Aim 1.1.3 Use term templates to bootstrap new phenotype ontologies

[matentzn]

Where phenotype ontologies do not yet exist, we will generate them using uPheno templates, auto-generating the classification using inference. We already have preliminary successes using this approach to draft phenotype ontologies for xenopus and zebrafish.

[matentzn]

Key results 2022/2023

• Revision and development of patterns for computational traits, which captures phenotype ontologies independent of their specific character state. The paper provides a lot of detail on how this works.
• Developing a new pipeline that allows to selectively generate trait terms from existing phenotypic abnormality EQs with minimal human curation. Implemented to integrate half of the MP terms relevant to IMPC phenotyping into OBA.
• Lots of OBA terms have been generated using the template approach
• Make some improvements to the ZP pipeline for generating a phenotype ontology entirely from existing annotations

Notes

I consider this goal mostly achieved. There is not much more that has to be done here, and we have shown repeatedly (XPO, ZP, OBA) that we can easily and effectively do this.

[matentzn]

Working on APO and FBBT alignments here: https://github.com/monarch-initiative/uphenotizer