incatools/ontology-access-kit issues and pull requests

#820 - Provide simple yaml-based output for release summary in `runoak diff`

Issue - State: open - Opened by matentzn 10 days ago - 1 comment

#819 - Adding more docs on how to use LLMs with OAK

Pull Request - State: closed - Opened by cmungall about 1 month ago

#818 - installing pandoc

Pull Request - State: closed - Opened by cmungall about 1 month ago

#817 - Adding step to build pandoc for sphinx docs

Pull Request - State: closed - Opened by cmungall about 1 month ago

#816 - Moved Jupter notebooks to be part of sphinx docs

Pull Request - State: closed - Opened by cmungall about 1 month ago

#815 - Ubergraph query throws SPARQL error

Issue - State: closed - Opened by ialarmedalien about 1 month ago - 1 comment

#814 - Remove outdated warning, fix minor typos

Pull Request - State: closed - Opened by ialarmedalien about 1 month ago

#813 - 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

Issue - State: open - Opened by turbomam about 2 months ago

#812 - OAK documentation and command line parsing should differentiate between TSV and CSV

Issue - State: open - Opened by turbomam about 2 months ago

#811 - Commands that treat empty lists as "all" should return no lists of a query that has zero results is passed

Issue - State: open - Opened by cmungall about 2 months ago

#810 - Consider adding --version option to `runoak`

Issue - State: open - Opened by turbomam about 2 months ago

#809 - Expand documentation on graph projections and allow finer grained control

Issue - State: open - Opened by cmungall about 2 months ago
Labels: documentation

#808 - update docs

Pull Request - State: closed - Opened by cmungall about 2 months ago

#807 - add SubClassOf ObjectHasValue to the recognized graph projection patterns

Issue - State: closed - Opened by turbomam about 2 months ago - 7 comments

#806 - graph projections and subset validation

Pull Request - State: closed - Opened by cmungall about 2 months ago

#805 - Oaklib annotate function does not return all substring containing values as expected

Issue - State: open - Opened by bsantan about 2 months ago

#804 - Update cli.rst (fixed very minor documentation error)

Pull Request - State: closed - Opened by DnlRKorn about 2 months ago

#803 - Annotate function emits lots of errors and is slow/verbose

Issue - State: closed - Opened by justaddcoffee 2 months ago - 3 comments

#802 - gilda tests failing - punkt is punked

Issue - State: closed - Opened by cmungall 3 months ago

#801 - Add test for all_by_all_pairwise_similarity() in semsimian using custom IC map

Pull Request - State: closed - Opened by justaddcoffee 3 months ago - 1 comment

#800 - Bug in calculating `all_by_all_pairwise_similarity`

Pull Request - State: closed - Opened by hrshdhgd 3 months ago - 3 comments

#799 - Add cache management features

Pull Request - State: closed - Opened by gouttegd 3 months ago - 4 comments

#798 - Enhanced heatmap functionality

Pull Request - State: closed - Opened by cmungall 3 months ago - 1 comment

#797 - Adding a .sample operator

Pull Request - State: closed - Opened by cmungall 3 months ago - 1 comment

#796 - Fix test suite

Pull Request - State: closed - Opened by gouttegd 3 months ago

#795 - Spurious warnings about invalid CURIEs cause `test_annotate_file` to fail

Issue - State: closed - Opened by gouttegd 3 months ago

#794 - Missing optional dependencies cause the test suite to fail

Issue - State: closed - Opened by gouttegd 3 months ago

#793 - Add --limit arg to similarity for fast testing, bump semsimian to 0.2.18

Pull Request - State: closed - Opened by justaddcoffee 3 months ago - 4 comments

#792 - Allow user to explicitly manage pystow cache (for downloaded sqlite dbs)

Issue - State: closed - Opened by cmungall 3 months ago - 5 comments

#791 - Implementing NodeDeletion which was earlier a comment.

Pull Request - State: closed - Opened by hrshdhgd 3 months ago

#790 - `diff` in KGCL format generates `create None`.

