ontology-access-kit
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INCATools
Ontology Access Kit: A python library and command line application for working with ontologies
Currently the notebooks in OAK are separate from the docs, and the user is invited to click on the ipynb file in github. This gives a decent rendering of the...
@cmungall can you provide a page docs page on how to use the obographs compliance framework? We are close to a robot release and we need this merged now: https://github.com/ontodev/robot/pull/1198...
Currently there are many failing open PRs with the same ruff warning. We should pin the ruff checks so that whenever ruff changes we don't get everything failing
I conducted a semantic similarity calculation experiment where I noticed that the Jaccard Similarity Score values of certain records differed when I used the `--information-content-file` option. I am unsure of...
See: - #171 Our current testing scenario doesn't test for a case where a core module depends on a package defined as an extra. All packages that are extras should...
## Overview I'm trying to use `runoak validate-mappings` on a SSSOM file, but I'm getting an error message, and it doesn't contain enough information to help me diagnose the problem....
I ran `runoak -i simpleobo:hp.obo diff -X simpleobo:hp-latest.obo -o diff.md -O md` and the `Classes added` section looked like this: Classes added: 932 | Term | ----| | Mosaic attenuation...
Version: oaklib 0.5.25 Replicates with both pronto and simpleobo adapters ## Minimal test ``` from oaklib import get_adapter example = """ format-version: 1.2 data-version: hp/releases/2024-02-25 ontology: hp.obo [Term] id: HP:0000001...
Most of the time the CLI commands use minimal formatting, but sometimes it's necessary to have lists, yaml blocks, etc E.g. the fill-table command is quite extensive This looks OK...