Annotation Conf. Call 2023-04-11
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Agenda and Minutes
Meetings and Announcements
Noctua
- Next regularly scheduled Noctua outages:
- Thursday, April 13th
- Outage tasks
Spring GOC Meeting - Almost here!
- 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
- Agenda and Logistics
- Please fill in survey on dinner choices
GO Release Pipeline
- April release out 2023-04-01
Annotation Data Flow
Change to products directory
- Rename products/annotations to products/upstream_and_raw_data to help avoid user confusion
- If your group retrieves files from the products/annotations directory, you will need to update the source location
PAINT
- Paul sent an email (2023-02-22) with a link to the draft of the human functionome paper
- Thanks to everyone for their feedback
- Current status?
AmiGO
Annotation
Annotation Reviews
GO Rules Reports by Assigned By
- Provide GORULE reports by "assigned by"
- Latest reports should be back tomorrow, 2023-03-22
- http://skyhook.berkeleybop.org/issue-go-site-1944-assigned-by-reports/reports/
- 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 again on 2023-03-22!
- Suggestions:
- Make sure there is a short summary for each rule in line with the actual lines flagged
- Add a horizontal sliding window bar at the top of the report, as well
- Copy the list of rules on the right-hand side of the table, as well
Annotation error reports and annotation review
Error reports
- Please remember to keep checking the reports generated by the pipeline and address any errors
Reannotating regulation of MF process terms
- Examples of annotations
- What level of granularity do we want in the corresponding MF terms?
- 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
- Working on MF-to-BP and BP-to-BP relations documentation (David, Pascale, Kimberly)
- https://github.com/orgs/geneontology/projects/130
- https://github.com/orgs/geneontology/projects/131
Ontology
Ongoing Projects
Is phagocytosis a type of endocytosis?
- Discuss ontology ticket
Term Merges and Obsoletions
- New proposed SOP for handling merges and obsoletions: No longer merge terms, only obsolete. When we used to merge, we'll now do obsolete + replaced by
- Noctua and P2GO automatically updates obsoleted terms that have a replaced_by; is this a problem for any group on the call?
- Note that QuickGO and AmiGO also repairs these annotations during the load process
- Streamline announcements for obsoleted terms having a replaced_by term: once per release (link to stats:
- For consistency with the OWL representation, and with other OBO ontologies, we would like to create obsolete terms for all alt_id entries. These would have a replaced_by link to the active term. After this, the ontology would contain no alt_id tags. (https://github.com/geneontology/go-ontology/issues/24467)
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 | 0 |
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 |
Attendees
- On call: Antonia, Dmitry, Dustin, Edith, Giulia, Karen, Kimberly, Leonore, Li, Mary, Pascale, Patrick, Raymond, Rob, Seth, Stan, Sridhar, Suzi, Val, Victoria