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

The list of Brenley's Suggested Terms- created by Brenley in OBO-Edit, and tweaked where necessary at the phage calls and jamborees.

People

  • Jane Lomax, Rebecca Foulger, Brenley McIntosh


Summary of Calls and Discussions

EDITS DONE

JANE'S EDITS

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


BECKY'S EDITS

AUGUST 6TH: 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'


AUGUST 10TH: Added 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.
  • Adjusted definition and placement of DNA recombinase mediator complex ; GO:0033061 to make it applicable to Prokaryotes [1]
  • New terms:
virion attachment, binding to host lipopolysaccharide ; GO:0039638
suppression by virus of host cell lysis in response to superinfection ; GO:0039639
cytolysis by virus via suppression of host peptidoglycan biosynthetic process ; GO:0039640


ACTION ITEMS

ACTION ITEMS FOR JANE AND BECKY

  • Bring up on an editors call how to handle multifunctional enzymes.
Decided that we can add these in (if the two functions always go together) with HAS_PART relationships to the individual activities.


  • Bring up the issue of tackling roles in GO, so we can describe holins and spanins Spanins and Holins
Decided that role terms are allowed IF the mechanism is known. So 'holin' is valid, but 'spanin' is not, because it's not yet known how spanins carry out their roles.


ACTION ITEMS FOR JANE

  • GO:0046739 spread of virus in host -- change to spread of virus in multicellular host
DONE
  • Add term for post-segregational killing: 'killing by virus of host cell by post-segregational killing'. Add comment that it occurs after plasmid partitioning.
DONE. killing by virus of host cell by post-segregational killing (GO:0044696). Brenley can you check it looks okay?
  • 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.
DONE. Also gave it a logical def the same.
  • Merge 'lytic viral release ; GO:0019077' with 'cytolysis by virus of host cell ; GO:0044659'. (point 11 from [2])
  • Create relationship: 'provirus excision ; GO:0032359' is_a: 'release from viral latency ; GO:0019046'. (point 18 from [3])


OBSOLETIONS FOR (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.


ACTION ITEMS FOR BECKY

  • Ask Philippe whether 'reversible bacteriophage attachment, binding of host cell surface receptor' and irreversible bacteriophage attachment, binding of host cell surface receptor' are specific to bacteriophages or whether this reversible process occurs in other viruses. (see Brenley's file for proposed terms).
HAVE EMAILED (AUG 22nd 2012). Philippe says:
To my knowledge this process is restricted to the bacteriophages. There are low affinity receptors for eukaryotic viruses as well, but we can't draw a line as reversible and irreversible attachment, and this phenotype is dependent on experimental procedures designed for bacterias.


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.
  • Brenley to give Jane and Becky a list of synonyms, db_xrefs, etc. added to existing GO terms, for incorporation into the live GO file.



UNRESOLVED ISSUES

  • terminase activity (Becky to add in multifunctional term).
  • escort proteins (Becky to find out how they help the viral genome enter the host cell, and how they offer protection).