Annotation Conf. Call 2023-02-21
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Agenda and Minutes
Meetings and Announcements
Noctua
- Next regularly scheduled Noctua outages:
- Thursday, February 23rd
- Outage tasks
Spring GOC Meeting Plans
- 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
- Registration deadline was Friday, February 17th
- Agenda and Logistics
GO Release Pipeline
- February release pending
- Issues with upstream sources
- There is a warning when IEA annotations reach the one-year mark
- Check the gorule-report regularly
Annotation Data Flow
- Survey on automated loads by groups that contribute to GO.
- Can groups update their spreadsheets in the Google drive or fill out the fields in the Summary spreadsheet?
AmiGO
Ontology
Ongoing Projects
- Timeline for obsoletions:
- extrinsic to membrane & histone modifications: end of Feb 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
- SOP
- 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.
We have the following structure: > x homeostasis >> cellular x homeostasis
- 'x homeostasis' has sometimes been used to mean 'organism-level' but not always.
- So, we will
- create new terms (where appropriate) for 'organismal x homeostasis'
- obsolete 'x homeostasis'
- change labels for 'cellular x homeostasis' to 'intracellular x homeostasis' to make the terms clearer
- change the definitions: current definition of 'cellular chemical homeostasis' is 'Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell.' -> proposed change to 'Any biological process by which a cell maintains a intracellular steady state level of a chemical."
- 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'. A suggestion by a Swiss-Prot curator was to use 'homeostasis' for compounds physiologically 'relevant', such as zinc, cobalt, and calcium, and use detoxification for others (aluminum, arsenic, possibly free iron, etc). We would like feedback from the group on this proposal.
- Ions versus monoatomic ions
- homestasis, transport, ion binding (no ticket yet)
Upcoming 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
Number of annotations by group (EXP/IC/TAS/NAS)
| Contributor (Assigned by) | Count |
|---|---|
| AgBase | 230 |
| Alzheimers_University_of_Toronto | 20 |
| ARUK-UCL | 380 |
| AspGD | 11 |
| BHF-UCL | 1198 |
| CACAO | 78 |
| CAFA | 115 |
| CGD | 20 |
| ComplexPortal | 365 |
| DFLAT | 5 |
| DIBU | 5 |
| dictyBase | 124 |
| DisProt | 4 |
| EcoCyc | 65 |
| EcoliWiki | 2 |
| FlyBase | 436 |
| GDB | 3 |
| GeneDB | 9 |
| GO_Central | 9 |
| HGNC | 1 |
| HGNC-UCL | 65 |
| JCVI | 2 |
| MGI | 935 |
| MTBBASE | 30 |
| PAMGO_MGG | 1 |
| ParkinsonsUK-UCL | 164 |
| PINC | 71 |
| PomBase | 34 |
| PseudoCAP | 41 |
| Reactome | 27 |
| RGD | 528 |
| SGD | 276 |
| SynGO | 71 |
| SynGO-UCL | 2 |
| TAIR | 100 |
| UniProt | 2200 |
| WB | 103 |
| ZFIN | 183 |
Annotation
Annotation Reviews
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 Rules Reports by Assigned By
- Provide GORULE reports by "assigned by"
- http://skyhook.berkeleybop.org/issue-go-site-1944-assigned-by-reports/reports/assigned-by-gorule-report.html
- We will await the full report so all groups can QC. Stay tuned!
GO-CAM and Noctua
- Automatic updates of MF-MF relations in existing GO-CAM models
- Report on what models will be updated and how.
Attendees
- On call: Antonia, Chris, David, Deborah, Dmitry, Dustin, Giulia, Kimberly, Leonore, Li, Malcolm, Mary, Pascale, Patrick, Petra, Raymond, Rob, Ruth, Sridhar, Seth, Suzi