Live and recent posts from across the Fediverse tagged #swat4hcls, aggregated by home.social.
📢 Submit your research to https://swat4hcls.org #SWAT4HCLS by 14.Sep.2026 at https://app.oxfordabstracts.com/stages/83041/submitter
Accepted papers will have the chance to submit an extended version to the conference collection at the Journal of Biomedical Semantics #JBMS
Topics around #knowledgeGraphs #ontologies #interoperability #datasets #Infrastructure #provenance #reproducibility #workflows #services #visualization for #Healthcare and #LifeSciences
short write up of #swat4hcls: https://doi.org/10.59350/bmxve-vry14 https://chem-bla-ics.linkedchemistry.info/2026/04/04/swat4hcls-2026.html
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
LS concluded her talk and mentioned their semantic mapping data is available from Zenodo: https://doi.org/10.5281/zenodo.18350592
last speaker before lunch is Lilly Schuckert about data for neuromuscular diseases
Final day at #SWAT4HCLS at AmsterdamUMC! Great to be here with Helmholtz KG team from HMC Hub Information & Health 🚀
Highlights included:
– Tutorials on #GraphRAG, SPARQL & provenance
– Inspiring keynotes by Hannah Bast (QLever) & Janna Hastings (LLMs)
– A buzzing poster session with fantastic discussions
And today we’re presenting:
👉 The Helmholtz Knowledge Graph
– building a semantic interoperability layer across @helmholtz
Come by and chat with us 🙌
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
the next speaker is Olga Endrich, taking about "Rx Norm for Europe - Toward the representation of medicinal products in the OMOP CDM"
the first talk after the coffee break is about STELA and "Unifying SNOMED CT Logical Expressions and Textual Descriptions"
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
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 with federated SPARQL!
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
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"
welcome to the live coverage of #SWAT4hcls !
We're kicking off day 2 of the symposium with a keynote by Janna Hastings!
Janna's @wdscholia page (and @ORCID_Org): https://qlever.scholia.wiki/orcid/0000-0002-3469-4923
Mastodon: @jannahastings
the last speaker today is Hannah Bast talking about QLever, now showing how it compares to alternatives
#SWAT4HCLS nice to see #qlever with a 1 trillion triple dataset. Or four UniProts ;)
@wikipathways more on Vodorezova's FDPcrawleR can be found here: https://github.com/vodor001/FDPcrawleR
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
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.
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
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
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
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
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
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
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"
@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!
new blog post: "SWAT4HCLS 2026 Amsterdam this week" https://doi.org/10.59350/mztnx-y1770 https://chem-bla-ics.linkedchemistry.info/2026/03/22/swat4hcls-2026-amsterdam-this-week.html
"Tomorrow, SWAT4HCLS 2026 will start, again in Amsterdam. The first SWAT4LS I attended was also in Amsterdam, and the second meeting in Amsterdam I was also there. And I was in Cambridge (see this post), Antwerp (no post), and at least to one of the two Leiden meetings (also no posts, it seems)."
Replies show up in the blog post.
@rupdecat there have been two reports from previous #SWAT4HCLS biohackathons:
"BioHackSWAT4HCLS25 report: Towards AI-Ready Datasets for the Life Sciences" https://doi.org/10.37044/osf.io/xqe8h_v1
and
"Publishing FAIR datasets from Bioimaging repositories" https://doi.org/10.37044/osf.io/7whtf
Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/