Phage call August 21st-23rd 2012: Difference between revisions

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==Topics for Aug 21-23rd discussion==
==QUESTIONS FROM BRENLEY==
==QUESTIONS FROM BRENLEY==


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* problems I have encountered:
* problems I have encountered:
* GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
* GO:0043493 viral terminase complex isn't under GO:0044423 virion part or better yet, 0019028 viral capsid
viral terminase complex ; GO:0043493
- host cell cytoplasm part
+ viron_part
* 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".   
* 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".   
  Changed definition to match Wikipedia: Icosahedral capsids have 12 pentamers and 10(T-1)hexamers, where T is the triangulation number.
**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.
**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
* need regulation of DNA integration terms -- GO:0015074 DNA integration
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====More issues from Bren====
====More issues from Bren====
2. What is the difference between GO:0019051 induction by virus of host apoptotic process and GO:0060139 positive regulation of apoptotic process by virus?  Why is 19 a child of 60?  Are they not the same thing?
2. What is the difference between GO:0019051 induction by virus of host apoptotic process and GO:0060139 positive regulation of apoptotic process by virus?  Why is 19 a child of 60?  Are they not the same thing?
* Paola reorganized the apoptosis terms, so Becky with check with her.  Before, induction was a specific kind of positive regulation.
Becky has emailed Paola, who's leading the apoptosis overhaul to check on what was decided about induction v pos regulation of apoptosis terms.
 
3. Is it going to be confusing to have GO:0039633 killing by virus of host cells and cytolysis (i.e. both kill the cells)
3. Is it going to be confusing to have GO:0039633 killing by virus of host cells and cytolysis (i.e. both kill the cells)
* Becky will make cytolysis a kind of KILLING
Add relationship:
killing by virus of host cell
--[isa]cytolysis by virus of host cell
 
 
4. GO:0075733 intracellular transport of viral material – confusing without indicating mean genome in term & not viral procapsid transport term.  Why is this separate from GO:0046788 egress of virus within host cell?
4. GO:0075733 intracellular transport of viral material – confusing without indicating mean genome in term & not viral procapsid transport term.  Why is this separate from GO:0046788 egress of virus within host cell?
*
Add relationship:
intracellular transport of viral material
--[isa]egress of virus within host cell
 
5. What about viral material transport out of nucleus?  Does that happen through proteins???
5. What about viral material transport out of nucleus?  Does that happen through proteins???
* leaving this for now - can add if people request terms for this.
* leaving this for now - can add if people request terms for this.
6. Is GO:0006948 induction by virus of host cell-cell fusion related to GO:0046739 spread of virus in multicellular host?
6. Is GO:0006948 induction by virus of host cell-cell fusion related to GO:0046739 spread of virus in multicellular host?
* the structure used for cell-cell fusion is not exclusively for spread.
* the structure used for cell-cell fusion is not exclusively for spread.
Add comment to 'host cell-cell fusion' to also consider spread of virus term.
7. Should we add a comment to GO:0046756 lytic viral exocytosis about how this is how dsDNA phages get out (by encoding a holin & lysozyme), ssDNA and ssRNA phages (by preventing host PG biosynthesis)
7. Should we add a comment to GO:0046756 lytic viral exocytosis about how this is how dsDNA phages get out (by encoding a holin & lysozyme), ssDNA and ssRNA phages (by preventing host PG biosynthesis)
* should use lytic viral release, Becky making this new relationships for holin activity under this
* should use lytic viral release, Becky making this new relationships for holin activity under this
** Becky may link cytolysis and lytic viral release via new term
** Becky may link cytolysis and lytic viral release via new term
Add in P/F relationships for holins:
lytic viral release
--[partof]holin activity
or
cytolysis by virus of host cell
--[partof]holin activity
create new term: lytic viral release by viral cytolysis of host cell ; GO:NEW
8. How does GO:0046754 non-lytic viral exocytosis work?  Why is it different from GO:0046755 non-lytic virus budding (which says it is a form of viral envelopment)?  Clarify that filamentous phage are the first & not the second in a comment???
8. How does GO:0046754 non-lytic viral exocytosis work?  Why is it different from GO:0046755 non-lytic virus budding (which says it is a form of viral envelopment)?  Clarify that filamentous phage are the first & not the second in a comment???
* defn of non-lytic exocytosis and release are basically the same thing, so what is the difference between those two terms & how does budding fit in???
* defn of non-lytic exocytosis and release are basically the same thing, so what is the difference between those two terms & how does budding fit in???
* ask Jane when she gets back!
* ask Jane when she gets back!
9. What happened to capsid formation around genome via self-assembly?
9. What happened to capsid formation around genome via self-assembly?
* Jane is working on these
* Jane is working on these
10. Have to have a term for the dsRNA viruses that pack a SINGLE strand of RNA & then replicate in the head.  OR clarify GO:0019074 viral RNA genome packaging to include this???
10. Have to have a term for the dsRNA viruses that pack a SINGLE strand of RNA & then replicate in the head.  OR clarify GO:0019074 viral RNA genome packaging to include this???
* Becky will add comment that the packaging can be ssRNA or dsRNA or dsDNA.
Add comment to GO:0019074 that the packaging can be ssRNA or dsRNA.
 
