Annotation Conf. Call 2023-04-11

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Agenda and Minutes

Meetings and Announcements

Noctua

  • Next regularly scheduled Noctua outages:

Spring GOC Meeting - Almost here!

  • Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th)
  • Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM
  • Agenda and Logistics
  • Please fill in survey on dinner choices

GO Release Pipeline

  • April release out 2023-04-01

Annotation Data Flow

Change to products directory

PAINT

  • Paul sent an email (2023-02-22) with a link to the draft of the human functionome paper
  • Thanks to everyone for their feedback
  • Current status?

AmiGO

Annotation

Annotation Reviews

GO Rules Reports by Assigned By

Annotation error reports and annotation review

Error reports

  • Please remember to keep checking the reports generated by the pipeline and address any errors

Reannotating regulation of MF process terms

  • 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

Ontology

Ongoing Projects

Is phagocytosis a type of endocytosis?

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)

Current 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 0
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

Attendees

  • On call: Antonia, Dmitry, Dustin, Edith, Giulia, Karen, Kimberly, Leonore, Li, Mary, Pascale, Patrick, Raymond, Rob, Seth, Stan, Sridhar, Suzi, Val, Victoria