Projects update meeting 2024-01-10

Attendees

• Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia
• Present:

Announcements

Calls are now scheduled for the 2nd and 4th Wednesday of the month.

Discussion points

Objectives Jan/Feb 2024

Assuming we still aim for 2-month sprints; maybe this work requires more than 2 months

Pipeline stabilization

Agree on objectives:

• for eg 1 snapshot a week
• minimally we need to produce the ontology and export annotations generated in Noctua.
• Maybe for stability, data export and import should be uncoupled
• Discussion
  • 8-9 hours on Noctua load and processing (Minerva GPAD ~ 5h), taxon constraints step,
  • more rules, more filtering also take more time

• Plan
  • February: new machine; hopefully this will allow to do more trials
  • Getting snapshots blessed to become releases; would stabilize release frequency
    • AI: Seth to make a project
  • Archiving step:
    • AI: Look into other DOI providers
    • Could we drop some products from the zenodo archive? for example the Solr index
  • AI: look into the products we want to produce and work backwards from there
• Longer term:
  • Creating a database
  • Rewriting the pipeline code

Noctua Form UI improvement

Paul, Tremayne

• Minimal changes to prevent exposing the GO-CAM model from users in the Form version of Noctua
  • Project and list of tasks: where is this?

Noctua form improvement specs

Kimberly

• List of 'selected' UI changes from discussion with curators
• Other high priority functionality (for example, metadata for curators to describe models as GO-CAM versus standard annotation)
  • Project and list of tasks: where is this?

Document and test devops documentation for GO services

Currently in the hopper: ok to move forward? while Abdou is still available (until the end of January)

Standardize isoform descriptions?

UniProt uses P12345-x; MGI uses PRO IDs; thus is causing apparent 'duplicate' annotations https://github.com/geneontology/go-site/issues/2043#issuecomment-1865209874

Progress Report

• What stats need collected?
• Draft doc to start filling in?

MDBD Evaluation

• Collab notebook: https://colab.research.google.com/drive/1BhjsacipBPDCAEk84O-r5JHqRUbw3Fgz#scrollTo=ZWtNO2K7QjS_

Projects status

• https://github.com/geneontology/project-management/issues/85

Next priorities

• Document and test devops documentation for GO services

Discussion topics

• "Reverse" dates from 2024? https://wiki.geneontology.org/Project_stand_up_meetings#2024
  • I did it! Cjm (talk) 20:43, 9 January 2024 (EST)
• Physical meeting soon?