Aim 2.2.2 Develop tools for reconciling information from different sources

[joeflack4]

A summary of what I've done regarding this work, by repository.

mondo-ingest

Integration of other ontologies into Mondo. Summary of major work:

• Automating slurp pipeline to integrate ontologies into Mondo
• Exclusions pipeline to discard terms / classes of terms from Mondo
• QA, e.g. analyses of invalid xrefs
• Synchronization (an extension of slurp) (WIP)
• Progress report (WIP) Many issues resolved Many PRs

OMIM

Querying its API, building RDF, and ingesting into Mondo. Many issues resolved. Several PRs.

ICD10CM

Analyses related to its ingest into Mondo. Not many issues/PRs to report.

ICD10WHO

Querying its API, building RDF, and ingesting into Mondo. Not many issues/PRs to report.

Other

Created and followed up on issues for various dependencies, including OAK (ontology access kit), ODK, and robot.

[matentzn]

Reporting period 2022/2023

• Continued coordinating the source update work with strong progress - we now have a first complete instance of the match/migrate pipeline, and making good progress towards syncing OMIM, ORDO, DO
• Developed a system for standardising Mondo towards American english and added British language synonyms to Mondo in request to one of our users
• First release a mondo rare disease subset with and inclusion of NORD rare disease viewpoint, including links to genes.
• Organised Mondo outreach calls series
• Integration of new GARD identifiers in Mondo
• Added the automatic source deprecation pipeline to Mondo which ensures that if a source is deprecating a term, this is reflected in Mondo
• OMIM: automated monthly build (shoulda done this awhile ago)
• Added a lot of missing documentation / makefile help for workflows
• Updates to mondo-ingest pipeline: exclusions, sorting, bugfixes, slurp
• Began work on Medgen, ICD11 ingests
• Finished Medgen to OWL conversion and repo setup (still need to connect to mondo-ingest)