v0.6.3

Highlights

Extension of SRS taxonomy

We extend the SRS taxonomy (described here) with some new types to be able to record

• mismatch between definition and definition reference
• retraction of definition reference

See

• #307
• #305

Definition Validation

This PR adds additional functionality to ValidatorInterface for definitions. This is exposed through the validate-definitions command:

runoak -i sqlite:obo:go validate-definitions .desc//p=i autophagy

In addition to doing lexical checks this will also check references e.g for retractions

This PR also adds an example notebook

LLM based validation of definitions

This will ask the LLM to align the text definition with the abstract of the references

To run:

runoak -i llm:{claude-3-opus}:sqlite:obo:go validate-definitions .desc//p=i autophagy

This PR also adds to the LLM guide

What's Changed

• Adding definition validation functionality by @cmungall in #738

Full Changelog: v0.6.2...v0.6.3