true path violation?, response to DNA damage

[gocentral]

Hi,

"response to DNA damage" is a child of "response to biotic stimulus". is this right? One of the plant genes is annotated to this term but falls under abiotic stimulus and can't fall under biotic stimulus .

So, here is the proposal: Option one: make "response to DNA damage" a direct child of GO:0009605.

Option two: create 2 terms, change the current GO:0006974 to "response to DNA damage by biotic stimulus" and create "response to DNA damage by abiotic stimulus" and make this a child of GO:0009628.

There are quite a few SGD, flybase and MGI genes annotated to this term and I wonder if the stimulus for these damages is biotic as it is right now?

Suparna

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/845":https://sourceforge.net/p/geneontology/ontology-requests/845

[gocentral]

Logged In: YES user_id=439222

You're right Suparna, this is a confused situation. Ack! SGD's annotations could reflect a response to abiotic or biotic damage-inducing agents. The biotic damage (screwed up replication or recombination) would most likely be an endogenous resopnse - which complicates matters.

I think this came up before, but I'm not sure it was ever resolved. maybe a GO editor remembers?

I would lean towards a modified option #2. My suggestion would be to obsolete GO:0006974 response to DNA damage because even though it now has the implicit definition of 'response to biotic stimulus', it would be good to alert people to this explicit change in meaning.

I like the creation of two new terms with strings similar to the ones you suggested. How about: response to abiotic induction of DNA damage response to biotic induction of DNA damage

So probably we'll have something like:

response to stress ; GO:6950 %response to DNA damage GO:new %response to abiotic induction of DNA damage GO:new %response to biotic induction of DNA damage GO:new response to external stimulus ; GO:9605 %response to abiotic stimulus ; GO: %response to abiotic induction of DNA damage GO:new %response to biotic stimulus ; GO: %response to biotic induction of DNA damage GO:new response to endogenous stimulus ; GO:9719 %response to endogenous biotic induction of DNA damage

??? This seems baroque.

Original comment by: clt4

[gocentral]

• summary: true path violation? --> true path violation?, response to DNA damage

Original comment by: clt4

[gocentral]

Logged In: YES user_id=439222

ugh. I just realized these terms are only children of physiological processes.

They are 'cellular responses' for unicellular organisms. Maybe David and Tanya have addressed this in their revisions of the process ontology? -C

Original comment by: clt4

[gocentral]

Logged In: YES user_id=451873

I think that the term 'response to DNA damage' is intended to describe the responses to DNA damage, regardless of how that damage occurred...as DNA is always within the cell, the stimulus to induce the response is always endogenous, and therefore biotic. So in the term 'response to biotic stimulus', biotic refers to the DNA damage itself, and not to the stimulus of that damage. For example, if an organism was exposed to an abiotic stimulus, such as ionizing radiation, which induced a set of genes, those genes might be annotated to 'response to abiotic stimulus'. At least that's how I always interpretted it - does that make sense?

Original comment by: jl242

[gocentral]

Logged In: YES user_id=439222

Ahh. Thanks Jane. That makes a lot of sense. Maybe it would be good to add a comment to 'response to DNA damage' to this effect?

Original comment by: clt4

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Was about to do just that when I realised that 'response to DNA damage' is also a child of 'response to external stimulus ; GO:0009605' which doesn't make sense at all - DNA damage can't always be both an external stimulus and a biotic stimulus.

Looking at the structure of the tree, both 'response to abiotic stimulus ; GO:0009628' and 'response to biotic stimulus ; GO:0009607' are only children of 'response to external stimulus ; GO:0009605' which must mean that they mean 'response to external abiotic stimulus' (e.g. radiation) and 'response to external biotic stimulus' (e.g. pathogens), so response to DNA damage can't really live under either of these terms.

I guess the important thing to capture here isn't how the DNA damage is caused - we already have lots of terms to cover that e.g. response to radiation - but the response to that damage. Most organisms/cells (I think) detect the damage itself e.g. double strand breaks which initiates some downstream response. So I think the best placing for this term is as a child of 'response to endogenous stimulus' and 'response to stress'. That way, if we ever needed to, we could make child terms e.g. response to DNA damage by UV light and also give an extra parent, in this case 'response to UV light'. I think that would work - I'll send round to the list.

I'm also not sure why 'DNA repair' terms aren't children of 'response to DNA damage' - I'll have to ask Eurie...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Actually, I've just realised that we're already working on 'response to DNA damage', so I'll just move this item over there...see instead [ 632111 ] apoptosis by DNA damage ; GO:0008630.

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242

[gocentral]

Logged In: YES user_id=614564

Hi Jane,

I am happy with the structure where 'DNA damage' is now a child of 'endogenous stimulus' and ' response to stress'. I think it makes most sense to take them out of abiotic and biotic. If you are adding them under 'endogenous stimulus', then should the term be, 'response to DNA damage stimulus' since the stimulus itself is DNA damage?

Suparna

Original comment by: smundodi