Annotation Conf. Call 2023-01-31

Agenda and Minutes

Meetings and Announcements

Noctua

• Next regularly scheduled Noctua outages:
  • Thursday, February 9th
  • Outage tasks

No GO Calls Week

• First full week of February (5th - 10th)

Spring GOC Meeting Plans

• Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th)
• Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM
• Registration fees will be less than $275/€300 including coffee breaks, 3 lunches & the group dinner.
• No payment is required to register; we will get in touch about how we are collecting these fees later.
• Registration deadline has been moved up to Friday, February 17th, 2023.
• Registration
• Agenda
• Lodging:
  • We are arranging a conference room, likely at the Hotel NH Padova. Room details including group rates to follow, but the recommended hotels are:
  • Hotel NH Padova, Via Niccolò Tommaseo, 61, 35131 Padova PD, Italy
  • Best Western Plus Hotel Galileo Padova Via Venezia 30, Padova, 35131 Italy

GO Release Pipeline

• January release out
• Error reports -
  • We have just ‘launched’ the project to produce GO rules reports by ‘assigned by’ rather than being the output of the file parser, see: https://github.com/geneontology/project-management/issues/23
  • Are there additional requirements from curators?
    • Curators would still like to see error reports based on submitting group (it can be helpful to see other groups' annotations for the organism(s) your group is responsible for)
    • May need to clarify who is responsible for some older groups' (retired sources) annotations, e.g. TAIR and TIGR
    • For inactive groups with multi-species annotations, should we consider parsing these out by organism?
    • Could we also generate custom reports for groups depending on what annotations they're responsible for?
    • In the future, we could also possibly generate curator-specific reports (using annotation properties in the GPAD file).

Ontology

Use of GO in other Ontologies

• Some discussion about use of GO BPs in other ontologies, particularly for defining phenotypes
• If terms are removed from GO, there needs to be another way to logically define some pheontpyes
• UPheno group will discuss this
• Other ontologies that use GO for this?

Annotation

Format of annotation review spreadsheets

• New github repo for generating lists of annotations for review
• Current SOP is very labor intensive for ontology editors
• Current spreadsheets may have more information than curators need and that information may not be organized ideally for efficient workflows
• Let's discuss what would be most useful for editors and curators to propose a new format that can be generated computationally
• Here’s a proposed new annotation report column and ordering:
  • https://docs.google.com/spreadsheets/d/11hm1kHDyu4CBUG_Zxcouq-rNDMUEmqw3YoMG8vNlWuU/edit#gid=1247173434

Annotation error reports and annotation review

• Currently, 195 open annotation review tickets
• Please remember to keep checking the reports generated by the pipeline and address any errors
• 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

Expanded set of MF-MF relations

• Noctua pathway editor with the expanded set of MF-MF relations is now on production
• The next step in this work will be to update existing models
  • Exploring doing this update computationally
• Small working meeting in Geneva next week to finish documentation for the new relations

Attendees

• On call: Antonia, Colin, David, Deborah, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Mahima, Malcolm, Mary, Pascale, Patrick, Raymond, Rob, Ruth, Sridhar, Seth, Suzi