Annotation Conf. Call 2021-09-07

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Agenda and Minutes

Meetings and Announcements

October Consortium Meeting - IMPORTANT UPDATES!

  • TUESDAY, OCTOBER 12th - THURSDAY, OCTOBER 14th
  • VIRTUAL
  • Agenda

Noctua Outage - Thursday, September 9th, 4 - 6pm PDT

Thank You Laurent-Philippe!

  • Friday is Laurent-Philippe's last day
  • Thank you very much for your contributions to GO!

Annotation Issues

Annotation Extension Relations

exists_during - TO BE RETIRED

  • Protein2GO now contains two new relations: 'existence overlaps' and 'existence starts and ends during' to replace 'exists during'
  • These relations are used to describe a developmental stage or cell cycle phase during which a cellular component exists.
  • 'exists during' is one of the gorel relations that is being retired in favor of Relations Ontology relations

activated_by - TO BE RETIRED

  • activated_by is also being retired
  • please see the remaining annotations in the spreadsheet to change or remove
  • if you have questions, get in touch - we can have more in depth discussion
    • 16 ARUK-UCL
    • 5 BHF-UCL
    • 6 Parkinson's
    • 4 PomBase
    • 3 SGD

Reannotation of methotrexate terms

  • We are proposing to obsolete all of the methotrexate terms in GO because methotrexate is a synthetic compound that is an analog of folic acid. It's effects on organisms are usually due to its similarity to folic acid, not due to any organism being evolved to deal with methotrexate specifically. Methotrexate binds with high affinity to dihydrofolate reductase (Dhfr), which it represses very effectively due to the greater affinity of Dhfr for methotrexate over folic acid. https://github.com/geneontology/go-ontology/issues/21998

Ontology update

Summary Ontology workshop - Chromatin-regulated transcription processes

Attendance

  • On call: Birgit, Chris, David, Dmitry, Dustin, Harold, Helen, Karen, Kimberly, Li, Mary, Midori, Pascale, Patrick, Petra, Raymond, Rob, Seth, Sierra, Stacia, Suzi, Tanya