SWAT4HCLS 2026 A bit over a week ago, SWAT4HCLS 2026 took place, with the matching biohackathon on Thursday (see this post. I attempted a bit of live coverage on mastodon: day 1 and day 2. But it seems the semantic web community interested in SWAT4HCLS has not found the fediverse yet. So, make sure to check this full list of abstracts. The meeting consisted of four keynotes, each one was quite interesting. Cornet gave a nice historic perspective of the venue and of the semantic web field, which is a great way to welcome the participants to your institute. The talk also touches on the main theme of the meeting: clinical data. It is a long standing (and important) research field, but progress is slow. Cornet comments along the lines that _we have been talking about reasoning over patient data for more than twenty years, but we still have not solve it_. The problem is really not only privacy, but simple also lack of a common language. As Sabine Österle explains about sharing health/patient data in Switzerland, across 26 kantons and legislations and 4 national languages. Another issue is more technical, running SPARQL across hospitals involves more than just aligning ontologies, but also requires (too much) fiddling with SPARQL queries. There was plenty of other content too, however. For example, I was pleasantly surprised by the RDF4RiskAssessment work, the RO-Crates for BioImaging, and FDPcrawleR. All these projects have direct links to research ongoing in our TGX team. Hanna Bast gave the second keynote of the first day, about QLever (doi:10.1145/3132847.3132921). She talked about some of the recent improvements, something we really needed for Scholia. She showed a technical approach to make federated queries faster, tho it currently only works between endpoints that both run QLever. One thing I am looking forward to, is playing with the notion of materialized views, but the biohackathon was too short to get around to that during the Thursday. The second day kicked off with a keynote by Janna Hastings, whose work I greatly admire. I was not disappointed today, and she showed the Behaviour Change Intervention Ontology and Chebifier (doi:10.1039/D3DD00238A). The last talk I want to mention in the blog is by two researcher working with Michel Dumontier. They presented a study about deduplication in/of knowledge graphs. This is something I want to read in more detail.

short write up of #swat4hcls: https://doi.org/10.59350/bmxve-vry14 chem-bla-ics.linkedchemistry.info/2026/04/04/swat4hcls-202...

Replies to this post show up as comments in the blog post.

#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

Semantic Mapping of TREAT-NMD Core Datasets to the CARE-SM Mapping of the TREAT-NMD Core Datasets to the CARE-SM version 1.0.0

LS concluded her talk and mentioned their semantic mapping data is available from Zenodo: https://doi.org/10.5281/zenodo.18350592

#swat4hcls

The Helmholtz KG team from HMC Hub Information & HMC Hub Health is here in full force 🚀

After two fantastic days with highlights like: - Tutorials on #GraphRAG, advanced SPARQL & provenance harmonization - An inspiring keynote by Hannah Bast on “What’s new in QLever”

Curious about how we unify distributed data into a queriable knowledge graph? Come by and chat with us 🙌

Final day at #SWAT4HCLS at Amsterdam UMC. The Helmholtz KG team (HMC Hub Information & Health) is here in full force! 🚀

Highlights so far:
• GraphRAG, SPARQL & provenance tutorials
• Keynote by Hannah Bast on QLever
• Great poster session

@swat4hcls.bsky.social

last speaker before lunch is Lilly Schuckert about data for neuromuscular diseases

#swat4hcls

GitHub - cmbi/AutoQ-RWD: Automated data Quality Metrics Assesment (AutoQ) in Real World Data (RWD) for Common Data Elements (CDE) Automated data Quality Metrics Assesment (AutoQ) in Real World Data (RWD) for Common Data Elements (CDE) - cmbi/AutoQ-RWD

third speaker is Sergi Aguiló-Castillo (@Radboud_uni) who will talk about Automated Quality Metrics Assessment in Real World Data for Rare Diseases Registries.

AutoQ-RWD: https://github.com/cmbi/AutoQ-RWD

#swat4hcls

the next speaker is Olga Endrich, taking about "Rx Norm for Europe - Toward the representation of medicinal products in the OMOP CDM"

#swat4hcls

the first talk after the coffee break is about STELA and "Unifying SNOMED CT Logical Expressions and Textual Descriptions"

#swat4hcls

the third talk is introduced by @Andrawaag and remotely given by Robert Hoehndorf, about ontological modelling of dynamic biodiversity consensus

Of course, this is also what the #Wikiblitz ongoing here is about

#swat4hcls

Original post on social.edu.nl

the 2nd talk is by a team of two speakers from the IDS team at Maastricht University (Dumontier's group) about Embedding-based Deduplication of Knowledge Graphs using Graph Neural Networks

I think this would be a very interesting alternative to find WikiPathways/Rhea matches we previous did […]

Screenshot of the Chebifier website in action in the SMILES CCCCCCO, recognizing it as a primary alcohol (and organooxygen compound).

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

new-app undefined

after covering some of her past ontology work, JH is introducing us to the Behaviour Change Intervention Ontology (BCIO): https://www.bciontology.org/

"here the key thing is a research report"

#swat4hcls

welcome to the live coverage of #SWAT4hcls !

We're kicking off day 2 of the symposium with a keynote by Janna Hastings!

@jerven maybe an @OpenAlex SPARQL end point is next?

#SWAT4HCLS

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

#SWAT4HCLS

#SWAT4HCLS nice to see #qlever with a 1 trillion triple dataset. Or four UniProts ;)

GitHub - vodor001/FDPcrawleR: Metadata Completeness check for FAIR Data Point index of ERDERA Virtual Platform Metadata Completeness check for FAIR Data Point index of ERDERA Virtual Platform - vodor001/FDPcrawleR

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

#SWAT4hcls

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

Original post on social.edu.nl

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 […]

Original post on social.edu.nl

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 […]

It actually turns out that many speakers do not have Wikidata pages #SWAT4HCLS

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

Original post on social.edu.nl

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 […]

And www.swat4ls.org/workshops/amsterdam2026/... #SWAT4HCLS

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

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

Redirecting

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

Photo of Cornet talking about the growth of ontologies reigstered in BioPortal (visibile on the slide in the background), in a Amsterdam UMC lecture hall, with a replica of Rembrand's "The Anatomy Lesson of Dr. Nicolaes Tulp" on the wall on the left side.

#swat4hcls

Scholia

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

@Andrawaag is kicking off the #swat4hcls main symposium. yesterday was the tutorial day, but all the talks (including a short talk by me) will be today.

Plz ping me if you read this and are also at SWAT4HCLS!