Remote

Egon Willighagen

@egonw@social.edu.nl

mastodon 4.7.3

This account is used for tooting conferences and about the Dutch academic system. Sometimes Dutch. Toots are personal and searchable. he/him

706 Followers

381 Following

50 Posts

Joined August 06, 2023

ORCID:

https://encyclia.pub/0000-0001-7542-0286

Website:

https://egonw.github.io/

Blog:

https://chem-bla-ics.linkedchemistry.info/

OWL:SAMEAS:

https://mastodon.social/@egonw

Egon Willighagen @egonw@social.edu.nl

· 2mo ago

new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921

"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk@fosstodon.org developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."

Replies to this post show up in the blog.

#chemistry #cheminformatics #inchi #openscience

5

0

9

0

Egon Willighagen @egonw@social.edu.nl

· 4mo ago

RE: @osflimburg@social.edu.nl

I will be there for chats and networking, and and I love to talk about @tgx_um@social.edu.nl, @cdk@fosstodon.org, @blueobelisk@fosstodon.org, @wikipathways@fosstodon.org, @wikidata@wikis.world, @wdscholia@wikis.world, @bridgedb@fosstodon.org, @elixir_europe@mstdn.science, @fair4chemnl, @vhp4safety, @biohackrxiv@fediscience.org, @oscmaastricht@social.edu.nl, or just about #openscience in general!

7

0

10

0

Egon Willighagen @egonw@social.edu.nl

· 2mo ago

every now and then I end up in a situation where the research article will not be published under a CC-BY license.

This week, six more (publisher version) papers are now freely available, from venues like a IEEE journal, a book chapter, and from the Communications of the ACM.

Green #openaccess via the Dutch Taverne law. I hope the "free PDF" info spreads widely

2

0

1

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

for example, it found this IUPAC name in the past hour: tert-butyl (tert-butoxycarbonyl)(9-((2R,3R,4R,5R)-4-((tert-butyldimethylsilyl)oxy)-5-(((tert-butyldimethylsilyl)oxy)methyl)-3-(((E)-4-(diisopropoxyphosphoryl)-4,4-difluorobut-2-en-1-yl)oxy)tetrahydrofuran-2-yl)-9H-purin-6-yl)carbamate #chemistry

3

1

2

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

congrats to all .nl users!

3

0

3

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

the last speaker today is Hannah Bast talking about QLever, now showing how it compares to alternatives #SWAT4HCLS

3

0

1

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

or take this beauty :) 2,2-dimethylpropanoyloxymethyl (5R)-3-[[(2-amino-2-oxo-ethyl)-methyl-amino]methyl]-6-[(1R)-1-hydroxyethyl]-7-oxo-4-thia-1-azabicyclo [3.2.0]hept-2-ene-2-carboxylate interestingly, searching this in Google Scholar does not show which article this name is from. Neither does searching for the InChIKey. So, is this just an incomplete name from that article? Are we not yet indexing all chemistry that well yet?

2

2

1

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

a quick update, it works like a charm. getting many new IUPAC names this way, and it seems the 500k will be reached in about 2 weeks, which is quite amazing realizing it was around 290k 2 days ago, when it ran for about a year. (it's 332k right now) I think the difference is simply the many article JATS that come in late, and missed when doing API searches for a certain time period

2

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 4mo ago

Replying to

Nice to see the Maastricht Day already has 100 registrations! The Heerlen Day still have spots left. I am attending both, and will bring my #meshcore device to see how things are working out in the south of Limburg.

1

0

1

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

first speaker is Ronald Cornet (https://qlever.scholia.wiki/orcid/0000-0002-1704-5980) talking about the history of ontologies, reasoning, and more "we have been talking about reasoning over patient data for more than 20 years, but we still have not solve it" #swat4hcls

qlever.scholia.wiki

2

2

1

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Happy birthday, @OpenScienceNL@akademienl.social !!!!

