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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

Chore: gen-doc commands in fails when linkml>=1.9 Open

chore

INCATools/ontology-access-kit#850 · 7 comments · 1 assignee · Opened Feb 20, 2026
Allow exceptions when checking alignment Open

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

INCATools/odk-robot-plugin#6 · Opened Jan 26, 2026
Replace `dataclasses-jsonschema` Open

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

INCATools/odkcore#1 · Opened Dec 25, 2025
Importing Subclass Object Properties Open

question

Difficulty 4/5 3-5 days Newbie friendliness 30/100

INCATools/ontology-development-kit#1311 · 6 comments · Opened Dec 8, 2025
Automatic generation of the schema documentation is broken Open

bug

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

INCATools/ontology-development-kit#1310 · 8 comments · Opened Dec 7, 2025
statistics --compare-with output is opposite to expectation Open

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

INCATools/ontology-access-kit#847 · Opened Dec 5, 2025
Create a claude SKILL for ODK Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

INCATools/ontology-development-kit#1303 · Opened Nov 7, 2025
Request: new field for synonym permutations Open

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

INCATools/dead_simple_owl_design_patterns#87 · 2 comments · Opened Oct 22, 2025
match table skos predicates incorrect Open

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

INCATools/semantic-sql#101 · 1 comment · Opened Oct 18, 2025
Add `author_cell_type_annotations` (JSON) to Pandasaurus Open

INCATools/pandasaurus_cxg#97 · 1 assignee · Opened Sep 15, 2025
Add text embedding vectors Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

INCATools/ubergraph#168 · Opened Jul 31, 2025
Bioportal mappings fail with `AttributeError` Open

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

INCATools/ontology-access-kit#844 · Opened Jul 18, 2025
Adding, removing, and modifying cross-references to node metadata Open

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

INCATools/kgcl#99 · Opened Jun 29, 2025
Change `clean` to a double colon rule? Open

enhancement

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

INCATools/ontology-development-kit#1284 · 3 comments · Opened Jun 17, 2025
output subsequent scores for singleton mappings Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

INCATools/boomer#459 · 1 comment · Opened May 30, 2025
ODK should support parallel builds Open

enhancement wishlist

INCATools/ontology-development-kit#1248 · 4 comments · 1 assignee · Opened May 21, 2025
Publish the Protégé plugin on Maven Central? Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

INCATools/whelk#277 · Opened May 5, 2025
Broken Link for Enrichment Notebook (Update Documentation) Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

INCATools/ontology-access-kit#842 · Opened Apr 23, 2025
Excessive "unknown" Nodes Created for Metadata Fields with Unknown Ontology IDs Open

INCATools/pandasaurus_cxg#94 · 1 assignee · Opened Apr 15, 2025
transform DisjointUnion to DisjointWith Open

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

INCATools/whelk#275 · Opened Apr 15, 2025
chore: update poetry.lock, resolve errors Open

INCATools/ontology-access-kit#841 · 1 assignee · Opened Apr 14, 2025
similarity compare fails on CLI using `-set1-file` & `-set2-file` args with complaint about missing `@` Open

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

INCATools/ontology-access-kit#840 · Opened Apr 11, 2025
chore: improve dev-testing ergonomics Open

chore

INCATools/ontology-access-kit#838 · 1 assignee · Opened Apr 9, 2025
Add Upheno Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

INCATools/ubergraph#163 · 2 comments · Opened Mar 28, 2025
Provide more examples of custom mirrors Open

documentation

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

INCATools/ontology-development-kit#1201 · 2 reactions · Opened Mar 21, 2025
Update documentation to explain when cleaning the cache might be necessary Open

documentation

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

INCATools/ontology-development-kit#1191 · 5 comments · Opened Feb 24, 2025
Would adding a dcterms:created triple to the import modules & release artefacts make sense? Open

enhancement needs discussion

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

INCATools/ontology-development-kit#1188 · Opened Feb 21, 2025
Handling KEGG Prefixes with Identical URI Resolution Open

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

INCATools/semantic-sql#98 · 2 comments · Opened Feb 21, 2025
Add graph column to main schema Open

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

INCATools/semantic-sql#97 · Opened Feb 21, 2025
add link to paper in README and schema Open

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

INCATools/kgcl#98 · Opened Feb 17, 2025
add FBbt to coherency check Open

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

INCATools/ubergraph#161 · Opened Feb 14, 2025
Export formats Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

INCATools/semantic-sql#96 · 2 comments · Opened Feb 14, 2025
Broken link in docs Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

INCATools/ontology-access-kit#827 · Opened Jan 31, 2025
`prefix` parameter is incompletely defined for `process-issue` command Open

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

INCATools/ontobot-change-agent#99 · Opened Jan 27, 2025
Update actions/cache in workflow Open

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

INCATools/kgcl#94 · Opened Dec 11, 2024
Update docs on pystow/sqlite cache management Open

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

INCATools/ontology-access-kit#823 · Opened Dec 10, 2024
add a matrix view of relationships, like one can get for logical definitions Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

INCATools/ontology-access-kit#822 · Opened Dec 9, 2024
Extend adapters to support versions Open

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

INCATools/ontology-access-kit#821 · 3 comments · Opened Nov 27, 2024
Provide simple yaml-based output for release summary in `runoak diff` Open

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

INCATools/ontology-access-kit#820 · 1 comment · Opened Nov 13, 2024
Ensure docker file matches the actually used image Open

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

INCATools/ubergraph#159 · Opened Oct 16, 2024
Document (or remove) the `baselite` artefact Open

documentation

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

INCATools/ontology-development-kit#1102 · 1 comment · Opened Oct 14, 2024
Installation issue Open

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

INCATools/obographviz#34 · Opened Oct 11, 2024
requesting a new `sqlite:obo:xyz` input only says "urllib.error.HTTPError: HTTP Error 404: Not Found" if an ontology with abbreviation xyz can't be found Open

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

INCATools/ontology-access-kit#813 · Opened Oct 3, 2024
OAK documentation and command line parsing should differentiate between TSV and CSV Open

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

INCATools/ontology-access-kit#812 · Opened Oct 3, 2024
Include other graph projection patterns Open

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

INCATools/relation-graph#270 · Opened Oct 3, 2024
Commands that treat empty lists as "all" should return no lists of a query that has zero results is passed Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

INCATools/ontology-access-kit#811 · 1 reaction · Opened Oct 3, 2024
Expand documentation on graph projections and allow finer grained control Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 30/100

INCATools/ontology-access-kit#809 · 2 reactions · Opened Oct 2, 2024
Oaklib annotate function does not return all substring containing values as expected Open

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

INCATools/ontology-access-kit#805 · Opened Sep 27, 2024
Weirdness in Ubergraph around RO and BFO labels (two labels for one CURIE) Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

INCATools/ubergraph#156 · 1 comment · Opened Sep 26, 2024
MONDO: unobsolete term Open

not implemented

Difficulty 1/5 Under an hour Newbie friendliness 35/100

INCATools/ontobot-change-agent#97 · Opened Sep 17, 2024

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