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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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starvation response #262

Closed gocentral closed 9 years ago

gocentral commented 22 years ago

Could a term like "starvation response" be added to cover multicellular organisms? We are looking for ways to annotate proteins involved in the perception of hunger and your definition of starvation response seems perfect except that it seems to apply only to cells:

A change in the state or activity of a cell (in terms of enzyme production, changes in gene expression etc.) as a result of deprivation of nourishment.
definition_reference: GO:jl

Reported by: lmatthews

Original Ticket: "geneontology/ontology-requests/262":https://sourceforge.net/p/geneontology/ontology-requests/262

gocentral commented 22 years ago

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I think that, like respiration, there needs to be distinction between cellular and physiological starvation. For the respiration discussion, refer to http://sourceforge.net/tracker/index.php? func=detail&aid=576886&group_id=36855&atid=440764.

Original comment by: ceyockey

gocentral commented 22 years ago

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Changed definition to: A change in the state or activity of an organism or cell (in terms of enzyme production, changes in gene expression etc.) as a result of deprivation of nourishment. so that now covers whole organisms. Am considering moving the 'xxx response' terms out from 'cell communication' and 'cell growth and/or maintenance' because these terms mostly refer to whole organisms.

Original comment by: nobody

gocentral commented 22 years ago

Original comment by: nobody

gocentral commented 22 years ago

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Hi Jane, This seems like it would cover it, though a concern that an editor voiced is that she viewed the behaviorial response to hunger would be different than the starvation response of single cells. Knowing that one of the goals of GO is to be "species generic" as possible, I am not sure how to get around this. Any ideas?

Original comment by: lmatthews

gocentral commented 22 years ago

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Okay - that was a bad/lazy decision! The response to starvation of a whole organism is clearly going to be very different to that of a single cell. Have reverted the defintion to how it was formerly.

Solution: two terms, one for each concept - need to work on the text strings though. Possibly create a new parent for them both too so they can be linked.

Original comment by: nobody

gocentral commented 22 years ago

Original comment by: nobody

gocentral commented 21 years ago

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Will fix this when we have cellular processes and multi- cellular processes separated, as discussed in the last meeting.

Original comment by: nobody

gocentral commented 21 years ago

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How about we change the current term to "response to cellular starvation", synonym "physiological response to starvation" and create a new term "behavioral response to starvation", which would apply to changes in the behavior of the organism. We could even keep the current term and make the definition less specific, and then have the children "physiological response to starvation" and "behavioral response to starvation".

Original comment by: nobody

gocentral commented 21 years ago

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This sounds good to me, thanks Jane

Original comment by: lmatthews

gocentral commented 21 years ago

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The problem with that solution is that not all responses to starvation are cellular or behavioural - some physiological responses occur at the level of the whole organism e.g. breakdown of fat reserves. How about:

response to starvation ---%response to cellular starvation % cellular processes ---%behavioural response to starvation % behaviour

the top term can be defined something like: 'the response of a cell, tissue or organism to a lack of nutrients'.

?

Original comment by: nobody

gocentral commented 21 years ago

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Added

response to starvation ; GO:0042594 ---%behavioural response to starvation ; GO:0042594

and changed the name of GO:0009267 to 'cellular response to starvation' keeping the same definition.

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gocentral commented 21 years ago

Original comment by: nobody

gocentral commented 21 years ago

Original comment by: nobody