Phage jamboree- I July 31st 2012
From GO Wiki
Phage Jamboree Number 1: July 31st 2012
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.