GO:0043575 detection of osmotic stimulus

[ValWood]

GO:0043575 detection of osmotic stimulus

Definition (GO:0043575 GONUTS page) The series of events in which a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell is received and converted into a molecular signal.

This has a single annotation. I suggest merging into parent

GO:0006970 response to osmotic stress

'sensors' belong in the MF ontology GO:0140299 small molecule sensor activity

[pgaudet]

I merged that one, but there are others that should also be merged, to be consistent (note that the list is not exhaustive; some children are not shown) :

• detection of stimulus 13040 DNA damage response, detection of DNA damage 96 ** detection of DNA damage stimulus involved in DNA damage checkpoint 7 detection of DNA damage stimulus involved in G2 DNA damage checkpoint 0 ** detection of DNA damage stimulus involved in mitotic G2 DNA damage checkpoint 0 ** detection of DNA damage stimulus involved in intra-S DNA damage checkpoint 0 detection of DNA damage stimulus involved in mitotic G1 DNA damage checkpoint 0 detection of stimulus involved in DNA replication checkpoint 0 detection of stimulus involved in meiotic DNA replication checkpoint 0 * detection of stimulus involved in mitotic DNA replication checkpoint 0 * detection of abiotic stimulus 2496 detection of electrical stimulus 0 detection of gravity 17 detection of humidity 0 detection of light stimulus 1441 detection of mechanical stimulus 931 detection of osmotic stimulus 2 detection of temperature stimulus 140 detection of activity 0 detection of muscle activity 0 detection of muscle activity involved in regulation of muscle adaptation 0 detection of biotic stimulus 373 detection of molecule of bacterial origin 110 detection of molecule of fungal origin 18 detection of molecule of oomycetes origin 0 detection of other organism 177 detection of cell density 114 detection of endogenous biotic stimulus 6 detection of endoplasmic reticulum overloading 0 detection of external biotic stimulus 232 detection of tumor cell 18 detection of chemical stimulus 10228 ** detection of cAMP 0 detection of calcium ion 127 detection of carbohydrate stimulus 46 detection of carbon dioxide 6 detection of chemical stimulus involved in sensory perception 9732 detection of glutamine 0 detection of hormone stimulus 8 detection of hydrogen ion 0 detection of hypoxic conditions in blood by chemoreceptor signaling 7 detection of jasmonic acid stimulus 0 detection of misfolded protein 0 detection of molecule of bacterial origin 110 detection of molecule of fungal origin 18 detection of molecule of oomycetes origin 0 detection of nutrient 8 detection of organic substance 0 detection of oxygen 66 detection of pheromone 17 detection of phosphate ion 7 detection of redox state 4 detection of salicylic acid stimulus 0 detection of unfolded protein 0 methyl accepting chemotaxis protein complex 7 soluble molecule recognition 1 detection of endogenous stimulus 26 ** detection of nodal flow 12 detection of nuclear:cytoplasmic ratio 0 detection of external stimulus 2497 detection of wounding 7 detection of inactivity 0 detection of muscle inactivity 0 ** detection of muscle inactivity involved in regulation of muscle adaptation 0 detection of stimulus involved in G1 DNA damage checkpoint 0 detection of stimulus involved in meiotic spindle checkpoint 0 detection of stimulus involved in sensory perception 10259 detection of electrical stimulus involved in sensory perception 0 detection of humidity stimulus involved in sensory perception 0 detection of light stimulus involved in sensory perception 156 detection of mechanical stimulus involved in sensory perception 301 *** detection of stimulus involved in sensory perception of pain 154

I can probably obsolete the terms with no annotations, and we can review the others.

What do you think ?

Thanks, Pascale

[ValWood]

Yes. One question. Is it OK to merge processes into activities. I thought that caused problems for some users. @hattrill did this cause issues for FB?

I think it is OK to obsolete the unused ones. For the others some people use in more. of a general signalling context, I believe.

I would be tempted to obsolete and tell people to annotatate either: I) to the appropriate signalling pathway OR, if they are annotating a sensor ii) request a term under MF molecular sensor

You can't do everything!

[hattrill]

wrt GO:0043575 detection of osmotic stimulus - can't say, no annotations to this.

Agree with "...OK to obsolete the unused ones."

Things under sensory perception can be hard to pin down - neuronal circuits are sometimes a bit hard to pindown. You might be pretty sure that you are looking at a machanoreceptor or phermone receptor for example, but assay is not detailed enough to put a MF to it, so the best you can say is that it is required to detect that stimulus but how that is translated at the cellular level is opaque.

[ValWood]

You might be pretty sure that you are looking at a machanoreceptor or phermone receptor for example, but assay is not detailed enough to put a MF to it

Why is that? could you use "EXP" in these cases, i.e experiments confirm it, and it is author intent but you don't really want to say it has been assayed? Or would a "signalling pathway" annotation not be more appropriate? Do you have an example where you would not feel confident to annotate to "sensor" I'm trying to figure out why you could say 'detection' and not say 'sensor' or signalling'?

[pgaudet]

You might be pretty sure that you are looking at a machanoreceptor or phermone receptor for example, but assay is not detailed enough to put a MF to it

Would you not annotate to 'signaling receptor activity' and some neuronal process ?

[hattrill]

e.g. Might be a behavioural assay. So it could be a receptor that binds the ligand, but it could be a downstream signaling component or be a screted factor that does something. Sometimes the 'author intent' + background knowledge is enough, other times it is not.