Virus ontology devt July 2012

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Overview

  • BM got the go ahead to work on this for the month of July 2012, so that started the project again
  • we need to fix the existing terms & relationships as well as add additional terms
  • Incorporating some MeGO terms

People

  • Jane Lomax, Rebecca Foulger, Brenley McIntosh

Timeline

  • July - devt
  • July 31st - 9am EST
    • Skype call to discuss
  • Aug 2nd - 8am EST
    • Skype call to discuss
  • Aug 9th - 10am EST
    • Skype again

Summary of Calls and Discussions


Change Parentage

  • GO:0060144 host cellular processes involved in virus induced gene silencing
  • GO:0015074 DNA integration
  • GO:0006310 DNA recombination


Clarify term or definition

Topics for Aug 21-23rd discussion

  1. GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
  2. GO:0019030 icosahedral viral capsid - definition is a bit confusing b/c it says "the subunits are arranged to form an icosahedron, a solid with 20 faces and 12 vertices".
    • Is that true always (i.e. pseudo-T3)? But there isn't an icosahedral viral capsid, major subunit... I just ran into this when annotating the major head protein of lambda (gpE). I could annotate to both (GO:0019030 and GO:0098017), but that seems kind of redundant.
  3. need regulation of DNA integration terms -- GO:0015074 DNA integration

Topics to cover for July 31st discussion

  • 54 terms BM added to GO (some from MeGO, but not all)
  • BM rearranged a BUNCH of relationships
  • BM put in new MeGO dbxrefs for ~50 existing terms in GO


  • Things BM needs help with:
  • Where does restriction alleviation fit? (GO:0019048 virus-host interaction)
    • Change GO:0019049 evasion of host defenses by virus to suppression of ""
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?!)
    • response to virus -- suppression by virus of host cell lysis in response to superinfecting virus
  • Where does immunity fit? (lysogenized host is immune to superinfection)
    • add in immunity to viral latency definition
    • Jane has 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)
    • BM will look into this & we will talk about it on Thurs
  • Are the MeGO terms for secretion system parts necessary?
    • No. Becky will add type V ss complex terms
DONE. Added:
type V protein secretion system complex ; GO:0098046
    • BM will look into shared parts of the ss
  • 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.


    • need children that are site-specific and not site-specific; then grandchildren are tyrosine, serine or DDE based
  • 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. 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.

  • Should we include the complexes transpososome, intasome, resolvasome, relaxasome?
done.  BM will send tomorrow. 
  • 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 are the types of proteins?? BM will find out.
  • What should the definition of terminase activity be? Is it necessary?
done.  BM will send tomorrow.
  • Need to redefine GO:0046797, GO:0019061 & GO:0004803.
  • Is GO:0098034 ok?
  • 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?
    • has part transposition, DNA-mediated (GO:0006313)
    • under viral genome replication (BM)
  • 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?
    • toss it. obsolete.

More discussion

  • 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.



    • Jane
  • capsid self-assembly term
    • under viral capsid assembly


EDITS DONE

EDITS DONE BY JANE

New terms:

  • GO:0044659 cytolysis by virus of host cell & children
  • GO:0044662 disruption by virus of host cell membrane
  • GO:0098046 type V protein secretion system complex
  • GO:0019042 viral latency & children



EDITS: AUGUST 6TH, BECKY

Added new terms that Brenley had created in OBO-Edit. At the August 2nd jamboree, Jane, Becky and Brenley went through these terms and tweaked the names, definitions and position where necessary.

name: virus tail assembly ; GO:0098003
name: virus tail fiber assembly ; GO:0098004
name: virus head-tail joining ; GO:0098005
name: viral DNA genome packaging, headful ; GO:0098006
name: virus terminase, large subunit ; GO:0098009
name: virus tail ; GO:0098015
name: viral capsid, major subunit ; GO:0098017
name: viral capsid, minor subunit ; GO:0098018
name: virus tail, major subunit ; GO:0098019
name: virus tail, minor subunit ; GO:0098020
name: viral capsid, decoration ; GO:0098021
name: viral capsid, fiber ; GO:0098022
name: virus tail, tip ; GO:0098023
name: virus  tail, fiber ; GO:0098024
name: virus tail, sheath ; GO:0098027
name: virus tail, shaft ; GO:0098028
name: icosahedral viral capsid, spike ; GO:0098029
name: icosahedral viral capsid, neck ; GO:0098030
name: icosahedral viral capsid, collar ; GO:0098031
name: icosahedral viral capsid, collar fiber ; GO:0098032
name: icosahedral viral capsid, neck fiber ; GO:0098033
name: viral DNA genome packaging via site-specific sequence recognition ; GO:0098035
name: viral DNA genome packaging, 3' extended cos packaging ; GO:0098036
name: viral DNA genome packaging, 5' extended cos packaging ; GO:0098037
name: non-replicative transposition, DNA-mediated ; GO:0098038
name: replicative transposition, DNA-mediated ; GO:0098039
name: virus baseplate assembly ; GO:0098045
name: viral capsid, internal space ; GO:0098061
name: RNA translocase activity ; GO:0039630
ID: GO:1901217 Label: regulation of holin activity
ID: GO:1901218 Label: negative regulation of holin activity
DNA translocase activity involved in viral DNA genome packaging ; GO:0039631
RNA translocase activity involved in viral RNA genome packaging ; GO:0039632
  • Changed 'GO:0019049 evasion of host defenses by virus' to 'evasion or tolerance of host defenses by virus ; GO:0019049'


