Annotation Conf. Call 2023-01-24
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Agenda and Minutes
Meetings and Announcements
- Next regularly scheduled Noctua outages:
- Thursday, January 26th
- 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
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 ticket closing jamboree
- Last week the ontology editors focused on closing tickets
- Any remaining questions about tickets?
- Timeline for obsoletions:
- extrinsic to membrane  & histone modifications : end of Jan 2023?
- generally: we have been leaving 1-2 weeks for terms with a few annotations, but we never discussed how long to leave when there are a lot of annotations - is 3 months OK ?
- Agreed on call: 3 months is sufficient time before obsoleting ontology terms with lots of annotations
- Should we use http://purl.obolibrary.org/obo/IAO_0006012 "scheduled for obsoletion on or after"?
- BP refactoring: split into 'cellular' processes and 'organism-level' processes. Currently working on the 'homeostasis' branch.
- detoxification versus homeostasis: some chemicals are important/essential (zinc, cobalt, calcium, etc) but toxic at high levels. We had started to create some specific detoxification terms (such as cobalt detoxification). The issue is that it becomes very difficult to chose whether to annotate 'homeostasis' or 'detoxification'. The current proposal is to use 'homeostasis' for compounds physiologically 'relevant', such as zinc, cobalt, and calcium, and use detoxification for others (aluminum, arsenic, etc).
Obsolete "Regulation of molecular function" processes terms
- 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
Number of annotations by group (EXP/IC/TAS/NAS)
|Contributor (Assigned by)||Count|
Format of annotation review spreadsheets
- 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
- 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
- We will soon be updating the Noctua pathway editor with the expanded set of MF-MF relations
- New decision tree
- The next step in this work will be to update existing models
- Hope to do this computationally
- Working on a format for systematically capturing/documenting conditional replacements
- regulates -> directly regulates
- Hope to do this computationally
- On call: Antonia, Deborah, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Leonore, Li, Pascale, Patrick, Raymond, Rob, Ruth, Seth, Sridhar, Suzi, Val, Petra