As always, update your local ODK with docker pull obolibrary/odkfull.
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.
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)
Fixing some issues with default values when using robot_report in your ODK config (pull request)
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.