Annotation Conf. Call 2022-11-15

From GO Wiki
Revision as of 12:37, 15 November 2022 by Vanaukenk (talk | contribs) (→‎Attendees)
Jump to navigation Jump to search

Agenda and Minutes

Meetings and Announcements

Noctua

  • Next regularly scheduled Noctua outage:

Spring GOC Meeting Plans

  • Survey - please reply
    • Padua, Italy - late April, before the ISB meeting
      • Another Italy option - the two days after the ISB (this was not on the original survey, but is now also an option) - email Pascale if you have strong feelings one way or the other wrt before/after the ISB meeting
    • Baltimore, MD - late May/early June (two options)

GO Release Pipeline

  • November release out on November 3rd
    • Encourage people to check #release-pipeline channel on Slack for up-to-date info
  • If your group changes any practice that would alter significantly the number of annotations, please let Pascale know
  • Next release in Dec should have IBAs from new PANTHER 17.0. Breakdown of changes by GAF file: https://docs.google.com/spreadsheets/d/1ShFwfNGk67v9XKj9COVPdHGaUfqIICtMi7wY-wkFcfY/edit#gid=1051461976
    • Drop of 7.91% (-316642 IBAs) compared to previous IBA release 2022-09-26. A significant portion of this drop (2.95 of the 7.91%) is due to a code change that removes redundant IBAs, meaning generic term annotations were dropped when a more specific term annotation exists.

Using PRO in GO Annotation

  • Presentation from Darren Natale on using PRO to create modified forms of proteins for GO annotation

AmiGO

Ontology

Annotation

Annotation Reviews

Contributor (Assigned by)

  • ARUK-UCL 6
  • BHF-UCL 13
  • ParkinsonsUK-UCL 4
  • SynGO-UCL 3
  • CAFA 1
  • CGD 1
  • EcoCyc 3
  • EcoliWiki 6
  • GeneDB 4
  • PomBase 5
  • RGD 9
  • SynGO 82
  • UniProt 146
  • WB 2

Annotation Questions on Slack Channel

Annotating to transcription coactivator term (Antonia)

  • ZMYND8 directly binds the P-TEFb complex and stimulates phosphorylation of RNA pol II CTD to stimulate transcription. The authors call it a coactivator - can I annotate to this term or is P-TEFb function downstream?

Annotation of cortical proteins attached to the cell membrane (Val)

  • How would you curate the location of a proteins that is described as "cortical", acts as a "membrane adaptor" and attaches to the "plasma membrane" by a prenylation signal?
  • "Here we describe a cortical protein, mod5p, that regulates the dynamic behaviour of tea1p. In mod5Delta cells, tea1p is efficiently transported on microtubules to cell tips but fails to anchor properly at the cortex and thus fails to accumulate to normal levels. mod5p contains a signal for carboxy-terminal prenylation and in wild-type cells is associated with the plasma membrane at cell tips."
  • I think in the discussion we said the "plasma membrane". and "cell cortex" were mutually exclusive, but researchers do not seem to make the same distinction?
  • Decision on 2022-11-15 call: annotate this protein, mod5p, to 'plasma membrane' based on its attachment via a prenylation modification

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: David, Deborah, Dmitry, Dustin, Edith, Giulia, Harold, Karen, Kimberly, Li, Mary, Pascale, Patrick, Petra, Raymond, Rob, Ruth, Seth, Suzi