11. I thought GO:0045090 retroviral genome replication was going away?
11. I thought GO:0045090 retroviral genome replication was going away?
* obsolete request going to go out from Jane
* on Jane's list for obsoletion
 
12. How is GO:0019081 viral protein biosynthetic process different from protein biosynthetic process?  Is this the whole cellular problem???
12. How is GO:0019081 viral protein biosynthetic process different from protein biosynthetic process?  Is this the whole cellular problem???
* discussing at Editors call, going to change the defintion of cellular in GO
* discussing at Editors call, going to change the defintion of cellular in GO
* separate cellular based on single or multi-organism process
* separate cellular based on single or multi-organism processes.
 
 
13. Should there be “escort functions” for A2 and similar proteins that escort the genomes into the host & protect the genome from degradation???
13. Should there be “escort functions” for A2 and similar proteins that escort the genomes into the host & protect the genome from degradation???
* similar to chaperone terms, no.
* similar to chaperone terms, no.
* synonym for GO:0046596 of viral escort (hopefully will point people here)
Add 'viral escort protein' as synonym for 'regulation of viral entry into host cell ; GO:0046596'.
 
 
14. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly?  They are the SAME!!
14. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly?  They are the SAME!!
* Becky is merging phage assembly into virion assembly
Merge 'phage assembly ; GO:' into 'virion assembly ; GO:'
 
15. What is the difference between GO:0019046 release from viral latency and GO:0032359 provirus excision?  Should GO:0032359 be a child of GO:0019046???
15. What is the difference between GO:0019046 release from viral latency and GO:0032359 provirus excision?  Should GO:0032359 be a child of GO:0019046???
* ask Jane when she gets back!
* ask Jane when she gets back!
16. Does GO:0019066 translocation of virus into host cell for host proteins or the viral proteins that escort the genome into the cell?  Does this need clarification?
16. Does GO:0019066 translocation of virus into host cell for host proteins or the viral proteins that escort the genome into the cell?  Does this need clarification?
* for both (host & virus) - Becky will add comment
  Add comment to GO:0019066 that the term can be used to annotate viral escort proteins AND host proteins.
* Becky will read up on escort proteins
* Becky will read up on escort proteins. Escort proteins protect the viral genome from degradation, but not sure on the mechanisms.
 
17. I think GO:0075001 adhesion of symbiont infection structure to host should have children viral attachment b/c the tail is a specialized structure meant to do that!
17. I think GO:0075001 adhesion of symbiont infection structure to host should have children viral attachment b/c the tail is a specialized structure meant to do that!
* doesn't always hold true b/c some tails are single proteins (A, A2), and others don't even have tails
* doesn't always hold true b/c some tails are single proteins (A, A2), and others don't even have tails.
 
