Annotation Conf. Call 2022-08-16

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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
    • 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?

AmiGO

Ontology

Histone modifications

Added many MFs for histone modifications -

  • histone acetyltransferase activity
    • 'histone H2A acetyltransferase activity'
      • 'histone H2AK5 acetyltransferase activity'
      • 'histone H2AK9 acetyltransferase activity'
    • 'histone H2B acetyltransferase activity'
      • 'histone H2BK12 acetyltransferase activity'
      • 'histone H2BK5 acetyltransferase activity'
    • 'histone H3 acetyltransferase activity'
      • 'histone H3K14 acetyltransferase activity'
      • 'histone H3K18 acetyltransferase activity'
      • 'histone H3K23 acetyltransferase activity'
      • 'histone H3K27 acetyltransferase activity'
      • 'histone H3K36 acetyltransferase activity'
      • 'histone H3K4 acetyltransferase activity'
      • 'histone H3K56 acetyltransferase activity'
      • 'histone H3K72 acetyltransferase activity'
      • 'histone H3K9 acetyltransferase activity'
    • 'histone H4 acetyltransferase activity'
  • histone methyltransferase activity
    • 'histone arginine N-methyltransferase activity'
      • 'histone H2AR3 methyltransferase activity'
      • 'histone H3R17 methyltransferase activity'
      • 'histone H3R2 methyltransferase activity'
      • 'histone H3R8 methyltransferase activity'
      • 'histone H4R3 methyltransferase activity'
    • 'histone glutamine N-methyltransferase activity'
    • 'histone lysine N-methyltransferase activity'
      • 'histone H3K27 methyltransferase activity'
      • 'histone H3K36 methyltransferase activity'
      • 'histone H3K37 methyltransferase activity'
      • 'histone H3K4 methyltransferase activity'
      • 'histone H3K56 methyltransferase activity'
      • 'histone H3K79 methyltransferase activity'
      • 'histone H3K9 methyltransferase activity'
      • 'histone H4K20 methyltransferase activity'
  • histone kinase activity (this branch needs to be changed to be organized by histone, not by modified residue)
    • 'histone arginine kinase activity'
    • 'histone serine kinase activity'
      • 'histone H2AS1 kinase activity'
      • 'histone H2AS121 kinase activity'
      • 'histone H2AS139 kinase activity'
      • 'histone H2BS14 kinase activity'
      • 'histone H2BS36 kinase activity'
      • 'histone H3S10 kinase activity'
      • 'histone H3S28 kinase activity'
      • 'histone H3S57 kinase activity'
      • 'histone H4S1 kinase activity'
      • 'histone threonine kinase activity'
      • 'histone H2AT120 kinase activity'
      • 'histone H3T11 kinase activity'
      • 'histone H3T3 kinase activity'
      • 'histone H3T45 kinase activity'
      • 'histone H3T6 kinase activity'
      • 'histone tyrosine kinase activity'
      • 'histone H2AY142 kinase activity'
      • 'histone H3Y41 kinase activity'


  • 'histone deacetylase activity'
  • 'histone demethylase activity'
  • 'histone phosphatase activity'
  • 'histone decrotonylase activity'
  • 'histone ubiquitin ligase activity'
  • 'histone lactyltransferase activity'


etc. etc.

Annotation

Review of histone modification annotations

  • Annotation review spreadsheet: https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=1052081963
  • Grouped by
    • Is in a Panther family that is one of the 134 enzymes? -> yellow
      • ARUK-UCL: 18
      • AspGD: 2
      • BHF-UCL: 2
      • CACAO: 9
      • CAFA: 17
      • CGD: 2
      • dictyBase: 5
      • FlyBase: 1
      • HGNC: 109
      • HGNC-UCL: 3
      • MGI: 2
      • PomBase:95
      • RGD:3
      • SGD: 9
      • UniProt 49
      • WB: 230
      • ZFIN:42
    • Is in a Panther family annotated to dbTF? -> blue
    • Is GO annotated to coTF or a descendant -> green
    • Is GO annotated to GTF or a descendant -> orange
    • In more than one category -> purple

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: Antonia, David, Deborah, Dmitry, Dustin, Harold, Karen, Kimberly, Leonore, Li, Pascale, Patrick, Raymond, Rob, Seth, Sridhar, Suzi
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