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Ontology Development Kit

Matentzoglu, Nicolas; Mungall, Chris; Goutte-Gattat, Damien

v1.3.0 (24 February 2022)

As always, update your local ODK with docker pull obolibrary/odkfull.

New features:
  • New DOSDP workflow for matching patterns: This is a powerful workflow that "matches" your DOSDP YAML templates against your ontology to actually create TSVs - so the other way around of what we usually do.
    • To set this up, you introduce a new "pattern_pipelines_group" called matches, which can then be invoked with sh run.sh make dosdp-matches-% to match all configured DOSDP tempates with the ontology.
    • Example see here.
  • Experimental feature-diff feature: When creating a pull request, the ODK can now automatically make a comment to the pull request informing editors of changes to the ontology (issue)
  • Adding Relation Graph to ODK (pull request, pull request)
  • New QC checks:
    • IRIs in labels: Often when using autogenerated labels in DOSDP we do not realise we are accidentally missing labels to for generating class names. We introduced a QC check to protect against that (pull request, issue)
    • Ensuring that the range of never_in_taxon:, present_in_taxon: , oboInOwl:inSubset, rdfs:seeAlso, foaf:depicted_by and dcterms:contributor is always IRI (issue, pull request)
  • Switched the default Ontology documentation theme from readthedocs to material (pull request)
  • New DOSDP tools version 0.19.1
Bugfixes:
  • Many faulty dependencies in the Makefile that triggered unnecessary re-runs of make were removed (issue)
  • Some major refactoring of the main Makefile (pull request). This includes, in particular, a smarter way to deal with web-dependencies (mirrors, dosdp-templates, components).
  • Fixes to documentation (Managing dependencies with base files, Import seed system)
  • Some fixes to DOSDP pipeline setup (issue)
  • Git main branch was hardcoded to master during the seeding process, now uses the ODK config file (pull request, issue)
  • Making sure the repo seeding process preserves file privileges. This ensures, in particular, that run.sh is executable and can be run using ./run.sh instead of sh run.sh (issue, pull)
  • DOSDP Validation now uses python up to date library
  • Auto-deployment of ODK docs fixed (ODK internal, pull request), but much of ODK's docs has moved to OBOOK (OBO Academy)
  • Fixing some issues with default values when using robot_report in your ODK config (pull request)
New commands:
  • sh run.sh make help: show frequently used ODK commands and their usage (issue)
  • sh run.sh make TSV=my.tsv validate-tsv: Experimental TSV validation feature with TSValid (issue)
  • sh run.sh make validate-all-tsv: Validate all TSV tables configured in repo with TSValid (issue)
  • sh run.sh make dosdp-matches-%: Run the "matches" pipeline, see above. (issue)
  • sh run.sh make clean: Clean up some temporary files created by the build. (issue)
Recommendations for ontology maintainers:
  • We have overhauled the SPARQL query management to make it more customisable (pull request). We recommend, before updating to the latest ODK, to delete old and potentially stale SPARQL queries like this: rm ../sparql/owldef-violation.sparql ../sparql/nolabels-violation.sparql ../sparql/def-lacks-xref-violation.sparql ../sparql/obsolete-violation.sparql ../sparql/redundant-subClassOf-violation.sparql.
  • You should periodically review the contents of your src/ontology/custom.Makefile - if you overwrite a lot of goals, you should review wether the overwrite is still necessary. This ODK release has a lot of revisions to the Makefile, so this should be a good opportunity to check this!
If you use this software, please cite it as below.
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