Issue - State: closed - Opened by hrshdhgd 3 months ago - 3 comments

#789 - set_label will INSERT if label not already presented. Fixes #788

Pull Request - State: closed - Opened by cmungall 4 months ago

#788 - lexmatch --add-label option will update but not create new labels for sql backend

Issue - State: closed - Opened by cmungall 4 months ago

#787 - Sphinx documentation for CLI has disappeared from website

Issue - State: closed - Opened by cmungall 4 months ago - 2 comments

#786 - add max depth for `vskit expand`

Issue - State: closed - Opened by turbomam 4 months ago - 2 comments

#785 - structured_format.pattern-style permissible value creation eg for MIxS

Pull Request - State: closed - Opened by turbomam 4 months ago - 2 comments

#784 - vskit expander should support PVs in the MIxS label [id] style

Issue - State: closed - Opened by turbomam 4 months ago - 3 comments

#783 - Added change handler for `kgcl.RemoveNodeFromSubset`

Pull Request - State: closed - Opened by hrshdhgd 4 months ago - 2 comments

#782 - Update sql_implementation.py to include sqlachemy output in debug logging.

Pull Request - State: closed - Opened by DnlRKorn 4 months ago - 1 comment

#781 - information content enhancements

Pull Request - State: closed - Opened by cmungall 5 months ago

#780 - Solves ClassCreation duplication & formats Mappings md table properly

Pull Request - State: closed - Opened by hrshdhgd 5 months ago

#779 - [OAK diff] Markdown output misformatted on `Mappings` section

Issue - State: closed - Opened by anitacaron 5 months ago - 1 comment

#778 - Duplicated ClassCreation changes in CSV diff output

Issue - State: closed - Opened by gouttegd 5 months ago - 5 comments

#777 - Add a way of detecting all usages of an ontology term

Issue - State: closed - Opened by cmungall 6 months ago

#776 - New functionality: term usages

Pull Request - State: closed - Opened by cmungall 6 months ago

#775 - rename edge to mapping

Pull Request - State: closed - Opened by twhetzel 6 months ago - 3 comments

#773 - py-horned-owl #438

Pull Request - State: open - Opened by cmungall 6 months ago

#772 - Improve python level access to expression language

Issue - State: closed - Opened by cmungall 6 months ago

#771 - Adding link to ontogenesis chapter on annotations.

Pull Request - State: closed - Opened by cmungall 6 months ago

#770 - Allow passing in of ontology terms on command line when using enrichment in ontology-only mode

Issue - State: closed - Opened by cmungall 6 months ago

#769 - Python level access to query expression language

Pull Request - State: closed - Opened by cmungall 6 months ago

#768 - Adding MRCA example to expression docs

Pull Request - State: closed - Opened by cmungall 6 months ago

#767 - Making retrieval of axiom annotations for synonyms faster

Issue - State: open - Opened by matentzn 6 months ago

#766 - Supporting skos mappings for simpleobo and pronto.

Pull Request - State: closed - Opened by cmungall 6 months ago

#765 - Adding has-part glyph to config.

Pull Request - State: closed - Opened by cmungall 6 months ago

#764 - More efficient association-based IC calculation.

Pull Request - State: closed - Opened by cmungall 6 months ago - 1 comment

#763 - Calculating ICs with an annotation corpus as background is slow

Issue - State: closed - Opened by cmungall 6 months ago

#762 - removing unneccessary quotes in expression language guide

Pull Request - State: closed - Opened by cmungall 6 months ago

#761 - Making prefix mapping less strict, fixes #702

Pull Request - State: closed - Opened by cmungall 6 months ago - 1 comment

#760 - Define behavior when conflicting idspaces are specified

Issue - State: open - Opened by cmungall 6 months ago

#759 - Pass custom IC map to Semsimian through CLI

Pull Request - State: closed - Opened by caufieldjh 6 months ago - 3 comments

#758 - Integrate notebooks into sphinx documentation (will break URLs)

Issue - State: closed - Opened by cmungall 7 months ago - 2 comments

#757 - Make ruff happy

Pull Request - State: closed - Opened by cmungall 7 months ago

#756 - Pin ruff checks and codespell checks

Issue - State: open - Opened by cmungall 7 months ago - 1 comment

#755 - Update to support new semsimian IC map functionality

Pull Request - State: closed - Opened by caufieldjh 7 months ago

#754 - Update SemSimianImplementation and CLI to allow using custom IC maps and frequencies

Issue - State: closed - Opened by caufieldjh 7 months ago

#753 - Berkeley Hackathon: Enhancing semsim docs.