EDITS: AUGUST 10TH, BECKY

new terms:

killing by virus of host cells ; GO:0039633
killing by virus of host cells during superinfection exclusion ; GO:0039634
suppression by virus of host peptidoglycan biosynthetic process ; GO:0039635
suppression by virus of host cell wall biogenesis ; GO:0039636
catabolism by virus of host DNA ; GO:0039637
  • Added comment to 'genetic transfer ; GO:0009292' that it doesn't include lysogeny. GO:0009292 should not be used for annotation of phage lysogeny (integration of the bacteriophage nucleic acid into the host bacterium's genome).
  • Added comment to 'mating ; GO:' to consider instead using 'conjugation ; GO:0000746': For single-celled organisms, consider instead annotating to 'conjugation ; GO:0000746' or its children.
  • Deleted following relationship because a virus responding to another virus can be annotated with GO:0009597: added a comment to make this clearer.
detection of symbiont ; GO:0009602
--[isa]detection of virus ; GO:0009597
  • Tweaked definition of transposase activity ; GO:0004803 to make it clearer that the enzyme is site-specific for viral DNA/element but isn't always site-specific for the host DNA insertion site.
  • Created relationship:
adhesion of symbiont to host cell ; GO:0044650
--[isa]viral attachment to host cell ; GO:0019062
  • Added to comment of 'growth of symbiont in host cell ; GO:0044119' that the term is not suitable for viral replication in a host cell.



ACTION ITEMS

ACTION ITEMS FOR JANE AND BECKY

  • Bring up on an editors call how to handle multifunctional enzymes.


ACTION ITEMS FOR JANE

  • GO:0046739 spread of virus in host -- change to spread of virus in multicellular host
  • Add term for post-segregational killing: 'killing by virus of host cell by post-segregational killing'. Add comment that it occurs after plasmid partitioning.
  • Look at the 'capsid morphogenesis by nucleation' terms that Brenley has suggested (e.g. 'viral RNA genome packaging, nucleation ; GO:0098034') and add in appropriate self-assembly terms.
  • As part of the viral latency edits, add relationships and synonyms to 'GO:0008979 prophage integrase activity': integrase activity involved in establishment of integrated proviral latency.


OBSOLETIONS_TO_DO (JANE)

  • GO:0045090 retroviral genome replication & its children (JANE)
    • ultimately, not different from processes already described in GO & we aren't delineating between the types of viruses, only the attributes of the gene products
  • GO:0019038 provius
    • SO term, not GO
  • GO:0009293 transduction
    • per Jim Hu sourceForge item - not clear what gp you would annotate to this -- it is more a process characterizing phage
  • GO:0043498 cell surface binding & its children
    • already have host cell surface binding
  • genome types (DNA, RNA) in cellular component tree.
  • bacterial cell surface binding ; GO:0051635, and eukaryotic cell surface binding ; GO:0043499. Instead capture this information at the annotation stage.


ACTION ITEMS FOR BECKY

  • DNA recombinase mediator complex ; GO:0033061
    • Request from Brenley to make the complex annotatable to Prokaryotes too.
    • See SF item for issues (including current nuclear parentage) [1]
  • Create terms: 'LPS binding involved in viral attachment to host cell', and 'receptor binding involved in viral attachment to host cell'.


ACTION ITEMS FOR BRENLEY

  • Ask Arrianne exactly what is the difference btwn rolling circle transposition & conservative transposition?!
  • 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 an 'RNA transport from capsid to cytoplasm' term should go.

UNRESOLVED ISSUES

  1. capsid self assembly (under virus capsid assembly)
  2. viral membranes
  3. GO:0000150 recombinase activity -- relationships
  4. GO:0033061 DNA recombinase mediator activity -- definition includes nuclear localization (not in prok/arch), but will change a bunch of relationships...
  5. GO:0008907 integrase activity (GO:0008979 prophage integrase activity) -- cellular process
  6. Spanins and Holins