INCATools/ontology-access-kit

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Ontology Access Kit: A python library and command line application for working with ontologies

Stars: 198
Forks: 35
Open beginner issues: 1
Indexed issues: 183
Avg merge: 3d 4h
Merged PRs (30d): 1

Dominant language: Python
License: Apache-2.0
Last GitHub push: Aug 21, 2026
Latest indexed: Sep 17, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue

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183 open issues indexed

Finalize naming conventions and method signatures for all interfaces Open

design

INCATools/ontology-access-kit#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add an owlery implementation Open

enhancement

INCATools/ontology-access-kit#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add example of how to do gene set enrichment Open

documentation

INCATools/ontology-access-kit#32 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Write a complete tutorial Open

documentation

INCATools/ontology-access-kit#33 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
remove print statements in tests Open

good first issue

INCATools/ontology-access-kit#37 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Support for reasoning Open

enhancement

INCATools/ontology-access-kit#38 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add a generate-categories method Open

enhancement

INCATools/ontology-access-kit#41 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
actions take too long Open

repo-hygeine

INCATools/ontology-access-kit#44 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
reinstate wikidata tests and ensure wikidata querying respects limis Open

repo-hygeine

INCATools/ontology-access-kit#46 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
review cross-ontology-diff datamodel prior to implementing Open

design

INCATools/ontology-access-kit#61 · 4 comments · 0 reactions · 2 assignees · Indexed Sep 17, 2026
Align metrics with robot measure? Open

design

INCATools/ontology-access-kit#68 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
set_label_for_curie not implemented for owl files? Open

bug

INCATools/ontology-access-kit#73 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
High-level interface via the Bioregistry Open

design

INCATools/ontology-access-kit#74 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Test with sssom schema Open

repo-hygeine

INCATools/ontology-access-kit#82 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Search behavior on obo files not as expected Open

bug

INCATools/ontology-access-kit#88 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
is there documentation on the search stuff (eg t~ etc.)? Open

workshop

INCATools/ontology-access-kit#104 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
On fetching ancestors — is this stated or reasoned? Does the query invoke the reasoner or are we assuming pre-classified? Open

workshop

INCATools/ontology-access-kit#105 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Can you tell viz to include a legend? Open

enhancement workshop

INCATools/ontology-access-kit#107 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
consider adding list of ontologies for annotate subcommand Open

workshop

INCATools/ontology-access-kit#108 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
consider pystow for API keys Open

workshop

INCATools/ontology-access-kit#110 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Create table of implementation x interface/method Open

workshop

INCATools/ontology-access-kit#112 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Document outputs more in tutorial Open

workshop

INCATools/ontology-access-kit#113 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
And SOP to PRs Open

workshop

INCATools/ontology-access-kit#114 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
ensure CLI and interfaces are closely aligned Open

design workshop

INCATools/ontology-access-kit#115 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Protect main branch Open

repo-hygeine

INCATools/ontology-access-kit#122 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 17, 2026
annotator should provide string similarity between input and matched term Open

enhancement

INCATools/ontology-access-kit#129 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
annotator should provide finer-grained model of match type Open

enhancement

INCATools/ontology-access-kit#130 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add a TSV enricher command that does performant lookup on ontological elements of ids Open

enhancement

INCATools/ontology-access-kit#135 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
where does the sqlite database go when I do something like --input sqlite:obo:envo Open

question

INCATools/ontology-access-kit#136 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Unify the two contributing docs Open

documentation

INCATools/ontology-access-kit#143 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Define general patterns for CLI commands Open

design

INCATools/ontology-access-kit#145 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 17, 2026
Document coding conventions Open

design

INCATools/ontology-access-kit#149 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Implement flake8 rules Open

repo-hygeine

INCATools/ontology-access-kit#160 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add ability to retrieve and cache prefix maps Open

design

INCATools/ontology-access-kit#165 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Externalize OntoPortal client functions (e.g., for BioPortal, AgroPortal, EcoPortal) Open

design

INCATools/ontology-access-kit#168 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Design of semantic similarity data model Open

design

INCATools/ontology-access-kit#169 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Decide on default colors for each ontology in OAK configuration Open

design

INCATools/ontology-access-kit#170 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Document if and when to write plugins, and what the alternatives are Open

design

INCATools/ontology-access-kit#171 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Decide whether to split out OMK or fully fold in Open

design

INCATools/ontology-access-kit#172 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Define and implement strategy for giving incubated datamodels their own homes Open

design

INCATools/ontology-access-kit#175 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
push bioportal/ontoportal client code upstream Open

design

INCATools/ontology-access-kit#179 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Home for curify_table, uri_to_curie, curie_to_uri, and irify_table? Open

INCATools/ontology-access-kit#186 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 17, 2026
Include UMLS implementation Open

enhancement

INCATools/ontology-access-kit#187 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
wrap fenominal Open

enhancement

INCATools/ontology-access-kit#193 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Create a generic Jupyter notebook parameterizable by ontology selector Open

documentation

INCATools/ontology-access-kit#195 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Create a demo fastAPI layer on top of OAK Open

enhancement

INCATools/ontology-access-kit#198 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Add solr backend Open

enhancement

INCATools/ontology-access-kit#200 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
split cli.py into sub-packages Open

design

INCATools/ontology-access-kit#203 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
`get_label*` issues Open

INCATools/ontology-access-kit#212 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
`FunOwlImplementation`: `.entities()` and `.axioms()` produced 0 results Open

INCATools/ontology-access-kit#218 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026

INCATools/ontology-access-kit

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