Annotation Conf. Call 2023-05-23
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Agenda and Minutes
Meetings and Announcements
Noctua
- Next regularly scheduled Noctua outage:
- Thursday, May 25th, 4-6pm PDT
Fall GOC Meeting
- Virtual meeting
- October 17th - 19th (Tuesday - Thursday)
GO Release Pipeline
- May release is out (May 10th, 2023)
- #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.
Follow up on the case of missing GO annotations
- Last week, Ruth reported on a group that found changes in the number of human proteins annotated to generation of precursor metabolites and energy (GO:0006091)
- Detective work revealed that this was due to a change in parentage
Question MAP kinase kinase activity and protein tyrosine kinase activity
GP2Term Relations for Cellular Component Annotations
- External2GO mappings should use 'located in'
- HTP CC annotations should use 'located in'
Annotations to Terms Due to be Obsoleted
- Apply a 'do not annotate' or 'do not manually annotate' subset tag to prevent more annotations from being created
PAINT
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)
- Status meeting today
GO-CAM and Noctua
- Model copy with evidence is available to test on noctua-dev
- 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.
- Scope?
- Ontology changes?
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: Antonia, David, Deborah, Dustin, Edith, Helen, Karen, Kimberly, Leonore, Li, Malcolm, Mary, Pascale, Patrick, Raymond, Rob, Seth, Shur-Jen, Sierra, Sridhar, Stan, Steven, Suzi