Annotation Conf. Call 2022-11-29

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Agenda and Minutes

Meetings and Announcements

Noctua

  • Next regularly scheduled Noctua outage:

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?

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

Upcoming Projects

Obsolete "Regulation of molecular function" processes terms

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: