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#Cheminformatics

1 post1 participant0 posts today
Egon Willighagen

Fwd: "Unleashing 4 million IUPAC names into the wild" chembl.blogspot.com/2025/08/un

"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:"

chembl.blogspot.comUnleashing 4 million IUPAC names into the wildIn support of Egon Willighagen's ' One Million IUPAC Names ' project, we have just released more than 4 million IUPAC names text-mined from...
#cheminformatics#chemistry#iupac
Blue Obelisk

Oscar4 5.3.0 has been released: github.com/BlueObelisk/oscar4/

"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."

[maven-release-plugin] copy for tag 5.3.0
GitHubRelease 5.3.0 · BlueObelisk/oscar4[maven-release-plugin] copy for tag 5.3.0
#cheminformatics#chemistry
Egon Willighagen

heading tomorrow to the InChI Technical Exchange Meeting Summer 2025 in Aachen/DE

Looking forward to it, and particularly talking about the InChI for inorganics and trying that in @wikidata :) See doi.org/10.26434/chemrxiv-2025

And also the nano InChI, see doi.org/10.3390/nano10122493

ChemRxivScholia Chemistry: access to chemistry in WikidataSharing knowledge on chemicals in the digital age has been the playground of databases such as the Chemical Abstract Services and PubChem. Wikipedia complements this field by providing context to chemicals aimed at a broad audience, but is not easily read by machines. Wikidata was started as a database service to improve the machine readability of the knowledge captured in Wikipedia. Wikidata has an open license, application programming interfaces, and a strong provenance model. Scholia uses the features to provide access to chemical knowledge. This study reviews the chemistry in Wikidata, shows how thousands of new chemicals were added, extends Wikidata with new properties for chemical representation and external links to additional databases, and shows how we extended Scholia to represent the chemistry in Wikidata.
#nanoinformatics#cheminformatics#inchi
*
Egon Willighagen

I think I am going to try to recover a bit of #cheminformatics / #chemistry #history, and make the index of the Internet Journal of Chemistry (IJC) FAIR in @wikidata

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 #Wikidata: w.wiki/Eide

Egon Willighagen

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.

But Letters to the Editor are preserved, for better or worse. if not mistaken, it was @dalke that pointed me at #ICCS2025 to a 1977-1978 discussion via such letters. I looked them up, and annotated some of the citations with the Citation Typing Ontology, made @nanopub and put them in @wikidata

#openscience#cheminformatics
Egon Willighagen

"How many of the compounds that appear in the chemical literature are mentioned just once?" doi.org/10.59350/rzepa.28802

"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)

Henry Rzepa's Blog · How many of the compounds that appear in the chemical literature are mentioned just once? - Henry Rzepa's BlogTom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once? Intrigued, I first set out to find out how many substances, as Chemical Abstracts refers to the them, there were as of 5 June, 2025. There is a […]
#chemistry#cheminformatics
Blue Obelisk

new preprint with #opensource #cheminformatics by @Kohulan et al.: "Cheminformatics Microservice V-3: A Web Portal for Chemical Structure Manipulation and Analysis" doi.org/10.26434/chemrxiv-2025

"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."

ChemRxivCheminformatics Microservice V-3: A Web Portal for Chemical Structure Manipulation and AnalysisThe widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. 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. This latest version features a newly developed, interactive web-based frontend built with React, providing users with an intuitive graphical interface for manipulating and analysing chemical structures. The frontend supports essential cheminformatics operations, including structure editing, PubChem database integration, batch molecular processing, and standardised InChI/RInChI identifier generation. The microservice V3 addresses critical accessibility barriers in computational chemistry by providing researchers with immediate access to analytical tools, eliminating the need for specialised technical expertise or complex software installations. This approach facilitates reproducible research workflows and broadens the utilisation of cheminformatics methodologies across interdisciplinary research communities. The platform is publicly accessible at https://app.naturalproducts.net, and the complete source code and documentation are available on GitHub.
Egon Willighagen

so, maybe you are wondering how we're doing with the 1 million IUPAC names? chem-bla-ics.linkedchemistry.i chem-bla-ics.linkedchemistry.i

Well, last week the 200k milestone was passed. But we're also running out of #openaccess articles from Europe PMC.

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.

But first #ICCS2025 and teaching grading first.

chem-bla-ics · One Million IUPAC namesNames of chemicals are part of the human user experience when browsing a chemical database. And literature too, of course. Chemical names are also not easy to use, and what a chemical name means is not always clear. This is why the IUPAC started a standardizing nomenclature in chemistry, the IUPAC names. Each IUPAC name uniquely defines the chemical structure it defines. For example, methane is the IUPAC name for the chemical CH4.
#cheminformatics
Andrew Dalke

When I started chemfp, PubChem and CAS had <100M records. Real-world #cheminformatics data doubles about every 10 years (since WWII), so I figured 200M was good enough.

Chemfp's FPB format fails at around 268M recs due to its hash table format layout. (I stored 16*X instead of X in a 4 byte field.)

I've now been working with bigger synthetic data sets.

I've tweaked the FPB format to handle 1B records. 🎉

Can't go much bigger as id lookups get slow due to 32-bit hash collisions/pigeon-holing.

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