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INCATools

30 indexed repositories · View on GitHub

ontology-development-kit
Ontology lifecycle management

Dockerfile · 375 stars
ontology-access-kit
Ontology Access Kit: A python library and command line application for working with ontologies

Python · 198 stars
semantic-sql
SQL and SQLite builds of OWL ontologies

Python · 69 stars
ubergraph
Integrated OBO ontology store

Makefile · 53 stars
dead_simple_owl_design_patterns
A simple system for specifying OWL class design patterns for OBO-ish ontologies.

Python · 49 stars
whelk
Whelk is an OWL EL reasoner

Scala · 46 stars
boomer
Bayesian OWL ontology merging

Scala · 37 stars
dosdp-tools
Utility for working with DOSDP design patterns and OWL ontologies

Scala · 33 stars
obographviz
Customizable translation of OBO graphs to dot for visualization using graphviz and other tools

JavaScript · 27 stars
kgcl
Datamodel for KGCL (Knowledge Graph Change Language)

Python · 23 stars
relation-graph
Materialize OWL existential relations

Scala · 23 stars
whelk-rs
Whelk is an OWL EL reasoner

Rust · 23 stars
kgcl-rdflib
Tools for working with KGCL

Python · 20 stars
ontobot-change-agent
A GitHub bot for modifying ontology resources.

Python · 9 stars
environments2wikidata
Mapping of GAZ and ENVO to Wikidata

Makefile · 7 stars
fantom5-ontology
ontology categorizing samples from FANTOM5 project

Web Ontology Language · 6 stars
intelligent-concept-assistant

6 stars
neoplasmer
Neoplasm Entity Recognition: matching disease names to ontology classes

Prolog · 5 stars
rdf_matcher
swi rdf_matcher

Prolog · 5 stars
oakx-grape
Experimental OAK plugin for Grape

Python · 5 stars
10 more repositories live on View on GitHub

Beginner friendly Everything

Open All

Null values in configuration cause issues Open

INCATools/odkcore#31 · 2 comments · 1 assignee · Opened Sep 17, 2026
Review the relevance of development tools in ODKFull Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

INCATools/ontology-development-kit#1378 · Opened Sep 13, 2026
Include uv Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

INCATools/ontology-development-kit#1375 · 3 comments · Opened Sep 11, 2026
precompute_lookups() costs 2.62 GB on NCBITaxon with no docstring or indication that cost scales with ontology size Open

Difficulty 3/5 1-2 days Newbie friendliness 56/100

INCATools/ontology-access-kit#910 · Opened Sep 10, 2026
prefix table: 774 redundant rows, and 3 prefixes carrying another resource's base Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

INCATools/semantic-sql#124 · Opened Sep 10, 2026
Several methods return set-derived lists, so their order changes between processes Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

INCATools/ontology-access-kit#909 · Opened Sep 9, 2026
Add Markdown formatting at end of ODK seed command Open

Difficulty 3/5 1-2 days Newbie friendliness 66/100

INCATools/ontology-development-kit#1371 · 1 comment · Opened Sep 9, 2026
Review release artefacts Open

Difficulty 4/5 3-5 days Newbie friendliness 50/100

INCATools/ontology-development-kit#1369 · 4 comments · Opened Aug 29, 2026
Consistently use URIBASE / ONTBASE Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

INCATools/ontology-development-kit#1367 · 1 comment · 1 reaction · Opened Aug 16, 2026
Must “export” release artefacts use a format-dependent ontology IRI? Open

Difficulty 3/5 1-2 days Newbie friendliness 56/100

INCATools/ontology-development-kit#1366 · 4 comments · Opened Aug 16, 2026
Can we release? Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

INCATools/whelk-rs#35 · 1 comment · 1 reaction · Opened Aug 15, 2026
Properly document `use_custom_import_module` Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

INCATools/ontology-development-kit#1365 · 2 comments · Opened Aug 13, 2026
Intel Macs are reaching their end-of-life Open

community random musing

Difficulty 5/5 Over a week Newbie friendliness 25/100

INCATools/ontology-development-kit#1364 · 2 reactions · Opened Aug 4, 2026
Extend UI to support a curie-curie view to help with Translator provenance Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

INCATools/ubergraph#177 · Opened Jul 30, 2026
Remove upper version pin for python from OAK Open

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

INCATools/ontology-access-kit#905 · 2 comments · Opened Jul 15, 2026
Unify the versions of all actions and updating them to latest Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

INCATools/ontology-access-kit#904 · Opened Jul 15, 2026
tests/test_implementations/test_bioportal.py is fragile Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

INCATools/ontology-access-kit#903 · 3 comments · Opened Jul 15, 2026
Add Python 3.14 to the compatibility matrix Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

