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I recently switched a workflow that includes `peaceiris/actions-gh-pages` to use a self-hosted runner.
When using `peaceiris/actions-gh-pages@v3` and when the output branch doesn't already exist, t…
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It's nice that `jsonlite::read_json` supports URLs for paths:
```R
url = "https://github.com/related-sciences/nxontology-data/raw/71cf538dc5c258ada880d58663b0205b7b7f8561/087_chembl_target_tree.js…
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I encountered the following mypy error when type checking a module that does `import bioregistry`:
```
nxontology_data/utils.py:77: error: "Module bioregistry" does not explicitly
export attribut…
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While investigating issues with disease mappings to EFO in Open Targets we have realised that labels and synonyms are not unique as we would expect for the majority of the terms. We have done a system…
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### Discussed in https://github.com/JamesIves/github-pages-deploy-action/discussions/993
Originally posted by **curiousdannii** January 7, 2022
I'd like to be able to include the source commi…
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explodes https://github.com/related-sciences/nxontology-ml/issues/35#issuecomment-1766560619
We currently ignore non-diseases, by only training and predicting on terms that are diseases as per [`ge…
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There are several EFO term classifications that could be useful. I propose we start with trying to assign a certain `precision` to terms based on the following definitions:
- `high`: High precision…
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At @related-sciences, we created a Python library called [nxontology](https://github.com/related-sciences/nxontology) for computing intrinsic semantic similarity between pairs of nodes in an ontology.…
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One nice aspect of pronto is that it seems able to read most ontologies using a consistent API, even though ontologies don't always follow the same standards. As seen in [these docs](https://github.co…
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background in https://github.com/EBISPOT/efo/issues/935
We currently extract database cross-references for EFO using the `oboInOwl:hasDbXref` predicate. However, MONDO is providing xrefs with great…