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July 02, 2026 software Open access Aachen paper

INCATools/ontology-access-kit: v0.7.0.0

Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.21134053 Full text (OA) OpenAlex

Abstract

What's Changed Ensuring that pronto definition objects are stringified (730) by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/731 Adding a notebook demonstrating statistics command. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/724 Fixed test by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/723 Added diff markdown for AddNodeToSubset by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/736 Ran formatter and minor code cleanup by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/737 Adding definition validation functionality by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/738 Adding option for non-redundant entialed relationships. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/740 Enriched mapping documentation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/741 Adding defusedxml dependency. Fixes #743 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/744 Refactored mappings to more generic relationships in diff markdown output by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/750 Update obo compliance suite using latest robot by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/747 Make ruff happy by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/757 Adding additional docs on the OAK expression language by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/749 Berkeley Hackathon: Enhancing semsim docs. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/753 Adding skos-xref-duplicate to obo compliance suite by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/752 Update to support new semsimian IC map functionality by @caufieldjh in https://github.com/INCATools/ontology-access-kit/pull/755 removing unneccessary quotes in expression language guide by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/762 Adding has-part glyph to config. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/765 More efficient association-based IC calculation. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/764 Pass custom IC map to Semsimian through CLI by @caufieldjh in https://github.com/INCATools/ontology-access-kit/pull/759 Adding MRCA example to expression docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/768 Adding link to ontogenesis chapter on annotations. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/771 Python level access to query expression language by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/769 New functionality: term usages by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/776 Making prefix mapping less strict, fixes #702 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/761 rename edge to mapping by @twhetzel in https://github.com/INCATools/ontology-access-kit/pull/775 Solves ClassCreation duplication & formats Mappings md table properly by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/780 information content enhancements by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/781 Added change handler for kgcl.RemoveNodeFromSubset by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/783 Supporting skos mappings for simpleobo and pronto. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/766 structured_format.pattern-style permissible value creation eg for MIxS by @turbomam in https://github.com/INCATools/ontology-access-kit/pull/785 Update sql_implementation.py to include sqlachemy output in debug logging. by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/782 set_label will INSERT if label not already presented. Fixes #788 by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/789 Implementing NodeDeletion which was earlier a comment. by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/791 Fix test suite by @gouttegd in https://github.com/INCATools/ontology-access-kit/pull/796 Bug in calculating all_by_all_pairwise_similarity by @hrshdhgd in https://github.com/INCATools/ontology-access-kit/pull/800 Add test for all_by_all_pairwise_similarity() in semsimian using custom IC map by @justaddcoffee in https://github.com/INCATools/ontology-access-kit/pull/801 Add cache management features by @gouttegd in https://github.com/INCATools/ontology-access-kit/pull/799 Enhanced heatmap functionality by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/798 Adding a .sample operator by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/797 graph projections and subset validation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/806 Update cli.rst (fixed very minor documentation error) by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/804 update docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/808 Remove outdated warning, fix minor typos by @ialarmedalien in https://github.com/INCATools/ontology-access-kit/pull/814 Moved Jupter notebooks to be part of sphinx docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/816 Adding step to build pandoc for sphinx docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/817 installing pandoc by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/818 Adding more docs on how to use LLMs with OAK by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/819 Adding crawl and chain commands by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/826 association graphs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/828 Adding ability to specify obographviz config inside a crawl config by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/829 Value Set examples and docs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/830 Add definition method to OLS implementation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/831 Add enrichment guide to OAK documentation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/832 Extend OntoportalImplementation with entities() and node() methods by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/833 Allow choice of closure fields in amigo by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/835 Additional utilities for handling boomer. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/843 Fix broken links to notebooks by @justaddcoffee in https://github.com/INCATools/ontology-access-kit/pull/837 Pyproject.toml Update to python standard/UV Update For Oak by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/849 Add --version option to runoak by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/859 Adding Python 3.13 support, removing Python 3.9 support by @DnlRKorn in https://github.com/INCATools/ontology-access-kit/pull/864 [codex] migrate funowl integration to py-horned-owl by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/868 [codex] fix release build versioning by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/869 [codex] fix owl input format detection by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/870 Switch PyPI release workflow to trusted publishing by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/872 Align PyPI publish workflow with existing trusted publisher by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/873 fix: set PyPI publish environment by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/874 [codex] fix: support info and tree for functional owl inputs by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/876 [codex] fix owl selector routing by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/884 Increase default cache TTL from 1 week to 1 month by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/879 Implement destructor for sqlite session and engine cleanup by @rly in https://github.com/INCATools/ontology-access-kit/pull/846 New Contributors @twhetzel made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/775 @turbomam made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/785 @DnlRKorn made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/782 @gouttegd made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/796 @ialarmedalien made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/814 @rly made their first contribution in https://github.com/INCATools/ontology-access-kit/pull/846 Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.6.0...v0.7.0.0

Authors 28

  1. Chris J Mungall

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  2. Harshad
  3. Patrick Kalita

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  4. Charles Tapley Hoyt Aachen

    RWTH Aachen University

    Affiliation as printed

    RWTH Aachen University

  5. Sagar Patil

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  6. Marcin P. Joachimiak

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  7. Harry Caufield

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  8. Joe Flack
    Affiliation as printed

    @jhu-bids

  9. Justin Reese

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Lab

  10. David Linke

    Leibniz Institute for Catalysis

    Affiliation as printed

    Leibniz Institute for Catalysis (LIKAT)

  11. Daniel Korn
  12. Nomi L. Harris

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Laboratory

  13. Sierra Moxon

    Lawrence Berkeley National Laboratory

    Affiliation as printed

    Lawrence Berkeley National Lab

  14. Deepak

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    SIB Swiss Institute of Bioinformatics

  15. Nicolas Matentzoglu
    Affiliation as printed

    semanticly.ai

  16. Kim Rutherford

    University of Cambridge

    Affiliation as printed

    Uni of Cambridge / @PomBase

  17. Damien Goutte-Gattat

    German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse

    Affiliation as printed

    German BioImaging e.V

  18. Parker Bremer
  19. V Reis de Souza

    European Bioinformatics Institute

    Affiliation as printed

    EBI - European Bioinformatics Institute

  20. Yaroslav Halchenko

    Dartmouth College

    Affiliation as printed

    Dartmouth College, @dandi, @Debian, @DataLad, @neurodebian, @PyMVPA, @fail2ban

  21. Jules Jacobsen

    Queen Mary University of London

    Affiliation as printed

    Queen Mary University of London

  22. Kevin Schaper
  23. Manuel Lera-Ramirez

    University College London

    Affiliation as printed

    University College London

  24. Ryan Ly
  25. Shawn Tan
  26. Tiago Lubiana

    German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse

    Affiliation as printed

    German BioImaging GMB-eV

  27. Trish Whetzel
  28. i alarmed alien

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