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152 Open 194 Closed
152 Open 194 Closed
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Issues list

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
#813 opened Oct 3, 2024 by turbomam
OAK documentation and command line parsing should differentiate between TSV and CSV
#812 opened Oct 3, 2024 by turbomam
Commands that treat empty lists as "all" should return no lists of a query that has zero results is passed
#811 opened Oct 3, 2024 by cmungall
Consider adding --version option to runoak
#810 opened Oct 3, 2024 by turbomam
Expand documentation on graph projections and allow finer grained control documentation Improvements or additions to documentation
#809 opened Oct 2, 2024 by cmungall
Oaklib annotate function does not return all substring containing values as expected
#805 opened Sep 27, 2024 by bsantan
Making retrieval of axiom annotations for synonyms faster
#767 opened May 16, 2024 by matentzn
Define behavior when conflicting idspaces are specified
#760 opened May 15, 2024 by cmungall
Pin ruff checks and codespell checks
#756 opened May 8, 2024 by cmungall
1
Document instructions for running the obographs-compliance suite documentation Improvements or additions to documentation
#751 opened May 5, 2024 by matentzn
4
Jaccard similarity differences when using information content
#746 opened May 1, 2024 by souzadevinicius
2
Run subset of tests in environment with no extras installed
#745 opened Apr 27, 2024 by cmungall
validate-mappings: NotImplementedError: ... NoneType bug Something isn't working
#742 opened Apr 25, 2024 by joeflack4
ValueSetExpander is too eager in using sqlite:obo as a default resolver
#718 opened Mar 15, 2024 by cmungall
Extended prefix map support
#699 opened Jan 26, 2024 by joeflack4
3
Hard coded CURIES in OAK code cause confusion when ontologies use different prefix maps
#698 opened Jan 20, 2024 by matentzn
3
.entities() typedef update
#690 opened Dec 19, 2023 by joeflack4
1
2
Dumpers and loaders: Separate concept of syntax and datamodel
#687 opened Dec 6, 2023 by cmungall
1
OAK Adapters vs. Invalid URI/CURIEs
#684 opened Dec 4, 2023 by glass-ships
5
relationships: Add warning/error when invalid predicates
#680 opened Nov 15, 2023 by joeflack4
2
Performance: SqlImplementation.entity_metadata_map()
#676 opened Nov 9, 2023 by joeflack4
1
5
Add an option to have a default count of 1 for all terms when calculating IC
#674 opened Nov 6, 2023 by cmungall
sort the return of 'ancestors' by the chain of relations such that the nodes are arranged in order from leaf to root good first issue Good for newcomers
#670 opened Oct 17, 2023 by realmarcin
Optimization: SqlImplementation.relationships_metadata() enhancement New feature or request
#660 opened Sep 27, 2023 by joeflack4
1
Add How to Cite in FAQ
#653 opened Sep 14, 2023 by amc-corey-cox
1
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