Annotation Conf. Call 2023-04-18

Agenda and Minutes

Meetings and Announcements

Noctua

• Next regularly scheduled Noctua outage:
  • No outage on Thursday, April 25th - GOC meeting in Padua
  • Next outage: Thursday, May 11th
    • Outage tasks

Spring GOC Meeting - Next week!

• Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th)
• Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM
• Rideshare to/from airport - arrival and departure in separate tabs
• Please let Pascale know if you haven't filled the survey on dinner choices
• Agenda and Logistics
  • Settle on breakout session topics
  • Discussion of GO-CAM strategies - groups invited to present (flash talks)

GO Release Pipeline

• April release out 2023-04-01

PAINT

• Paul sent an email (2023-02-22) with a link to the draft of the human functionome paper
• Thanks to everyone for their feedback
• Current status?

AmiGO

• Patrick Kalita is working on a project to display GO-CAMs on AmiGO
  • Will add pathways widget as seen on the Alliance gene pages and in Noctua (separate workbench)

Annotation

Annotation error reports and annotation review

Error reports

• Please remember to keep checking the reports generated by the pipeline and address any errors

Reannotating regulation of MF process terms

• Examples of annotations
• What level of granularity do we want in the corresponding MF terms?

• Also check annotation review tickets assigned to you/your group in go-annotation repo on github
• Questions about either - please bring to the meeting

GO-CAM and Noctua

• 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

Term Merges and Obsoletions

• New proposed SOP for handling merges and obsoletions: No longer merge terms, only obsolete. When we used to merge, we'll now do obsolete + replaced by
  • Noctua and P2GO automatically updates obsoleted terms that have a replaced_by; is this a problem for any group on the call?
  • Note that QuickGO and AmiGO also repairs these annotations during the load process
• Streamline announcements for obsoleted terms having a replaced_by term: once per release (link to stats:
• For consistency with the OWL representation, and with other OBO ontologies, we would like to create obsolete terms for all alt_id entries. These would have a replaced_by link to the active term. After this, the ontology would contain no alt_id tags. (https://github.com/geneontology/go-ontology/issues/24467)

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

Attendees

• On call: Antonia, Chris, Colin, Debby, Dmitry, Dustin, Giulia, Helen, Karen, Kimberly, Leonore, Li, Mahima, Malcolm, Mary, Pascale, Patrick, Raymond, Rob, Ruth, Seth, Sierra, Sridhar, Tom