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)
Ongoing Projects
- 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."
- Ions versus monoatomic ions
- homestasis, transport, ion binding (no ticket yet)
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: Antonia, Colin, David, Deborah, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Leonore, Pascale, Patrick, Raymond, Seth