monarch-initiative / phenomics_first_resource

Project Management repository for anything in and around the Phenomics First Resource (PFR)
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Aim 2.3 Design governance process for and coordinate co-development of MONDO with other disease resources #15

Open sagehrke opened 1 year ago

sagehrke commented 1 year ago

Objective

Clear and agreed standardized curation, contribution, and governance processes are needed for MONDO and associated disease annotations to become a global community resource. We will create a formal vetting process, documentation, a library of examples, and a quality assurance pipeline. We will formalize the "lumping and splitting" guidelines that many participants in the MONDO workshop have worked on together, and are already being implemented in ClinGen.​

Key results

Key personnel

@nicolevasilevsky @mellybelly @cmungall (leadership) @nicolevasilevsky @sabrinatoro (curation) @matentzn @joeflack4 @hrshgd (technical support)

nicolevasilevsky commented 1 year ago

From the grant:

Clear and agreed standardized curation, contribution, and governance processes are needed for MONDO and associated disease annotations to become a global community resource. We will create a formal vetting process, documentation, a library of examples, and a quality assurance pipeline. We will formalize the "lumping and splitting" guidelines that many participants in the MONDO workshop have worked on together, and are already being implemented in ClinGen (Rehm LoS). There will be four guideline components:

nicolevasilevsky commented 1 year ago

note:

matentzn commented 1 year ago

2022 Grainyhead output

Event Total Internal External Ext. (%)
Issues opened 805 340 465 57.76
Issues closed 934 849 85 9.10
Pull requests opened 1467 992 475 32.38
Pull requests closed 1482 1391 91 6.14
Pull requests merged 1295 1242 53 4.09
Comments 1988 1331 657 33.05
Commits 3880 3200 680 17.53
Contributors 93 10 83 89.25
Releases 15
joeflack4 commented 1 year ago

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

mondo-ingest

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

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 commented 1 year ago

@joeflack4 can you please move your comment to https://github.com/monarch-initiative/phenomics_first_resource/issues/26

nicolevasilevsky commented 11 months ago

see: https://mondo.readthedocs.io/en/latest/editors-guide/curation-workflow-overview/