ontology-access-kit
ontology-access-kit copied to clipboard
INCATools
Ontology Access Kit: A python library and command line application for working with ontologies
This also reduces some test verbosity (move print -> logging.info, but the logger is not configured to completion) adds a short-cut `make lint-fix` target.
- [ ] improve dev control over test outputs (e.g., move `print` to `logging`/`logger`) - [ ] improve test run speed (currently takes ~ 38 mins locally to run the...
to fix #836 Updated all links pointing to /notebooks/Commands/ to now point to /docs/examples/Commands/ following repository reorganization. This includes links in: - README.md - src/oaklib/cli.py - docs/faq/commandline.rst - docs/guide/mappings.rst -...
On [this documentation page](https://incatools.github.io/ontology-access-kit/cli.html#runoak-associations) page, we link to https://github.com/INCATools/ontology-access-kit/blob/main/notebooks/Commands/Associations.ipynb but this is broken. I think it should point here instead: https://github.com/INCATools/ontology-access-kit/blob/main/docs/examples/Commands/Associations.ipynb I think might be several other places in the...
The "Selectors" link on https://linkml.io/schema-automator/packages/annotators.html#annotators to https://incatools.github.io/ontology-access-kit/selectors.html returns a 404.
We have a FAQ entry "My cached SQLite ontology is out of date" https://incatools.github.io/ontology-access-kit/faq/troubleshooting.html#my-cached-sqlite-ontology-is-out-of-date This recommends low-level navigating to the pystow `.data` directly and explicitly clearing old .db files. However,...
I am working with a great bioinformatician on a project which involves doing oaking with PHENIO and loading data from the Monarch KG (separately). PHENIO is large, and it frequently...
In Mondo (and similarly in HPO) we have ``` reports/difference_release_base.md: tmp/mondo-released.obo $(KGCL_ONTOLOGY) runoak -i simpleobo:tmp/mondo-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type md ``` to generate a nice diff output with...