matentzn
commented
1 year ago Update reporting period 08/2022 - 07/2023
The has been a lot of work on ODK, too much to list in great detail. The best way to track is to probably look at the 1.4 milestone release (and its changelog): https://github.com/INCATools/ontology-development-kit/milestone/6
Some highlights:
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Integration of SSSOM into the general ontology workflow
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Support for
singularityas an alternative to docker -
Various improvements to quality control checks and release pipelines
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Expansion of the ODK toolbox especially to support linkml and oak related efforts
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Various talks at conferences and workshops about ODK
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Coordinated the set up of a Monarch specific OBO Dashboard (https://monarch-initiative.github.io/monarch-ontology-dashboard/dashboard/index.html) and promoted fixing of a number of quality issues across Monarch ontologies
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Made a big push with the Tech team to finally release Protege 5.6.1 (the main development environment in our ontology worl), ODK 1.4.1 and ROBOT 1.9.4 (including the long-awaited ROBOT subset command based on relation graph (key piece for knowledge graph integration).
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Wrote a draft spec for the base module approach and finalised the base process in ODK itself. The base file is a central concept for interoperability moving forward.
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Other tooling
- Various extensions to SSSOM Toolkit for managing mappings
- Improvements to oak mappings command produces (almost) legal SSSOM which is used especially for phenotype matching.
The ODK is now very widely used in our community and a central piece and many development workflows. This goal can be considered more than achieved.
The ODK [65] is already used by some phenotype ontologies to drive template-driven development, QC, and ontology releases. We will extend the ODK to make QC reports more powerful and easier to understand, and more configurable for evolving ontology release requirements.