Annotation Conf. Call 2022-11-29: Difference between revisions
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Number of annotations by group (EXP/IC/TAS/NAS) | Number of annotations by group (EXP/IC/TAS/NAS) | ||
{| | {| border="1" cellpadding="5" cellspacing="0" | ||
!Contributor (Assigned by)!!Count | !Contributor (Assigned by)!!Count | ||
|- | |- | ||
| AgBase | | AgBase | ||
| 230 | | 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 == |
Revision as of 04:21, 29 November 2022
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: