#inchi #cheminformatics #fairdata #iupac #openscience #chemicaldata #standards | Sonja Herres-Pawlis

Two weeks ago, we had the pleasure of hosting the Technical InChI Meeting (March 25–26), bringing together contributors from across the global InChI community - both in person and online. Over two intensive days, discussions focused on one central theme: how to evolve InChI as a robust, future-proof standard while maintaining trust, usability, and scientific rigor. Key outcomes and directions: 🔹 Beta release of Molecular Inorganics InChI A major milestone: the current version for molecular inorganics was approved as a beta release. This marks the most significant extension of the InChI standard in years, expanding coverage into new areas of chemical space. The beta release will undergo at least four months of broad community testing, aligned with IUPAC provisional recommendation procedures. 🔹 Testing, infrastructure, and community engagement The beta phase will actively involve: - major chemoinformatics platforms, - working group members and external testers, and broader community feedback via defined channels. Please have a look here: https://lnkd.in/eTP4xQzh (and choose “latest with Molecular Inorganics”) 🔹 Priorities for upcoming development Current focus areas include: - inorganic stereochemistry - advanced organic stereochemistry (MDL enhanced stereochemistry, atropisomers) - mixtures and reactions (with strong demand and existing IUPAC groundwork) - continued work on polymers, 🔹 FAIR cheminformatics and standards in practice Discussions on day two highlighted the broader context: How can chemical representations and standards like InChI support FAIR data principles, reduce ambiguity, and bridge the gap between academic definitions and industrial practice? Beyond the technical details, one message was clear: +++InChI is not just a format—it is a community effort.+++ With the beta release now underway, we invite the community to engage, test, and contribute to shaping the next generation of the standard. 📩 If you are interested in testing or contributing, feel free to reach out or follow upcoming updates. All these developments are only possible by the ongoing support of the InChI and the InChI Trust, NFDI4Chem, the VolkswagenStiftung and the Beilstein-Institut. #InChI #Cheminformatics #FAIRData #IUPAC #OpenScience #ChemicalData #Standards   Thank you for participation to Gerd Blanke, Ian Bruno, Ray Boucher, Jonathan Goodman, Anne Nijs, Steffen Pauly, Wendy Patterson , Ulrich Schatzschneider, Andrei Erin, Christoph Müller, Felix Bänsch, Markus Nietfeld, Richard Hartshorn, Thomas Doerner, Leah McEwen, Jan Brammer, Djordje Baljozovic, Jochen Ortmeyer, Evan Bolton

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chemfp 5.1 is out, my package for #cheminformatics fingerprints

Most of the new features are related to "superimposed" binary coding of count fingerprints. These do a good job of approximating the count Tanimoto when using the binary Tanimoto.

- integrated "superimposed" into RDKit binary fp generation

- added:
- EState count&superimposed fps (RDKit and OEChem)
- Gobbi 2D pharmacophore count fps (RDKit)
- LINGO count&superimposed fps from SMILES strings

More at https://chemfp.com/docs/whats_new_in_51.html .

What’s new in chemfp 5.1 — chemfp documentation 5.1 documentation

#SWAT4HCLS is over.

Today, I am at the #KNCV CTC meeting, where we are launching the #Cheminformatics and #DrugDiscovery working group, as part of the CTC Section

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

#swat4hcls #cheminformatics

Two papers for the ICCS Collection in the Journal of Cheminformatics have been tagged as accepted now. With another 4 under review, and at least one more paper to be submitted. The deadline was extended one last time.

But we are looking forward to a nice collection of work presented at the ICCS 2025!

#cheminformatics #noordwijkerhout #ICCS2025

OPSIN 2.9.0 has been released: https://chembl.blogspot.com/2026/03/opsin-v290-released.html

OPSIN is an IUPAC name parser that returns SMILES

"The release notes describe a mixture of minor bug fixes and improvements:"

#smiles #chemistry #iupac #cheminformatics #openscience

OPSIN v2.9.0 released

Just a quick note to say that Daniel Lowe has released OPSIN v.2.9.0 , the first release since Oct 2023. This is now available via the EMBL-...

Here's an #RDKit #cheminformatics quiz for you all. What do you think this code will output?

from rdkit import Chem
mol = Chem.MolFromSmiles("C" + "C(C)(C)" * 50 + "C")
pat = Chem.MolFromSmarts("[$([CD4H0X4](-*)(-*)(-*)-*)]")
print(len(mol.GetSubstructMatches(pat)))

No cheating by actually running the code! :) Feel free to explain your reasoning in the comments.

0
0%
38
0%
42
50%
50
50%
Poll ended at .

Spent most of the week writing an EState count #cheminformatics fingerprint for #chemfp .

It should have been a few hours to build on RDKit's EState code. Perhaps a bit longer to implement a faster version using the same SMARTS patterns.

I then realized the RDKit implementation and patterns had problems, eg, not matching both atoms in "CC", and unexpected handling of explicit hydrogens, like in deuterated [2H]. See https://git.sr.ht/~dalke/rdkit/log

The hard part was finding good test cases.

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They use Google Analytics to track my visit.

I sent email to the #EMBL data controller via [email protected] to highlight issues with Google and the US, and asked they stop using Google Analytics, or clarify why they couldn't use one of https://european-alternatives.eu/alternatives-to .

You should email them too. #cheminformatics

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