2

0

3

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

yeah, not quite the list that I hoped for... new blog post: "FAIR Implementation Profiles: Chemistry" https://doi.org/10.59350/x115q-m5f95 #fair #chemistry #INTOXICOM #FAIR4ChemNL

"I have had this on my todo list for way too long: writing about FAIR Implementation Profiles, or FIPs for short" https://chem-bla-ics.linkedchemistry.info/2026/05/05/fair-implementation-profiles.html

Replies to this post will show up in the blog

1

0

2

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

RE: @tgx_um@social.edu.nl

nice work by my colleagues. Direct link to this new knowledge base: https://cnvpathwayatlas.github.io/cnv-website/

1

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

@uint8_t@chaos.social well, no worries, at the current speed, it will be way past A.D. 2060 before we have all names

1

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

@MsPhelps @OpenAlex @HLdeJonge each time with a major update, my metadata got corrupted again there is a significant risk with using big numbers: loss of interest in details

1

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

@wikipathways more on Vodorezova's FDPcrawleR can be found here: https://github.com/vodor001/FDPcrawleR #SWAT4hcls

1

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

I stepped out from the session bc of a cough from last week that doesn't want to go away, and because my batteries were running out and I have a demo to give later this afternoon I am sitting in the biohackathon area, with a RDF4RiskAssessment poster from four people from the German BfR @bfr, is Taras Guenther or one of the other authors also on the #fediverse #swat4hcls

1

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

third speaker is Pedro Paulo Favato Barcelos, of Health-RI about ontologies in patient history provenance he quotes: "the opposite of an ontology is not a non-ontology, but a bad ontology" -- someone #swat4hcls

1

9

0

0

Egon Willighagen @egonw@social.edu.nl

· 7mo ago

Replying to

@dalke@toots.nu @cdk@fosstodon.org I had a look, and a search for 'getCountFingerprint' says to have >700 results. I browsed 5 pages (<700, so maybe the initial is guess?), and that was mostly just the method as part of the interface IFingerprinter.

1

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 8mo ago

Replying to

@olibrendel PhD theses are notoriously hard to find. Where are you collecting them? Would be awesome to link to PhD theses from platforms like https://academictree.org/ and with @wikidata

academictree.org

The Academic Family Tree

1

3

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu btw, the current primary reference for PubChemRDF is https://doi.org/10.1186/s13321-015-0084-4

1

7

0

0

Egon Willighagen @egonw@social.edu.nl

· 10mo ago

@Bibliothecaris @SURF ah, great to hear they are further opening their #peertube trial!

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

we're back from lunch (no signs, so not clear what I had), and now started the first session after lunch by Samaneh Jozashoori and Nirmal Raman Kannaiyan using KGs and LLMs on literature for the purpose of drug repurposing #swat4hcls

0

6

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

the second talk in the session also shows that RDF in hospitals is there. Enough that people are now focusing on querying across databases, and no longer just aligning ontologies. Also, it shows that writing efficient SPARQL queries is something that requires tweaking SPARQL queries. The order of instructions matter, but a SPARQL query does not have a clear linear direction #SWAT4hcls

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

after my Scholia demo (during the poster session), now listening to two talks before the final keynote of today. First, Yael Tirlet is speaking about SPARQL modules, so that people can focus on what they want to query, rather than how. Thinking about my talk and that of others, we need a higher level SPARQL "programming language" indeed. #swat4hcls

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu oh, actually one more. I cannot find the copyright and license info for the data in the SPARQL endpoint. I see a MIT license in the GitHub repo (on the 200+ MB Turtle file), but that's not a data license. But if that is the intention (it's metadata, mostly), why not tag it as CCZero, which will make it nicely compatible with Wikidata?

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

@NFDI4Chem congrats! What are "your" highlights? Are there data sets that stand out because of their reuse, for example?