INCATools/ontology-access-kit#901 · 3 comments · Opened Jul 14, 2026
Migrate direct raw-S3 bbop-sqlite consumers to the semanticsql CDN Open

help wanted

INCATools/semantic-sql#115 · 7 comments · 1 assignee · Opened Jul 14, 2026
[bot] Cut a semsql release including the semanticsql.berkeleybop.io default Open

enhancement

INCATools/semantic-sql#114 · 2 comments · 1 reaction · 1 assignee · Opened Jul 14, 2026
Evaluate sqlite-zstd compression as alternative to gzip Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

INCATools/semantic-sql#111 · 1 comment · Opened Jul 2, 2026
Epic: reduce dependencies on central sqlite database Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

INCATools/ontology-access-kit#889 · Opened Jul 2, 2026
Ubergraph descendants() treats bare string CURIE input as characters Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

INCATools/ontology-access-kit#887 · Opened Jun 20, 2026
OLS adapter graph traversal lacks descendants() and reflexive keyword parity Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

INCATools/ontology-access-kit#886 · Opened Jun 20, 2026
OLS adapter label() returns None for OLS4 term payloads Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

INCATools/ontology-access-kit#885 · Opened Jun 20, 2026
Proposed new module type: minimal Open

enhancement needs discussion

Difficulty 5/5 Over a week Newbie friendliness 38/100

INCATools/ontology-development-kit#1352 · 18 comments · 1 reaction · Opened Jun 19, 2026
The ODK needs its own reference documentation Open

documentation

INCATools/ontology-development-kit#1351 · 1 comment · 1 assignee · Opened Jun 15, 2026
Provenance? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

INCATools/ubergraph#174 · 1 comment · Opened Jun 7, 2026
Slow "naive approach" root detection: no adapter overrides the base impl, hits noticeably at 2.7M-node scale Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

INCATools/ontology-access-kit#881 · 1 comment · Opened May 20, 2026
Consider using marocchino/sticky-pull-request-comment@v3 instead of NejcZdovc/comment-pr@v1.1.1 Open

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

INCATools/odkcore#15 · 3 comments · Opened May 20, 2026
Update `actions/checkout` in GitHub Actions workflow Open

bug

INCATools/ontology-development-kit#1346 · 3 comments · 1 assignee · Opened May 13, 2026
`test_text_fields` validator ignores `dataProperties` and `annotationProperties` Open

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

INCATools/dead_simple_owl_design_patterns#89 · Opened May 13, 2026
Reduce S3 egress costs for bbop-sqlite database downloads Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

INCATools/ontology-access-kit#880 · Opened May 11, 2026
axioms of `info` output have wrong labels Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

INCATools/ontology-access-kit#877 · Opened May 8, 2026
Schema: add author_label_column, author_synonym_columns, Open

INCATools/pandasaurus_cxg#100 · 1 assignee · Opened Apr 10, 2026
Optimize horned-owl text search for large local OWL ontologies Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

INCATools/ontology-access-kit#871 · Opened Apr 7, 2026
Warn users not to use make -B in their workflows Open

documentation

INCATools/ontology-development-kit#1333 · 5 comments · 1 assignee · Opened Apr 3, 2026
Install "just" in ODK Open

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

INCATools/ontology-development-kit#1332 · 2 comments · Opened Apr 3, 2026
oaklib fails to import with linkml-runtime 1.10.0: Format.JSON removed Open

Difficulty 2/5 1-3 hours Newbie friendliness 67/100

INCATools/ontology-access-kit#867 · 1 comment · Opened Apr 1, 2026
Integrate ENERO Foundry ontologies into Semantic-SQL Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

INCATools/semantic-sql#107 · Opened Mar 30, 2026
Revise documentation Open

documentation

INCATools/ontology-development-kit#1330 · 1 reaction · 1 assignee · Opened Mar 30, 2026
feature request: enhance term enrichment figures Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

INCATools/ontology-access-kit#866 · 1 comment · Opened Mar 24, 2026
broken link in enrichment demo Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

INCATools/ontology-access-kit#865 · Opened Mar 23, 2026
using semantic sql in R: a vignette Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 45/100

INCATools/semantic-sql#106 · 3 comments · Opened Mar 22, 2026
HPOA parser does not account for negation qualifier Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

INCATools/ontology-access-kit#862 · Opened Feb 26, 2026
Chore: Getting SADeprecationWarning in SQL code Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

INCATools/ontology-access-kit#861 · 1 comment · Opened Feb 24, 2026
Chore: Curies currently needs to be locked to version 11 Open

chore

INCATools/ontology-access-kit#855 · 1 comment · 1 assignee · Opened Feb 20, 2026
Chore: Gilda annotate changes return data format in release 1.5.0 Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

INCATools/ontology-access-kit#854 · Opened Feb 20, 2026
Chore: Backslash character in test data causes pronto to have error Open

chore

Difficulty 3/5 1-2 days Newbie friendliness 35/100

INCATools/ontology-access-kit#853 · 8 comments · Opened Feb 20, 2026
Chore: entrez eutils library needs to be replaced by API calls to remove dependency on pkg_resources/setuptools<82 Open

chore

INCATools/ontology-access-kit#852 · 6 comments · 1 assignee · Opened Feb 20, 2026

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