CamEds Ontology meeting 2012-07-3
From GO Wiki
BINDING AND CATALYTIC ACTIVITY
- SF item from Dianna. There's 2 types of ubiquitin ligases:
- Where substrate binding and ubiquitin transfer are done by the same protein.
- Where substrate binding is done by one subunit, and ubiquitin transfer is done by the second subunit.
- Can we create terms for the individual subunit activities?
- Does 'ubiquitin ligase activity' (catalysis of ....) encompass both substrate binding and ubiquitin transfer?
- Where do we stand on adding in specific types of locomotion and locomotory behavior terms? (E.g. request for 'swimming'). We have 'flight' but not walking. Chris M was keen to have 'limb development' but not 'leg development'.
- SF item from SIB: http://sourceforge.net/tracker/?func=detail&aid=3535440&group_id=36855&atid=440764
- Background: The SIB curator is annotating a rhodopsin kinase which phosphorylates opsin in cones. Phosphorylated opsin is bound by arrestin, which PREVENTS phototransduction.
Q1: Which of their requested new terms are phenotypes and which are processes?
- light adaptation: is the ability of the eye to adjust to various levels of light. (PMID:16039565, http://jgp.rupress.org/content/116/6/791.full).
- photosensitivity: Photosensitivity is the amount to which an object reacts upon receiving photons, especially visible light. (PMID:21486791).
- cone photoresponse recovery (PMID:16039565).
- Q2: Are the following terms too specific?
- receptor phosphorylation ; GO:NEW?
- GPCR phosphorylation ; GO:NEW?
- GPCR kinase activity ; GO:NEW (we have rhodopsin kinase activity, already)
- GPCR phosphorylation involved in deactivation of rhodopsin mediated signaling ; GO:NEW
- Q3: We have this term that was obsoleted: phototransduction, visible light: light adaptation ; GO:0008085.
- Q4: I'm getting a bit confused about rhodopsin vs opsin, and cones vs rods. Do the rhodopsin signaling terms just refer to rod photoreceptors (and not cone opsins)?
Suggested plan of action:
- 1. Merge:
- rhodopsin mediated phototransduction ; GO:0009586
- rhodopsin mediated signaling pathway ; GO:0016056
- 2. New terms:
response to light stimulus ; GO:0009416 --[isa]response to light intensity ; GO:0009642 ----[isa]light adaptation ; GO:NEW
light adaptation ; GO:NEW Def: The process by which the eye adapts to a change/increase in illumination.
--%adaptation of rhodopsin mediated signaling ; GO:0016062 ----[partof]deactivation of rhodopsin mediated signaling involved in light adaptation ; GO:NEW
deactivation of rhodopsin mediated signaling involved in light adaptation ; GO:NEW Def: Restoring the photoreceptor cell to its unexcited state after termination of the stimulus (photon) that contributes to light adaptation at the photoreceptor level. synonym: rhodopsin desensitization synonym: phosphorylation-mediated desensitization [NARROW]