Difference between revisions of "Phage call August 9th 2012"

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(Created page with " DISCUSSION FROM CALL AUGUST 9TH 2012 ==Present== *Brenley *Jane *Becky * Jane working on high level entry/exit terms * holin & spanin terms (roles) are on agenda for editors ...")
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Latest revision as of 13:34, 10 July 2014



  • Brenley
  • Jane
  • Becky

  • Jane working on high level entry/exit terms
  • holin & spanin terms (roles) are on agenda for editors call next week.
  • Q: What should Bren do with her synonyms, db_xrefs, etc. that are in her flatfile?
    • A: Send them to Becky and Jane, and they'll add them to the live GO.
  • BM thinks exclusion killing should go as a child under GO:0034050 programmed cell death
    • A: The relationships between 'normal' GO and the multi-organism terms aren't worked out yet, but will come in due course.
  • Child of GO:0050658 RNA transport -- RNA transport out of viral capsid into host cytoplasm? This is when the capsid has been taken up into the cell, but the nucleic acid genome is then transferred from the capsid to the host cytoplasm.
    • AI: Brenley to look at the mechanism by which RNA is transported out of the viral capsid into the host cytoplasm, to help with deciding where in GO this term should go.
  • GO:0044119 growth of symbiont in host cell -- does this count for viruses?
    • A: NO... it refers to increase in mass of a symbiont, not increase in number. Becky will (and now has) added a comment to the term to this effect.
  • GO:0044037 multi-organism cell wall macromolecule metabolic process -- bacterial cell wall inhibition?
    • Where does cell lysis by inhibition of CW biosynthesis fit?? GO:0000270 peptidoglycan metabolic process or GO:0044659 cytolysis by virus of host cell
    • I am just not entirely sure about the definition including membranes b/c it is a passive process (inhibit cw synthesis = weaken cw as cell continues to remodel = ??? = loss of turgor & cell lysis)
  • GO:0052013 catabolism by symbiont of host macromolecule -- child for DNA? (protein & CHO are there)
  • GO:0009292 genetic transfer -- ok for viruses?
  • GO:0044650 adhesion of symbiont to host cell vs attachment to host?
  • GO:0044044 interaction with host via substrate in symbiont surface -- ok for fibers of viruses? glycoproteins of HIV surface?
  • GO:0075052 entry into host via a specialized structure -- tail?
  • GO:0007618 -- maybe clarify vs. conjugation.
  • Should GO:0009615 response to virus be a child of GO:0009608 response to symbiont?
  • GO:0004803 transposase activity -- definition says it is site-specific, but they are NOT all site-specific depending on how you define!!
    • site-specific ok -- are specific to sequences on insertion element or transposon
    • site-specific not ok -- some are NOT specific about where they insert
    • see PMID:6279020 - Three transposons (Mu, Tn1/Tn3, and Tn9/ IS1) insert efficiently at a great many different sites even within a region as short as a single gene.
  • GO:0052354 ! catabolism by organism of carbohydrate in other organism during symbiotic interaction