ontology-access-kit
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INCATools
Ontology Access Kit: A python library and command line application for working with ontologies
According to documentation, I should be able to use `lexmatch` with other ontology interfaces. However, while this here works fine: ``` runoak -i sqlite:foodon_wd.owl lexmatch -o foodon_wd_lexmatch.tsv ``` This here:...
## Overview I'm trying to use OAK to get an Obograph, and tried `ProntoImplementation`. I noticed that there are differences between what the `bioontologies` package gives me, and what `ProntoImplementation`...
[The docs entry for termset-similarity](https://incatools.github.io/ontology-access-kit/cli.html#runoak-termset-similarity) contains this example: ``` runoak -i go.db termset-similarity -p i,p nucleus membrane @ “nuclear membrane” vacuole -p i,p ``` Is this a typo? Does the...
This will implement ONLY TextAnnotator https://www.ncbi.nlm.nih.gov/research/pubtator/api.html Be sure to implement the throttle Note that certain ID transformations will need to be transformed Note: we may also want to extend the...
Currently there are different variants of ontologies available: - https://oboacademy.github.io/obook/explanation/owl-format-variants/ Depending on the use case, a user may wish to use different variants or different subsets - for visualizing locations...
## Overview I am trying to `pip` install on Python 3.11, but I get an error when trying to build `fastobo`. ## Error Short error: ` ERROR: Failed building wheel...
Currently there is one way to visualize ontology graphs, via graphviz. This involves 1. subgraph operation -> obo json [oak] 2. obo json to dot (mediated by stylesheet following kgviz...
Reference: https://github.com/monarch-initiative/mondo-ingest/issues/112#issuecomment-1329314132 - roman numerals: A function call to convert arabic to Roman numerals (or maybe vice versa? ) - stop word removal: similar to `--exclude-tokens` implemented in [PR here](https://github.com/INCATools/ontology-access-kit/pull/353)...
We have a PR for *exporting* FHIR JSON: - #320. This could be used for loading a HAPI FHIR server using any OAK-wrapped ontology It would be useful to have...
This issue arises from the process of accelerating the edge file generation in this PR: https://github.com/INCATools/oakx-grape/pull/15 While generating edge files with s, p and o, dangling nodes may not be...