Annotation Conf. Call 2023-01-10

From GO Wiki
Jump to navigation Jump to search

Agenda and Minutes

Meetings and Announcements

Noctua

  • Next regularly scheduled Noctua outages:

Spring GOC Meeting Plans

  • Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th)
  • Tentative schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM

GO Release Pipeline

  • January release out

AmiGO

Ontology

Ongoing Projects

  • Timeline for obsoletions:
    • extrinsic to membrane & histone modifications: end of Jan 2023?
    • generally: we have been leaving 1-2 weeks for terms with a few annotations, but we never discussed how long to leave when there are a lot of annotations - is 3 months OK ?
    • Agreed on call: 3 months is sufficient time before obsoleting ontology terms with lots of annotations
  • SOP
  • 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."
  • detoxification versus homeostasis: some chemicals are important/essential (zinc, cobalt, calcium, etc) but toxic at high levels. We had started to create some specific detoxification terms (such as cobalt detoxification). The issue is that it becomes very difficult to chose whether to annotate 'homeostasis' or 'detoxification'. A suggestion by a Swiss-Prot curator was to use 'homeostasis' for compounds physiologically 'relevant', such as zinc, cobalt, and calcium, and use detoxification for others (aluminum, arsenic, possibly free iron, etc). We would like feedback from the group on this proposal.


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

Error Report Usability

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

Expanded set of MF-MF relations

  • We will soon be updating the Noctua pathway editor with the expanded set of MF-MF relations
    • New decision tree
  • The next step in this work will be to update existing models
    • Hope to do this computationally
    • regulates -> directly regulates

Other Projects

Attendees

  • On call:
Retrieved from "https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2023-01-10&oldid=83873"