Phage jamboree- I July 31st 2012

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Phage Jamboree Number 1: July 31st 2012

Present:

  • Brenley
  • Jane
  • Becky
  • Shabnam


Progress Update from Brenley

  • 54 terms BM added to GO (some from MeGO, but not all). These are in a separate text file that Becky and Jane will go through with Brenley then copy-and-paste into the live GO file.
  • BM rearranged a BUNCH of relationships: Will need to go through these one-by-one with Jane and Becky, so they can do the edits in the live GO file.
  • BM put in new MeGO dbxrefs for ~50 existing terms in GO. Brenley will need to pass these to Jane and Becky.


Questions From Brenley

  • Where does restriction alleviation fit? (GO:0019048 virus-host interaction)
DONE (Becky). Changed to match parents and definition:
evasion by virus of host immune response ; GO:0030683
evasion of host defenses by virus ; GO:0019049
>
evasion or tolerance by virus of host immune response ; GO:0030683
evasion or tolerance of host defenses by virus ; GO:0019049


  • Where does lysis inhibition fit? (established virus vs newly-infecting virus in host?!)
    • Becky to add under response to virus: suppression by virus of host cell lysis in response to superinfecting virus ; GO:NEW.
  • Where does immunity fit? (lysogenized host is immune to superinfection)
    • add in immunity to viral latency definition
    • Jane to look at the latency terms.
DONE (Jane). Added a whole bunch of new terms under 'viral latency ; GO:0019042' and fixed up defs etc.
  • Where does exclusion fit? (2 different viruses in same cell at same time = ONLY get progeny from 1)
DONE (Becky). Added term: killing by virus of host cells during superinfection exclusion ; GO:0039634


  • Are the MeGO terms for secretion system parts necessary?
    • No. Becky will add type V ss complex terms
DONE (Becky). Added:
type V protein secretion system complex ; GO:0098046


  • Do we want the specific children for the terminases, invertases, excisionases?
    • Becky will fix relationships for recombinases
NOT DONE IN THE END (Becky). I was going to add 
recombinase activity ; GO:0000150
--[isa]site-specific recombinase activity ; GO:0009009
BUT, the comment of GO:0009009 states: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do  not break or form phosphodiester bonds. 
'GO:0000150' has a similar comment explaining the absence of the relationship, so I haven't added it in.
  • How do excisionase and invertase and integrase fit into DNA cleavage activities or are they separate?
    • Becky will do process:function relationships for these
DONE (Becky). Added P/F relationships as follows:
DNA integration ; GO:0015074
--[part_of]integrase activity ; GO:0008907
DNA recombination ; GO:0006310
--[part_of]recombinase activity ; GO:0000150
BUT... the GOEds need to look at the cellular parentage of the DNA metabolism terms. Causes disjoint TPVs when a protein metabolises the DNA of another organism. Several of the definitions & synonyms of child terms will be affected.


  • How do we describe the injected proteins?
    • not in scope of GO directly
    • functions possible -- RNA binding involved in genome entry into host cell


  • What should the definition of terminase activity be? Is it necessary?
    • It's a multifunctional enzyme (keeps coming up, so Becky and Jane will discuss with the other editors the best way to handle these multifunctional proteins).


  • Need to redefine GO:0046797, GO:0019061 & GO:0004803.


  • Is viral RNA genome packaging, nucleation ; GO:0098034 ok?
    • JANE TO LOOK AT AND ADD self-assembly terms.
  • What do we do with the plasmid virus terms?
    • new terms by Jane suit these fine


  • What do we do with replication by transposition terms?
    • Add a relationship: has part transposition, DNA-mediated (GO:0006313)
  • How do we handle the viral envelopes since some are INTERNAL, others are EXTERNAL, but the current defn is only for EXTERNAL?
    • merge virion membrane and viral envelope & make children for internal and external
 HELD OFF on the merge because I see viral membranes crop up again for our Thursday session.


  • What do we do with GO:0009293 (transduction) and children from BM?
    • Obsolete (Jane).


  • GO:0060144 - needs to be under multi-organism process
DONE (Jane). Fixed immediate parentage issue. Although virus-induced gene silencing is something that really needs looking at in more detail - the terms we have are really outdated with recent developments - RNAi etc. And in fact virus-induced gene silencing is now only ever mentioned as a technology rather than a biological process, so these terms are extra confusing. I'll make a SF ticket.