18. Is viral latency part of GO:0022611 dormancy process?
18. Is viral latency part of GO:0022611 dormancy process?
* for Jane!
* ask Jane!
* dormancy is a developmental process.  Do viruses have developmental processes or do they only replicate??
* dormancy is a developmental process.  Do viruses have developmental processes or do they only replicate??
19. I thought GO:0019038 provirus was going away???
* still there, but on the list for obsoletion
20.  New term -- GO:0009295 nucleiod -- child -- GO:00980xx ! virus nucleiod - The region of in the host cell to which viral DNA is confined.   
20.  New term -- GO:0009295 nucleiod -- child -- GO:00980xx ! virus nucleiod - The region of in the host cell to which viral DNA is confined.   
* Proteins (PhuZ) are responsible for centering the viral DNA for some bacterial viruses, Herpes virus, etc.  PMID:22726436
* Proteins (PhuZ) are responsible for centering the viral DNA for some bacterial viruses, Herpes virus, etc.  PMID:22726436
* Becky will add.
* Becky will look into adding a new term 'nucleoid' is_a: host cell part
 


====Other stuff====
====Other stuff====
1. GO:0046729 spread of virus in host
* change to spread of virus in multicellular host?
* done
11. I thought GO:0045090 retroviral genome replication was going away?
* Jane is doing these.
19. I thought GO:0019038 provirus was going away???
* still there, but on the list for obsoletion


* I have GO:0098035 viral DNA genome packaging via site-specific sequence recognition (3’ and 5’ extensions) & GO:0098006 viral DNA genome packaging, headful
* I have GO:0098035 viral DNA genome packaging via site-specific sequence recognition (3’ and 5’ extensions) & GO:0098006 viral DNA genome packaging, headful
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** replicative, non-replicative ok according to email exchange with Ariane T.
** replicative, non-replicative ok according to email exchange with Ariane T.
** need term for class III -- BM
** need term for class III -- BM
==QUESTIONS FROM BECKY==
*killing by virus of host cells during superinfection exclusion ; GO:0039634
** 1/ Is it ALWAYS a lysogenic virus that kills the host cell in response to a subsequent lytic viral infection?
** PMID: 22398285 suggests that the second virus can be the same or a closely related viral type.
*Do we need a term for SUPERINFECTION EXCLUSION (where a pre-existing virus prevents infection of a host cell by a second virus).
** is there another way this happens that doesn't include killing the host?  BM doesn't know.
[[Category:Meetings]]
[[Category:Ontology]]

Revision as of 06:20, 29 August 2012

QUESTIONS FROM BRENLEY

  • BM has been annotating phage lambda proteins (see 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
viral terminase complex ; GO:0043493
- host cell cytoplasm part
+ viron_part
  • 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".
 Changed definition to match Wikipedia: Icosahedral capsids have 12 pentamers and 10(T-1)hexamers, where T is the triangulation number.


    • 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
  • guess we need a terminase activity term (NOT specific to DNA or RNA!)

More issues from Bren

2. What is the difference between GO:0019051 induction by virus of host apoptotic process and GO:0060139 positive regulation of apoptotic process by virus? Why is 19 a child of 60? Are they not the same thing? 

Becky has emailed Paola, who's leading the apoptosis overhaul to check on what was decided about induction v pos regulation of apoptosis terms.

3. Is it going to be confusing to have GO:0039633 killing by virus of host cells and cytolysis (i.e. both kill the cells) 

Add relationship:
killing by virus of host cell
--[isa]cytolysis by virus of host cell


4. GO:0075733 intracellular transport of viral material – confusing without indicating mean genome in term & not viral procapsid transport term. Why is this separate from GO:0046788 egress of virus within host cell? 

Add relationship:
intracellular transport of viral material
--[isa]egress of virus within host cell

5. What about viral material transport out of nucleus? Does that happen through proteins???

  • leaving this for now - can add if people request terms for this.

6. Is GO:0006948 induction by virus of host cell-cell fusion related to GO:0046739 spread of virus in multicellular host?

  • the structure used for cell-cell fusion is not exclusively for spread.
Add comment to 'host cell-cell fusion' to also consider spread of virus term.


