Annotation Conf. Call 2023-01-17

Agenda and Minutes

Meetings and Announcements

Noctua

• Next regularly scheduled Noctua outages:
  • Thursday, January 26th
  • Outage tasks

Spring GOC Meeting Plans

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

GO Release Pipeline

• January release out

Ontology

Ongoing Projects

Ontology ticket closing jamboree

• This week the ontology editors are focusing on closing tickets
• Any tickets that need immediate attention from curators?

• 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
  • Should we use http://purl.obolibrary.org/obo/IAO_0006012 "scheduled for obsoletion on or after"?
• BP refactoring: split into 'cellular' processes and 'organism-level' processes. Currently working on the 'homeostasis' branch.
  • 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'. The current proposal is to use 'homeostasis' for compounds physiologically 'relevant', such as zinc, cobalt, and calcium, and use detoxification for others (aluminum, arsenic, etc).

• possible merges "actin filament REorganization

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

• actin filament reorganization https://github.com/geneontology/go-ontology/issues/14087
• Cobalt homeostasis https://github.com/geneontology/go-ontology/issues/24658
• RNA pol II C terminal phosphorylation processes : https://github.com/geneontology/go-annotation/issues/4408

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
    • Working on a format for systematically capturing/documenting conditional replacements
  • regulates -> directly regulates

Attendees

• On call: Antonia, Chris, Colin, Deborah, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Leonore, Li, Pascale, Patrick, Petra, Raymond, Seth, Sridhar, Stacia, Suzi, Val