Annotation Conf. Call 2022-09-06

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Agenda and Minutes

Meetings and Announcements

Fall 2022 Consortium Meeting

  • In person with remote accommodation
  • At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th
  • Registration form - PLEASE REGISTER by SEPT. 1st
    • See agenda for pswd
  • Please think about agenda items and breakout group topics

Noctua

  • Next regularly scheduled Noctua outage:
    • Thursday, September 22nd

GO Release Pipeline

  • August release still pending
    • Passed QC inspection, but held up by issues with Zenodo, where GOC releases are archived
    • Encourage people to check #release-pipeline channel on Slack for up-to-date info

Tracker summary emails for go-ontology and go-annotation

  • Thank you, Dustin!
  • From Seth: It has come to our notice that due to an issue we are having with our email delivery system (https://github.com/geneontology/go-site/issues/1891), we have been unable to send summaries since the 12th. As a stopgap measure until this issue has been fixed, we will manually send these emails on Fridays on a weekly interval, starting tomorrow. We hope to have a permanent resolution to this quickly and return to the previous daily summaries.

AmiGO

Ontology

Membrane CC Terms

Extrinsic component of membrane

Remaining: Extrinsic component of membrane Cannot be sure whether these were membrane or membrane-associated, so we need to obsolete with 'consider' the parent term 

  • extrinsic component of membrane 120
  • extrinsic component of cytoplasmic side of plasma membrane 98
  • extrinsic component of plasma membrane 70
  • extrinsic component of mitochondrial inner membrane 38
  • extrinsic component of synaptic vesicle membrane 22
  • extrinsic component of endoplasmic reticulum membrane 19
  • extrinsic component of mitochondrial outer membrane 19
  • extrinsic component of postsynaptic membrane 16
  • extrinsic component of external side of plasma membrane 13
  • extrinsic component of presynaptic membrane 13
  • extrinsic component of endosome membrane 10
  • extrinsic component of postsynaptic density membrane 9
  • extrinsic component of fungal-type vacuolar membrane 8
  • extrinsic component of synaptic membrane 8
  • extrinsic component of Golgi membrane 5
  • extrinsic component of presynaptic endocytic zone membrane 5
  • extrinsic component of neuronal dense core vesicle membrane 5
  • extrinsic component of periplasmic side of plasma membrane 4
  • extrinsic component of vacuolar membrane 4
  • extrinsic component of postsynaptic specialization membrane 4
  • extrinsic component of organelle membrane 4
  • extrinsic component of autophagosome membrane 3
  • extrinsic component of intraperoxisomal membrane 3
  • extrinsic component of presynaptic active zone membrane 3
  • extrinsic component of omegasome membrane 3
  • extrinsic component of plastid membrane 3
  • extrinsic component of lysosome membrane 2
  • extrinsic component of postsynaptic endosome membrane 2
  • extrinsic component of stromal side of plastid thylakoid membrane 2
  • extrinsic component of phagophore assembly site membrane 2
  • extrinsic component of cell outer membrane 1
  • subplasmalemmal coating 1
  • extrinsic component of nuclear outer membrane 1
  • extrinsic component of matrix side of mitochondrial inner membrane 1
  • extrinsic component of postsynaptic early endosome membrane 1
  • extrinsic component of thylakoid membrane 1


By group:

Contributor (Assigned by)

  • AgBase 2
  • ARUK-UCL 6
  • BHF-UCL 13
  • CACAO 2
  • CAFA 1
  • CGD 1
  • ComplexPortal 3
  • dictyBase 6
  • EcoCyc 21
  • EcoliWiki 6
  • FlyBase 18
  • GeneDB 4
  • GO_Central 3
  • MGI 27
  • ParkinsonsUK-UCL 4
  • PomBase 5
  • RGD 22
  • SGD 103 - done
  • SynGO 82
  • SynGO-UCL 3
  • TAIR 26
  • UniProt 157
  • WB 3
  • ZFIN 5

Side of membrane

  • Proposal for side of x membrane
  • From Pascale: "I would like to confirm that the term labels proposed are OK; I suspect that they are not always correct, because many times the level of the resolution of the experiment does not allow to define the position of the protein relative to the membrane. I think we also need to take the protein topology into account (ie transmembrane domains or anchors)."
  • @kimberly: is the use of ‘colocalizes with’ a membrane term more appropriate in some of these cases?
    • 'colocalizes with' has been used imprecisely in past GO curation.
    • We now also have 'located in' and 'is active in', with the latter being the main CC information we want to capture.
    • Does continued use of 'colocalizes with' add value to GO annotations?
    • Do curators have examples where they think its use is still warranted?
    • In AmiGO, there are currently 2,164 experimental CC annotations to ~100s of different terms that use 'colocalizes with'.
    • Over the past two years, WB reviewed 'colocalizes with' CC annotations and was able to remove them all in favor or more precise annotations.

Annotation

Review of histone modification annotations

Remaining enzymes to review (according to the spreadsheet):

  • ARUK-UCL 2
  • BHF-UCL 9
  • CACAO 17
  • CAFA 1
  • CGD 5
  • ComplexPortal 17
  • dictyBase 1
  • FlyBase 108
  • HGNC 3
  • HGNC-UCL 2
  • MGI 95
  • PomBase 3
  • RGD 9
  • SGD 48
  • UniProt 35
  • WB 42
  • ZFIN 24

The [Annotation review ticket https://github.com/geneontology/go-annotation/issues/4261] also has spreadsheets for dbTFs, coTFs and GTFs

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: Chris, David, Debby, Dustin, Edith, Giulia, Harold, Helen, Kimberly, Leonore, Li, Malcolm, Mary, Pascale, Patrick, Raymond, Rob, Ruth, Sierra, Stan, Val