7. Should we add a comment to GO:0046756 lytic viral exocytosis about how this is how dsDNA phages get out (by encoding a holin & lysozyme), ssDNA and ssRNA phages (by preventing host PG biosynthesis)

  • should use lytic viral release, Becky making this new relationships for holin activity under this
    • Becky may link cytolysis and lytic viral release via new term
Add in P/F relationships for holins:
lytic viral release
--[partof]holin activity

or 

cytolysis by virus of host cell
--[partof]holin activity

create new term: lytic viral release by viral cytolysis of host cell ; GO:NEW

8. How does GO:0046754 non-lytic viral exocytosis work? Why is it different from GO:0046755 non-lytic virus budding (which says it is a form of viral envelopment)? Clarify that filamentous phage are the first & not the second in a comment???

  • defn of non-lytic exocytosis and release are basically the same thing, so what is the difference between those two terms & how does budding fit in???
  • ask Jane when she gets back!

9. What happened to capsid formation around genome via self-assembly?

  • Jane is working on these

10. Have to have a term for the dsRNA viruses that pack a SINGLE strand of RNA & then replicate in the head. OR clarify GO:0019074 viral RNA genome packaging to include this??? 

Add comment to GO:0019074 that the packaging can be ssRNA or dsRNA.

11. I thought GO:0045090 retroviral genome replication was going away?

  • on Jane's list for obsoletion

12. How is GO:0019081 viral protein biosynthetic process different from protein biosynthetic process? Is this the whole cellular problem???

  • discussing at Editors call, going to change the defintion of cellular in GO
  • separate cellular based on single or multi-organism processes.


13. Should there be “escort functions” for A2 and similar proteins that escort the genomes into the host & protect the genome from degradation???

  • similar to chaperone terms, no.
Add 'viral escort protein' as synonym for 'regulation of viral entry into host cell ; GO:0046596'.


14. How is GO:0042963 phage assembly separate from GO:0019068 virion assembly? They are the SAME!! 

Merge 'phage assembly ; GO:' into 'virion assembly ; GO:'

15. What is the difference between GO:0019046 release from viral latency and GO:0032359 provirus excision? Should GO:0032359 be a child of GO:0019046???

  • ask Jane when she gets back!

16. Does GO:0019066 translocation of virus into host cell for host proteins or the viral proteins that escort the genome into the cell? Does this need clarification? 

 Add comment to GO:0019066 that the term can be used to annotate viral escort proteins AND host proteins.
  • Becky will read up on escort proteins. Escort proteins protect the viral genome from degradation, but not sure on the mechanisms.

17. I think GO:0075001 adhesion of symbiont infection structure to host should have children viral attachment b/c the tail is a specialized structure meant to do that!

  • doesn't always hold true b/c some tails are single proteins (A, A2), and others don't even have tails.

18. Is viral latency part of GO:0022611 dormancy process?

  • ask Jane!
  • dormancy is a developmental process. Do viruses have developmental processes or do they only replicate??

19. I thought GO:0019038 provirus was going away???

  • still there, but on the list for obsoletion

20. New term -- GO:0009295 nucleiod -- child -- GO:00980xx ! virus nucleiod - The region of in the host cell to which viral DNA is confined.

  • Proteins (PhuZ) are responsible for centering the viral DNA for some bacterial viruses, Herpes virus, etc. PMID:22726436
  • Becky will look into adding a new term 'nucleoid' is_a: host cell part


Other stuff

  • I have GO:0098035 viral DNA genome packaging via site-specific sequence recognition (3’ and 5’ extensions) & GO:0098006 viral DNA genome packaging, headful
    • struggling to describe (CLEARLY) ways dsDNA genomes are packaged b/c others have terminal proteins that are bound to ends of replicated genome (NOT produced as a concatamer like site-specific dudes)
  • Linear vs Rotary motors???


  • Transposition, DNA mediated
    • replicative, non-replicative ok according to email exchange with Ariane T.
    • need term for class III -- BM
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