children of GO:0009615: response to virus

[gocentral]

Hi,

I suggest reorganizing the placement of children GO:0009615: response to virus, as follows, based on how these processes take place in NATURAL conditions and not simulated ones.

response to virus (GO:0009615) --[i] virus induced gene silencing (GO:0009616)--BRING THIS BACK --[i] defense response to virus (GO:0051607) ----[i] phage shock (GO:0009271) ----[i] detection of virus (GO:0009597) ----[i] response to exogenous dsRNA (GO:0043330) ----[p] regulation of antiviral response (GO:0050688)

Pankaj

Reported by: jaiswalp

Original Ticket: "geneontology/ontology-requests/3591":https://sourceforge.net/p/geneontology/ontology-requests/3591

[gocentral]

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Pankaj,

Some comments regarding your proposal:

'virus induced gene silencing ; GO:0009616' is currently an is_a to 'defense response to virus ; GO:0051607.' Is it not a type of a defense response to virus? Also it is an is_a to 'innate immune response (sensu Viridiplantae) ; GO:0002226', which implies it is a plant-specific process involved in plant innate immunity, and it is an is_a to 'posttranscriptional gene silencing ; GO:0016441', which tells one something about its mechanism. I do wonder whether these are the correct linkages. There's no external reference associated with the term, so it is hard to know the inspiration for it. I'm guessing from PMID: 16409629, PMID:16368157, and PMID:15068886 that this term refers to a process common to all eukaryotes rather than just for plants, and thus should become a direct child of 'innate immune response ; GO:0045087', as well as being made an is_a to 'intracellular defense response ; GO:0002818,' which it obviously is. Also, I would regard it as an 'immune effector process ; GO:0002252' as well. That would make it an is_a to five terms, GO:0051607, GO:0016441, GO:0045087, GO: 0002818, and GO:0002252. Pretty amazing for one process, although perhaps it should really have a part_of relationships to GO:0051607, GO:0002818, and GO:0045087, since it a quite mechanistic term (I prefer the second approach, actually).

The term 'phage shock ; GO:0009271' describes stress responses to a variety of stimuli, including phage infection, and based on the references I've read, is not strictly a defense response per se, nor strictly a response to viruses per se. I judge its current placement as an is_a to 'response to stress ; GO:0006950' and 'response to virus ; GO:0009615' to be correct.

The term 'detection of virus ; GO:000959' is currently correctly placed as a direct child to 'response to virus ; GO:0009615'.
This is direct parallel to the relationship of all the other 'response to organism X' and 'detection of organism X' terms in the GO, and I'm not sure why viruses should be treated any differently.

I don't think 'response to exogenous dsRNA' should have any relationship to the 'response to virus' terms at all. Afterall, the definition states that dsRNA is only 'usually indicative' of viral infection, not always indicative. Certainly, dsRNA is not an organism per se, but only part of an organism. Also, endogenous dsRNA is sometimes indicative of a virus infection as well, so why make the distinction for the child term 'response to exogenous dsRNA' but not the parent term 'response to dsRNA.'
The best solution is to treat give this term a response to chemical and a response to biotic stimulus is_a parentage, and skip the organism specific stuff (virus) completely:

response to chemical --% response to dsRNA ----% response to exogenous dsRNA response to biotic stimulus --% response to dsRNA ----% response to exogenous dsRNA

I remind the readers that response to biotic stimulus is defined as "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism," the key words being "or produced by a living organism." A lot of so-called chemicals fall into this class of things as well.

I agree about the suggested placement of GO:0050688, but think that it might be renamed to "regulation of defense response to virus" with "regulation of antiviral response" as an exact_synonym, to clarify that it refers to defensive antiviral responses.

Thanks for your patience,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Comments on comments ...

> 'virus induced gene silencing ; GO:0009616'

At present, this term has four is_a parents:

GO:0016441 posttranscriptional gene silencing GO:0045087 innate immune response (GO:0002226 has been merged into this term as part of the sensu overhaul) GO:0051607 defense response to virus (seems reasonable to me based on definitions, though I'm no expert) GO:0052018 modulation by symbiont of host RNA levels (from PAMGO work, and I'm inclined to take your word for it)

I'm quite willing to accept Alex's suggestion to add two more parents: GO:0002252 immune effector process GO:0002818 intracellular defense response

The definitions of GO:0002252 and GO:0002818 suggest that each is a collection of processes, and that individual processes such as GO:0009616 should be is_a children.

The GO:0045087 def is more ambiguous, but seems a bit closer to collection-of-processes than a single large process.

Finally, a small picky thing: 'virus-induced' should be hyphenated.

> 'phage shock ; GO:0009271'

Agreed -- its parentage is OK (if anything, the 'response to virus' parent could perhaps be removed, if not all of the stresses that invoke the response actually result from viral infection).

> 'detection of virus ; GO:000959'

Agree completely -- the current parentage is consistent with all 'response to' and 'detection of' terms, and is correct.

> response to exogenous dsRNA ; GO:0043330

Alex's suggestion makes sense.

> regulation of antiviral response ; GO:0050688 (rename to 'regulation of defense response to virus'?)

Both suggestions make sense. Also, 'response to virus ; GO:0009615' has two synonyms, 'antiviral response' (exact) and 'antiviral response protein activity' (related), that would probably make more sense as synonyms of 'defense response to virus ; GO:0051607'.

Any further comments?

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

- I've made immune effector process (GO:0002252) an is_a parent of GO:0009616. For the moment, we can't add intracellular defense response or restore posttranscriptional gene silencing as a parent, because of the disjoint issue (maybe we'll come up with another way around the problem, at least for interactions between viruses and their hosts ... but I don't want to muddy this item further right now).

- removed relationship response to exogenous dsRNA GO:0043330 is_a response to virus GO:0009615; also removed bit about viral infection from GO:0009615 def and added comment

- renamed GO:0050688 to 'regulation of defense response to virus'

I think that's this one sorted, to the best of our ability at present.

m

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11