Annotation Conf. Call 2023-01-31
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Agenda and Minutes
Meetings and Announcements
- 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.
- 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).
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?
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:
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
- 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