Matentzoglu, Nicolas
Mungall, Chris
Goutte-Gattat, Damien
2021-07-11
v1.3.0 (24 February 2022)
<p>As always, update your local ODK with <code>docker pull obolibrary/odkfull</code>.</p>
New features:
<ul>
<li><em>New DOSDP workflow for matching patterns</em>: This is a powerful workflow that "matches" your DOSDP YAML templates against your ontology to actually <em>create</em> TSVs - so the other way around of what we usually do.<ul>
<li>To set this up, you introduce a new "pattern_pipelines_group" called <code>matches</code>, which can then be invoked with <code>sh run.sh make dosdp-matches-%</code> to match all configured DOSDP tempates with the ontology.</li>
<li>Example see <a href="tests/test-dosdp-matches.yaml">here</a>.</li>
</ul>
</li>
<li><em>Experimental feature-diff feature</em>: When creating a pull request, the ODK can now automatically make a comment to the pull request informing editors of changes to the ontology (<a href="https://github.com/INCATools/ontology-development-kit/pull/547">issue</a>)</li>
<li><em>Adding <a href="https://github.com/balhoff/relation-graph/">Relation Graph</a> to ODK</em> (<a href="https://github.com/INCATools/ontology-development-kit/pull/535">pull request</a>, <a href="https://github.com/INCATools/ontology-development-kit/pull/529">pull request</a>)</li>
<li><em>New QC checks</em>: <ul>
<li><em>IRIs in labels</em>: 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 (<a href="https://github.com/INCATools/ontology-development-kit/pull/542/files">pull request</a>, <a href="https://github.com/INCATools/ontology-development-kit/issues/536">issue</a>)</li>
<li>Ensuring that the range of never_in_taxon:, present_in_taxon: , oboInOwl:inSubset, rdfs:seeAlso, foaf:depicted_by and dcterms:contributor is always IRI (<a href="https://github.com/INCATools/ontology-development-kit/issues/520">issue</a>, <a href="https://github.com/INCATools/ontology-development-kit/pull/527/files">pull request</a>)</li>
</ul>
</li>
<li>Switched the default Ontology documentation theme from <code>readthedocs</code> to <code>material</code> (<a href="https://github.com/INCATools/ontology-development-kit/pull/530/files">pull request</a>)</li>
<li>New <a href="https://github.com/INCATools/dosdp-tools/releases/tag/v0.19.1">DOSDP tools version 0.19.1</a></li>
</ul>
Bugfixes:
<ul>
<li>Many faulty dependencies in the Makefile that triggered unnecessary re-runs of make were removed (<a href="https://github.com/INCATools/ontology-development-kit/issues/448">issue</a>)</li>
<li>Some major refactoring of the main <code>Makefile</code> (<a href="https://github.com/INCATools/ontology-development-kit/pull/530/files">pull request</a>). This includes, in particular, a smarter way to deal with web-dependencies (mirrors, dosdp-templates, components).</li>
<li>Fixes to documentation (<a href="https://github.com/INCATools/ontology-development-kit/issues/514">Managing dependencies with base files</a>, <a href="https://github.com/INCATools/ontology-development-kit/pull/519">Import seed system</a>)</li>
<li>Some fixes to DOSDP pipeline setup (<a href="https://github.com/INCATools/ontology-development-kit/issues/490">issue</a>)</li>
<li>Git <code>main</code> branch was hardcoded to <code>master</code> during the seeding process, now uses the ODK config file (<a href="https://github.com/INCATools/ontology-development-kit/pull/541">pull request</a>, <a href="https://github.com/INCATools/ontology-development-kit/issues/508">issue</a>)</li>
<li>Making sure the repo seeding process preserves file privileges. This ensures, in particular, that <code>run.sh</code> is executable and can be run using <code>./run.sh</code> instead of <code>sh run.sh</code> (<a href="https://github.com/INCATools/ontology-development-kit/issues/196">issue</a>, <a href="https://github.com/INCATools/ontology-development-kit/pull/538">pull</a>)</li>
<li>DOSDP Validation now <a href="https://github.com/INCATools/ontology-development-kit/pull/515">uses python up to date library</a></li>
<li>Auto-deployment of ODK docs fixed (ODK internal, <a href="https://github.com/INCATools/ontology-development-kit/pull/517">pull request</a>), but much of ODK's docs has moved to <a href="https://oboacademy.github.io/obook/">OBOOK (OBO Academy)</a></li>
<li>Fixing some issues with default values when using <code>robot_report</code> in your ODK config (<a href="https://github.com/INCATools/ontology-development-kit/pull/558">pull request</a>)</li>
</ul>
New commands:
<ul>
<li><code>sh run.sh make help</code>: show frequently used ODK commands and their usage (<a href="https://github.com/INCATools/ontology-development-kit/issues/531">issue</a>)</li>
<li><code>sh run.sh make TSV=my.tsv validate-tsv</code>: Experimental TSV validation feature with <a href="https://github.com/INCATools/ontology-development-kit/issues/532">TSValid</a> (<a href="https://github.com/INCATools/ontology-development-kit/issues/375">issue</a>)</li>
<li><code>sh run.sh make validate-all-tsv</code>: Validate all TSV tables configured in repo with <a href="https://github.com/ontodev/tsvalid">TSValid</a> (<a href="https://github.com/INCATools/ontology-development-kit/issues/375">issue</a>)</li>
<li><code>sh run.sh make dosdp-matches-%</code>: Run the "matches" pipeline, see above. (<a href="https://github.com/INCATools/ontology-development-kit/issues/540">issue</a>)</li>
<li><code>sh run.sh make clean</code>: Clean up some temporary files created by the build. (<a href="https://github.com/INCATools/ontology-development-kit/issues/300">issue</a>)</li>
</ul>
Recommendations for ontology maintainers:
<ul>
<li>We have overhauled the SPARQL query management to make it more customisable (<a href="https://github.com/INCATools/ontology-development-kit/pull/523">pull request</a>). We recommend, before updating to the latest ODK, to delete old and potentially stale SPARQL queries like this: <code>rm ../sparql/owldef-violation.sparql ../sparql/nolabels-violation.sparql ../sparql/def-lacks-xref-violation.sparql ../sparql/obsolete-violation.sparql ../sparql/redundant-subClassOf-violation.sparql</code>.</li>
<li>You should periodically review the contents of your <code>src/ontology/custom.Makefile</code> - 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!</li>
</ul>
If you use this software, please cite it as below.
https://doi.org/10.5281/zenodo.6257507
oai:zenodo.org:6257507
Zenodo
https://github.com/INCATools/ontology-development-kit/tree/v1.3.0
https://doi.org/10.5281/zenodo.4662066
info:eu-repo/semantics/openAccess
Other (Open)
Ontology Development Kit
info:eu-repo/semantics/other