Annotation Conf. Call 2023-05-30

Agenda and Minutes

Meetings and Announcements

No GO Calls Week

• Next week, June 5th - 9th

Noctua

• Next regularly scheduled Noctua outage:
  • Thursday, June 8th, 4-6pm PDT
    • Outage tasks

Fall GOC Meeting

• Virtual meeting
• October 17th - 19th (Tuesday - Thursday)

GO Release Pipeline

• June release will start this week
• #release-pipeline Slack channel for updates

Annotation

Contributor-based annotation reports

• GO rule reports organized by Contributor are now available, both in the monthly release and in snapshot.

GP2Term Relations for Cellular Component Annotations

• Now updated in files:
  • External2GO mappings should use 'located in'
  • HTP CC annotations should use 'located in'

Obsolete Terms

Obsolete Terms in Annotation Extensions

• Will now also be reported

Annotations to Terms Due to be Obsoleted

• Apply a 'do not annotate' subset tag to prevent more annotations from being created

AmiGO

• Patrick Kalita is working on a project to display GO-CAMs on AmiGO
  • Adding pathways widget as seen on the Alliance gene pages and in Noctua (separate workbench)
  • David and Kimberly will work on some additional requirements for information/metadata on model pages

GO-CAM and Noctua

• Model copy with evidence is now available on production
• Ability to search for obsolete ontology terms in now available on production
• Working on MF-to-BP and BP-to-BP relations documentation (David, Pascale, Kimberly)
• https://github.com/orgs/geneontology/projects/130
  • We now have a list of all causal relations between MFs and BPs in Noctua for review
• https://github.com/orgs/geneontology/projects/131

Ontology

Ongoing Projects

Signaling Cassettes

• Helen, Giulia, Ruth and Pascale have started to plan work for signaling cassettes.

Current Projects

Obsolete "Regulation of molecular function" processes terms

• https://github.com/geneontology/go-ontology/issues/22455
• Obsolete all terms with no annotations: https://github.com/geneontology/go-ontology/issues/22455#issuecomment-1326741419
• Obsolete other terms: https://docs.google.com/spreadsheets/d/1jO6KdfHndALNYWn24S_M6LHUYrCIBgOqBg34a5tsARk/edit#gid=0
• Start working on together as a group in early March
• Make suggestions for replacements, if possible
• Make sure we have an SOP to migrate miRNA annotations

ncRNAs

Essentially finished - fixed some labels to change 'ncRNA' to 'regulatory ncRNA

Attendees

• On call: Colin, Deborah, Dmitry, Dustin, Edith, Giulia, Karen, Kimberly, Leonore, Li, Mahima, Malcolm, Pascale, Patrick, Raymond, Ruth, Seth, Shur-Jen, Sridhar, Stacia, Suzi