a> <a href="https://scholar.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a>

Kohulan RajanNew Preprint Alert!We're excited to share our latest work on <a href="https://mastodon.social/tags/ChemRxiv" class="mention hashtag" rel="nofollow noopener" target="_blank">#ChemRxiv</a>! MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures) is a web-based platform for extracting chemical information from scientific papers.📄 Preprint: <a href="https://doi.org/10.26434/chemrxiv-2025-9p1q1" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.26434/chemrxiv-2025-9p1q1</a>🔗 Try it out: <a href="https://marcus.decimer.ai" rel="nofollow noopener" translate="no" target="_blank">https://marcus.decimer.ai</a><a href="https://mastodon.social/tags/Cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Cheminformatics</a> <a href="https://mastodon.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://mastodon.social/tags/ChemicalDatabases" class="mention hashtag" rel="nofollow noopener" target="_blank">#ChemicalDatabases</a> <a href="https://mastodon.social/tags/AIinScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#AIinScience</a> <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScientificSoftware</a> <a href="https://mastodon.social/tags/ResearchTools" class="mention hashtag" rel="nofollow noopener" target="_blank">#ResearchTools</a>

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...

Recent searches

Search options

Administered by:

Server stats:

#Cheminformatics