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Some benchmarks are being skipped even with inclusion of "--run-all" flag
**To Reproduce**
Steps to reproduce the behaviour.
"pytest benchmark --run-all"
**Stack trace**
What is the exact err…
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generic `id` field (uniqueness) and namespaces, etc.
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Based on https://github.com/biocypher/collectri and the build script therein
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- [ ] find an ontology related to medical terms able to describe patient card's fields
- [ ] design a mapping allowing to transliterate from the patient card to the ontology vocabulary (using BioCyphe…
jdreo updated
5 months ago
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# Connecting Preprints to Peer-reviewed Articles on Wikidata | Biopragmatics
After the BioCypher preprint went up on the arXiv, I checked in on the missing co-author items list on the Scholia page th…
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The [Biolink model](https://github.com/biolink/biolink-model) has a native adapter inside BioCypher core. See https://biocypher.org/tutorial-ontology.html
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[OBO Foundry](https://obofoundry.org) Ontologies can be accessed natively though BioCypher by providing a file location (local or remote). See https://biocypher.org/tutorial-ontology.html
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**Describe the bug**
LLM reply using KG-RAG is inconsistent and contradictory, see screenshot
**Reproduction and actual result**
Steps to reproduce the behavior:
1. Modify docker-compose config …
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BioCypher currently crashes on "Translating BioCypher config leaves to Biolink" step, e.g. in clean installation of [OTAR-BioCypher](https://github.com/saezlab/OTAR-BioCypher).
Stack trace:
```INF…
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Hi,
@GitteDecatBIT is working on a new adapter for Biocypher -
it would be an adapter for the consolidated protein-protein interaction dataset [iRefindex](https://irefindex.vib.be).
The adapt…