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spkw sensory transduction-> sensory perception + editorial #34

Closed gocentral closed 9 years ago

gocentral commented 20 years ago

I notice some Uniprot entries have a keyword 'sensory transduction'. I suspect that from a pombe perspective this really means signal transduction.

These currently map to GO:0007600 : sensory perception

this is incorrect as it has the parent GO:0050877 : neurophysiological process

I suspect the definiton of'sensory perception is inadequate...

"The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal."

because from this the annotation seem fine, but to me 'perception' implies a brain?

maybe this should go on both trackers....

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/34":https://sourceforge.net/p/geneontology/annotation-issues/34

gocentral commented 20 years ago

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Hi Val,

Perception requires a higher order neural processing. In order to perceive something, you have to take the neural input and process it in some way. Sensory transduction is simply the process of converting the stimulus like a sound into a neural impulse. It does not require any higher order neural processing. I think these annotations need to be looked at more closely. It sounds like there was a problem in assignment.

David

Original comment by: ukemi

gocentral commented 20 years ago

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Hmmm, I think our use of 'perception' has been ambiguous up 'til now. Looking at the terms that contain 'perception', I can't be sure whether they're intended to be specific for neural processing or if they just mean 'detection' (except for GO:0042769, which is obviously really a detection term).

If they're supposed to have the more restricted meaning, we'll need a suggestion for modifying the defs. Also, are the detection concepts (without the brainy part) useful for annotating any organisms out there? Might need new terms ...

Original comment by: mah11

gocentral commented 20 years ago

Original comment by: mah11

gocentral commented 19 years ago

Original comment by: ecamon

gocentral commented 19 years ago

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will discuss with Michele and get back to you Evelyn

Original comment by: ecamon

gocentral commented 17 years ago

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I will mail Kati to remove the keywords from the offending entries, but then this is now more of an ontology issue, so should it be moved to the annotation tracker?

Cheers

Val

Original comment by: ValWood

gocentral commented 17 years ago

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I think remapping the SP keyword would solve the problem.

GO is now OK: In the ages that have passed since this item was posted, GO has cleaned up its use of 'perception' in term names and definitions. We now use 'perception' only to refer to neural processing (or in related synonyms to help with searching, if perception had been misused in the past).

Given the definition of the 'sensory transduction' keyword. it could probably be mapped to 'response to stimulus' (GO:0050896) or its child 'detection of stimulus' (GO:0051606).

m

Original comment by: mah11

gocentral commented 17 years ago

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OK I think this can be closed. I now have nothing mapping to the term 'sensory perception' so I am happy. I think Kati removed the kw from the GP it was applied to as it wasn't even correct for the SPKW reported usage so Ev can keep any existing mappings :)

Original comment by: ValWood

gocentral commented 17 years ago

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Ok...

I am closingthis now...as sensory transduction kw is mapped to GO term 'response to stimulus'

Evelyn

Original comment by: ecamon

gocentral commented 17 years ago

Original comment by: ecamon