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 7mo ago

Replying to

@dalke@toots.nu sometimes all it needs is a good tutorial article

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 4mo ago

not just for people from Heerlen and Maastricht, but also for Sittard, Venlo, Hasselt, Aachen, Liege, and even Eindhoven and Cologne! #openscience

@oscmaastricht@social.edu.nl

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

second speaker is Ömer Durukan Kılıç from Maastricht University. He is talking about MIMIC-III, which I think is described here: https://doi.org/10.1016/j.ijmedinf.2026.106297 #swat4hcls

0

10

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

0

11

1

0

Egon Willighagen @egonw@social.edu.nl

· 8mo ago

Replying to

@olibrendel @wikidata in NL you are lucky (tho it happens more and more) to find them in university databases/repositories. But metadata is not systematically aggregated making them relatively hard to find. Belgium PhD thesis I really struggled with. It makes making academic trees non-trivial, but happy with how #wikidata has been helping with getting information together

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

@MatthiasMailaender@mastodon.social @cdk@fosstodon.org yes, indeed! I did not get around to that yet

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

second session just started with the first talk by Sabine Österle and Jan Armida about sharing health/patient data in Switzerland, across 26 kantons and legislations and 4 national languages #swat4hcls

0

8

0

0

Egon Willighagen @egonw@social.edu.nl

· 7mo ago

Replying to

@dalke@toots.nu @cdk@fosstodon.org my best guess would a search on github

0

5

0

0

Egon Willighagen @egonw@social.edu.nl

· 4mo ago

Replying to

@magnusmanske@wikis.world @Codeberg@social.anoxinon.de it has lists of all issues assigned to me and that I created

0

1

0

0

Egon Willighagen @egonw@social.edu.nl

· 4mo ago

Replying to

@magnusmanske@wikis.world how about "owner:magnusmanske is:issue is:open" ?

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

RE: @intconfchemstr@social.edu.nl

excited to see the first ICCS 2025 paper online!

0

0

1

0

Egon Willighagen @egonw@social.edu.nl

· 7mo ago

Replying to on discuss.systems

@dan@discuss.systems anything known about their academic tree? https://qlever.scholia.wiki/author/Q136505436#academic-tree

qlever.scholia.wiki

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu the webinterface of the SPARQL endpoint could use a horizontal scrollbar: https://ditrare.ise.fiz-karlsruhe.de/chemotion-kg/shmarql/?query=select%20%3Fs%20%3Fp%20%3Fo%20where%20%7B%3Fs%20%3Fp%20%3Fo%7D%20limit%201000%0A

ditrare.ise.fiz-karlsruhe.de

0

6

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu one last thought, I assume you also have SMILES in the datasets (since you have InChIs too), check out the work by Ammar Ammar that uses CDK Depict to visualize SMILES as 2D in SPARQL result tables: https://edu.nl/tuppe The column ?smilesDepict holds a SMILES value, but is automatically converted into a 2D depiction Source code: https://github.com/ammar257ammar/Snorql-UI/commits/master/ (see 2022-03-13 patch)

0

5

0

0

Egon Willighagen @egonw@social.edu.nl

· 6mo ago

Replying to

second speaker is Kristina Vodorezova about FDPcrawleR, working in the ERDERA project on rare diseases I wonder what the results are for the @wikipathways FDP #SWAT4hcls

0

2

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu @herreslab.bsky.social oh, and overlooked it the earlier, but you're using schema:ChemicalSubstance, cool! thank you so much!

0

2

0

0

Egon Willighagen @egonw@social.edu.nl

· 2mo ago

@inchi-trust.bsky.social @BorkLab@mstdn.science @shl@genomic.social @efsa.europa.eu

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 5mo ago

Replying to

follow up post: https://social.edu.nl/@egonw/116506249437053153

0

0

0

0

Egon Willighagen @egonw@social.edu.nl

· 11mo ago

Replying to

@lysander07@sigmoid.social @fizise@sigmoid.social @enorouzi@sigmoid.social @joerg@sigmoid.social @NFDI4Chem@nfdi.social @DiTraRe@social.kit.edu argh... one more. Do you already support the organometallic InChI as @herreslab.bsky.social's lab has been coordinating in @NFDI4Chem@nfdi.social ? it would an awesome early dataset with such InChIs for the #chemistry community to play with :)

0

3

0

0