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Published July 11, 2021 | Version 1.2.29
Software Open

Ontology Development Kit

Creators

  • 1. Semanticly Ltd
  • 2. Lawrence Berkeley National Laboratory (LBNL)
  • 3. Flybase

Description

  • Important: The way we install python packages has changed significantly: we are now using fixed version dependencies (issue). If there are problems with the versions of packages we are using, please let us know immediately.
  • We are now using multi-stage builds in ODK for docker. The obolibrary/odklite container is considerably lighter (smaller) than the normal odkfull container you have been using so far, and it should be sufficient for most ODK pipelines.
  • Mirrors are now downloaded with CURL instead of ROBOT, and configurable with mirror_retry_download and mirror_max_time_download in the import_group section of the ODK config file (PR). Note that the default mirror_max_time_download is 200 sec (a bit more than 3 minutes), which may be tight for some huge ontologies.
  • For those who are using DOSDP patterns we re-introduced the pattern schema check even if pattern generation is skipped (it is very fast).
  • Created a simple way to cite ODK from within GitHub, using the CITATION.cff file. If you go to https://github.com/INCATools/ontology-development-kit, you will now see a "cite this repo" section under the About section.
  • Changed the default README.md to include a better reference to ODK, the correct ontology description text and the correct edit file extension.
  • Added a GitHub action to deploy the ODK-based mkdocs documentation (issue).
  • Created a page for frequently used ODK commands.
  • Bugfixes:
    • project repo name was not read correctly during make update_repo causing it to be named "False" (commit)
    • Fixed a bug where mirrors were not considered precious
    • Fixed a bug where where the report directories where not created when running a sparql report command (commit)
    • Fixed a bug where report command incorrectly did not include components in the check (issue)
    • Fixed a bug where myont-odk.yaml was not created when using command line mode during seeding (issue)
    • Added some tests for external tools (issue) to ODK built process

Notes

If you use this software, please cite it as below.

Files

INCATools/ontology-development-kit-v.12.30.zip

Files (617.9 kB)

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md5:18529c8dfdf8d02b390d2ebc39b45cee
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Additional details

Related works

Is supplement to
https://github.com/INCATools/ontology-development-kit/tree/v.12.30 (URL)