ontology-access-kit
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INCATools
Ontology Access Kit: A python library and command line application for working with ontologies
This falls back to the pure python at the moment. This should call the rust code
Current Monarch work would benefit from having semsimian return an empty object (or something in the expected form, at least) as a result for termset similarity rather than a NotImplementedError....
Background: - #289 To have more consistent names we should have a generate-mappings command. Lexmatch should be a (default) method within this. (this robot export and `--method`). In future there...
## Overview I was reading through https://incatools.github.io/ontology-access-kit/intro/tutorial01.html#search and also compared against https://incatools.github.io/ontology-access-kit/cli.html#runoak-search, and in the former, there are some syntax that you can use, like `^`, and `~`, as well...
GO: ```yaml id: GO:0016805 name: dipeptidase activity def: "Catalysis of the hydrolysis of a dipeptide." [https://www.ebi.ac.uk/merops/about/glossary.shtml#DIPEPTIDASE, PMID:19879002] synonym: "cytosolic dipeptidase activity" NARROW [] xref: EC:3.4.13.- xref: EC:3.4.13.18 {source="skos:narrowMatch"} xref: EC:3.4.13.21...
Currently using the bioportal client with some ontologies like FBbt, WBbt results in failure, because bioportal uses different names eg FB-BT We should implement the mapping - using bioregistry? in...
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...
Is it possible to add [subsets()](https://incatools.github.io/ontology-access-kit/packages/interfaces/basic.html#oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.subsets) and [subset_members()](https://incatools.github.io/ontology-access-kit/packages/interfaces/basic.html#oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface.subset_members) methods to Ubergraph implementation?
Running somthing like ``` runoak --stacktrace -i simpleobo:ontologies/maxo_2022-06-24.obo diff -X simpleobo:ontologies/maxo_2023-03-09.obo --statistics -o stats/maxo_diff.txt.yaml ``` Results in non deterministic serialisation of stats/maxo_diff.txt.yaml. 
