Annotation Conf. Call 2022-08-30: Difference between revisions

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(Created page with "= 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 * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
 
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* PomBase 5
* PomBase 5
* RGD 22
* RGD 22
* SGD 103
* SGD 103 - done
* SynGO 82
* SynGO 82
* SynGO-UCL 3
* SynGO-UCL 3

Revision as of 15:19, 29 August 2022

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 8th

GO Release Pipeline

  • August release still pending (but passed QC inspection)

Tracker summary emails for go-ontology and go-annotation

  • 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

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

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:
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