change of reponse to arsenate

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GO term:response to arsenate GO id:GO:0046685 Definition: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to arsenate, a salt or ester of arsenic acid (H3AsO4).

However, using Amigo, one sees that the term is being used to include arsenite as well as arsentate (23 non IEA). Therefore, I suggest that the term be altered to response to arsenate, arsenite, or other forms of arsenic.
This way

1. obsoleting GO:0046685 does not occur, with destruction of the anotations.
2. If a separate "response to arsenite " term is created, then a parent to both terms will be needed.

Arsenic in water comes in two forms: arsenite and arsenate.Arsenate is toxic but arsenite 100 times more so. There are enzymes that conver one to the other. Arsenate is salt or ester of arsenic acid having a negative ion of AsO43- , arsenite is a salt or ester of arsenious acid having a negative ion of AsO43- derived from aqueous solutions of As4O6 and arsenide is a negative, trivalent binary arsenic compound such as H3As (arsine). So, I think the term could be modfied to say "arsenic compounds such as...arsenate, arsenite, etc.

Reported by: hdrabkin

Original Ticket: "geneontology/ontology-requests/2122":https://sourceforge.net/p/geneontology/ontology-requests/2122

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Sounds fine to me.

Original comment by: jl242

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Jane, after re-reading this morning, I'm not sure that I made it clear that I wanted to change the term name and def but keep the same id so that we wouldn't have to reannotate (#1). The other alternative (#2) was to make separate terms, but if we did that, we would need to make a parent that essentially would be the rewordced term in #1. I think I could use "response to aresentates and aresenites" as the new term name.

Original comment by: hdrabkin

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I'd just keep the same id.

Original comment by: jl242

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Great; I just thought the way I wrote it up yesterday looked like a rambling mess. Ok, if I don't hear any complaints by the end of the day here, I'll go ahead and do it.

Original comment by: hdrabkin

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It made perfect sense ;)

Original comment by: jl242

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How about "response to arsenic", or "response to arsenic ions" , and then the def would have the salts like arsenate, arsenite, etc.

I know the term is referring to the base metal, but in this case, Ii think we all know that it's the ions, and the def will reflect that. We have a similar situation with response to chromate, response to chlorate And I just noticed that "response to CO2" is under "response to inorganic substance" That doesn't seem right does it?

Under response to inorganic ions", we have sometimes "metal ion" (eg, aluminum, cadimium, etc.), but sometimes just response to x, like reponse to cesium.

I think what we are seeing here is that each term was created because someone needed something specific for a particular gene product, but didn't think about the larger picture.

Original comment by: hdrabkin

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I think we should just have 'response to arsenic', and have it as a child of 'response to inorganic substance' - this is what we've typically done in other parts of the ontology (def would be 'A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to compounds containing arsenic (As)'). I think response to metal ion is the wrong parent because it's describing the metal ion itself (e.g. Cu2+) rather than ionic compounds containing that metal.

Carbon dioxide is an inorganic compound - it doesn't have any carbon-hydrogen bonds (that's usually the distinction isn't it?).

response to cesium can be changed to 'response to cesium ion'.

Original comment by: jl242

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What do you think Harold?

Original comment by: jl242

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It appears that somehow the change I thought went through didn't;

Yes, I agree with your comment, and I will momentarily change the wording of the term to include all forms of arsenic.

Original comment by: hdrabkin

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• status: open --> closed

Original comment by: hdrabkin

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Done; I will close this

Original comment by: hdrabkin

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• status: closed --> closed-accepted

Original comment by: hdrabkin