Pull Request - State: closed - Opened by cmungall 7 months ago - 1 comment

#752 - Adding skos-xref-duplicate to obo compliance suite

Pull Request - State: closed - Opened by cmungall 7 months ago - 1 comment

#751 - Document instructions for running the obographs-compliance suite

Issue - State: open - Opened by matentzn 7 months ago - 4 comments
Labels: documentation

#750 - Refactored `mappings` to more generic `relationships` in diff markdown output

Pull Request - State: closed - Opened by hrshdhgd 7 months ago

#749 - Adding additional docs on the OAK expression language

Pull Request - State: closed - Opened by cmungall 7 months ago - 1 comment

#748 - Breaking change in Synonymizer?

Issue - State: closed - Opened by matentzn 7 months ago - 3 comments

#747 - Update obo compliance suite using latest robot

Pull Request - State: closed - Opened by cmungall 7 months ago - 1 comment

#746 - Jaccard similarity differences when using information content

Issue - State: open - Opened by souzadevinicius 7 months ago - 2 comments

#745 - Run subset of tests in environment with no extras installed

Issue - State: open - Opened by cmungall 7 months ago

#744 - Adding defusedxml dependency. Fixes #743

Pull Request - State: closed - Opened by cmungall 7 months ago

#743 - Missing `defusedxml` dependency

Issue - State: closed - Opened by gouttegd 7 months ago - 3 comments

#742 - `validate-mappings`: `NotImplementedError: ... NoneType`

Issue - State: open - Opened by joeflack4 7 months ago
Labels: bug

#741 - Enriched mapping documentation

Pull Request - State: closed - Opened by cmungall 7 months ago - 3 comments

#740 - Adding option for non-redundant entialed relationships.

Pull Request - State: closed - Opened by cmungall 7 months ago

#739 - Add option to `relationships` for walking up subclass hierarchy

Issue - State: closed - Opened by cmungall 7 months ago

#738 - Adding definition validation functionality

Pull Request - State: closed - Opened by cmungall 7 months ago

#737 - Ran formatter and minor code cleanup

Pull Request - State: closed - Opened by hrshdhgd 8 months ago

#735 - runoak diff erroneously names "relationships" --> "mappings" in markdown summary

Issue - State: closed - Opened by matentzn 8 months ago - 4 comments

#732 - simple obo diffs creates duplicate `Classes added`

Issue - State: closed - Opened by hrshdhgd 8 months ago - 8 comments

#724 - Adding a notebook demonstrating statistics command.

Pull Request - State: open - Opened by cmungall 8 months ago - 1 comment

#723 - Fixed test

Pull Request - State: open - Opened by hrshdhgd 8 months ago - 1 comment

#722 - Partial robot template implementation.

Pull Request - State: closed - Opened by cmungall 8 months ago - 1 comment

#721 - Added mock tests

Pull Request - State: closed - Opened by hrshdhgd 8 months ago - 1 comment

#720 - Handle `RemoveTextDefinition`

Pull Request - State: closed - Opened by hrshdhgd 8 months ago

#717 - Update semsimian dependency version

Pull Request - State: open - Opened by hrshdhgd 8 months ago - 2 comments

#716 - Remove flake8 and replace it by `ruff`

Pull Request - State: closed - Opened by hrshdhgd 8 months ago - 1 comment

#715 - OBO compliance suite (redux of #693)

Pull Request - State: closed - Opened by cmungall 8 months ago - 1 comment

#714 - Extending amigo and llm implementations

Pull Request - State: closed - Opened by cmungall 8 months ago - 1 comment

#713 - Adding pantherdb impl

Pull Request - State: closed - Opened by cmungall 9 months ago - 1 comment

#712 - Autoadding current year to footer, fixes #710

Pull Request - State: closed - Opened by cmungall 9 months ago - 1 comment

#711 - llm exception handling

Pull Request - State: closed - Opened by cmungall 9 months ago - 1 comment

#710 - Misleading copyright statement at the bottom of OAK documentation pages

Issue - State: closed - Opened by nlharris 9 months ago - 5 comments

#709 - Add link to llm how-to

Pull Request - State: closed - Opened by cmungall 9 months ago - 1 comment

#708 - revert semsimian

Pull Request - State: closed - Opened by cmungall 9 months ago - 1 comment

GitHub / incatools/ontology-access-kit issues and pull requests