Harry Caufield
Harry Caufield
The `runoak ontologies` command doesn't work as described in its docs: ``` $ runoak -i ubergraph ontologies FileNotFoundError: [Errno 2] No such file or directory: 'ubergraph' During handling of the...
Follow-up from #488 : The tests here still don't fully test RustsimImplementation itself. They should be updated accordingly.
[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...
As of this change: https://github.com/monarch-initiative/koza/commit/e2fb994971d707c82e6d3161cd7d983da1acadcd importing koza's main functions is done from `koza.cli_utils` rather than `koza.cli_runner`. This should be reflected in the docs.
Haven't been able to reproduce this consistently, but attempts to ground using the Translator endpoint (though OAK) will sometimes fail in an uncontrolled way. Stack trace c/o @enockniyonkuru ``` Traceback...
When missing API keys (and especially the Bioportal one), crashes can happen in the middle of operations. If a template requires Bioportal in its annotators, for example, using that template...
On the page: https://monarch-initiative.github.io/ontogpt/operation/ there are several links to templates, including one specifically to the GO-CAM template. All are 404 - likely because they should actually link to repository locations...
The knowledge engine class includes a `map_identifier` function: https://github.com/monarch-initiative/ontogpt/blob/e3a68ae8391b12559842089657799156c06fd2f0/src/ontogpt/engines/knowledge_engine.py#L418 This calls the NodeNormalizer API through OAK: https://github.com/INCATools/ontology-access-kit/blob/0a734a8383943891173eaf8b1fd95cf4fde1f65e/src/oaklib/implementations/translator/translator_implementation.py This process can take some time, especially when grounding many entities. In some...
The MIRO checklist is for the minimum information in reporting an ontology. Natural fit for an extraction template, as some responses may simply be IRIs, URLs, etc. See https://doi.org/10.1186/s13326-017-0172-7 See...
(related to discussion with @enockniyonkuru re: MAXO extraction on Apr 1 2024) SPIRES extraction does grounding recursively, but still doesn't always catch instances where the term to match is within...