Annotation Conf. Call 2022-11-29
Agenda and Minutes
Meetings and Announcements
Noctua
- Next regularly scheduled Noctua outage:
- Thursday, December 1st and December 15th
- Outage tasks
2022 - 2023 Annotation Calls
- Last call: Tuesday, December 6th, 2022
- No calls: December 13th and 20th
- Tentative: no GO calls first week of January
- Tentative: first annotation call: January 10th
Spring GOC Meeting Plans
- Padua, Italy - late April, the two days after the ISB (this was not on the original survey)
- Tentative plan: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM
GO Release Pipeline
- December release to start later this week
Protein2GO
- Noctua imports for WB and SGD
- Issue of contributor assignment for ISS annotations has come up (deja vu?)
- Changes to original experimental annotation result in contributor also being assigned to the ISS annotation
- Is this the desired behavior? Do we need to make changes in Protein2GO behavior?
- Issue of contributor assignment for ISS annotations has come up (deja vu?)
AmiGO
Ontology
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)
Upcoming Projects
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 |
---|---|
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-CAM and Noctua
Other Projects
Attendees
- On call: