Virus ontology devt July 2012: Difference between revisions

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* we need to fix the existing terms & relationships as well as add additional terms
* we need to fix the existing terms & relationships as well as add additional terms
* Incorporating some MeGO 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==
==People==
* Jane Lomax, Rebecca Foulger, Brenley McIntosh
* Jane Lomax, Rebecca Foulger, Brenley McIntosh


==Summary of Calls and Discussions==
==Summary of Calls and Discussions==
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*[[Phage jamboree- II August 2nd 2012]]
*[[Phage jamboree- II August 2nd 2012]]
*[[Phage call August 9th 2012]]
*[[Phage call August 9th 2012]]
 
*[[Phage call August 21st-23rd 2012]]
 
*[[Phage call August 30th 2012]]
==Topics for Aug 21-23rd discussion==
*[[Phage call September 6th 2012]]
* BM has been annotating phage lambda proteins (see [http://ecoliwiki.net/colipedia/index.php/Category:Gene_List:Phage_lambda Gene List of Lambda on EW])
* problems I have encountered:
# GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
# 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.
# need regulation of DNA integration terms -- GO:0015074 DNA integration
 
==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virus-induced gene silencing is something that really needs looking at in more detail - the terms we have are really outdated with recent developments - RNAi etc.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==


===EDITS DONE BY JANE===
===JANE'S EDITS===


New terms:
New terms:
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===BECKY'S EDITS===  
 
 
===EDITS DONE BY BECKY===  


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.
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.
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* Changed 'GO:0019049 evasion of host defenses by virus' to 'evasion or tolerance of host defenses by virus ; GO:0019049'
* Changed 'GO:0019049 evasion of host defenses by virus' to 'evasion or tolerance of host defenses by virus ; GO:0019049'




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* 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.
* 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 [https://sourceforge.net/tracker/?func=detail&aid=3554860&group_id=36855&atid=440764]
* 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==
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* Bring up on an editors call how to handle multifunctional enzymes.
* 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.




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* GO:0046739 spread of virus in host -- change to spread of virus in multicellular host
* 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.
* 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.
* 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.
* 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 [http://gocwiki.geneontology.org/index.php/Phage_call_August_21st-23rd_2012])
* Create relationship: 'provirus excision ; GO:0032359' is_a: 'release from viral latency ; GO:0019046'. (point 18 from [http://gocwiki.geneontology.org/index.php/Phage_call_August_21st-23rd_2012])






====OBSOLETIONS_TO_DO (JANE)====
====OBSOLETIONS FOR (JANE)====


* GO:0045090 retroviral genome replication & its children (JANE)
* GO:0045090 retroviral genome replication & its children (JANE)
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** already have host cell surface binding
** already have host cell surface binding
* genome types (DNA, RNA) in cellular component tree.
* 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.




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===ACTION ITEMS FOR BECKY===
===ACTION ITEMS FOR BECKY===


* DNA recombinase mediator complex ; GO:0033061
* 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).
** Request from Brenley to make the complex annotatable to Prokaryotes too.
 
** See SF item for issues (including current nuclear parentage) [https://sourceforge.net/tracker/?func=detail&aid=3554860&group_id=36855&atid=440764]
HAVE EMAILED (AUG 22nd 2012). Philippe says:
* Create terms: 'LPS binding involved in viral attachment to host cell', and 'receptor binding involved in viral attachment to host cell'.
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.
* Add under response to virus: suppression by virus of host cell lysis in response to superinfecting virus ; GO:NEW.
 
 


===ACTION ITEMS FOR BRENLEY===
===ACTION ITEMS FOR BRENLEY===
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* Ask Arrianne exactly what is the difference btwn rolling circle transposition & conservative transposition?!
* 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 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 MeGO dbxrefs she's added to approx 50 existing terms in 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==


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


==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).




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[[Category:Meetings]]
[[Category:Meetings]]
[[Category:Ontology]]
[[Category:Ontology]]
[[Category:Viruses]]

Latest revision as of 09:26, 15 July 2018

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).
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