Annotation Conf. Call 2023-02-28
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Agenda and Minutes
Meetings and Announcements
No GO Calls Week
- Next week, March 6th - 10th, is a no GO calls week
Noctua
- Next regularly scheduled Noctua outages:
- Thursday, March 9th
- 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
- Please respond to Suzi's email if you registered but won't be attending in-person
- Agenda and Logistics
GO Release Pipeline
- February release scrapped
- March release will hopefully start tomorrow
- Issues with upstream sources
- There is a warning when IEA annotations reach the one-year mark - filter now extended from two to three years
- Check the gorule-report regularly
Annotation Data Flow
- Survey on automated loads by groups that contribute to GO.
- Most groups have updated the spreadsheet in the Google drive or filled out the fields in the Summary spreadsheet
- Any questions about the spreadsheet?
PAINT
- Paul sent an email (2023-02-22) with a link to the draft of the human functionome paper
- Please use “suggest mode” when making suggestions directly in the text. We’ve tried to add the Consortium members who have been involved in creating and supporting manual experimental annotations (excluding directly to protein binding), which provided the basis for the integrated human functionome, but please review the list toward the end of the main paper text (the initial list was copied from the recent GO update paper).
- We request that you add comments by the end of the day on Thursday March 2. We’re looking forward to your feedback!
AmiGO
Ontology
Ongoing Projects
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
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
- Full list of group reports is now ready for review. Please check!
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: David, Deborah, Dmitry, Dustin, Edith, Giulia, Helen, Karen, Kimberly, Leonore, Li, Malcolm, Mary, Pascale, Patrick, Petra, Raymond, Rob, Ruth, Seth, Sridhar, Stacia, Stan, Suzi