Definition: Visual Perception

[gocentral]

GOA recently had a user request to delete an annotation to the Fibrillin-1 protein of 'Visual perception' (GO:0007601), which I agreed should be removed. In the course of our discussions, the user requested that the definition of 'visual perception' be made less ambiguous. He is an expert in Marfan Syndrome and Ectopia Lentis (lens displacement), disorders caused by mutations in Fibrillin-1, and as such is a good person to advise on the definition. I have copied our communications below, which include his thoughts on the definition of visual perception - please feel free to add your thoughts.

The term visual perception is perhaps a bit ambiguous >> " >> The series of events required for an organism to receive a visual >> stimulus, convert it to a molecular signal, and recognize and >> characterize the signal. Visual stimuli are detected in the form of >> photons and are processed to form an image. " >> >> >> If we include turning one's head to get a better look at something, >> then we would also need to annotate say muscle proteins to visual >> perception. :-} >> >> Somehow I would understand visual perception as something that begins >> in the retina and and goes through the visual cortex, and would not >> include processes involved in refraction as a part of visual >> perception. >> >> Fibrillin-1 is involved in mechanically keeping the lens in place, and >> does not play any known role in the retina or brain. So that is why I >> made the suggestion. >> >> >> By the way, all of the EL patients have myopia unless the slipped lens >> is surgically replaced. Some may also develop retinal detachment or >> glaucoma. >> >> Take care, >> Peter

Dear Peter, >> >> >> Thank you for your message to correct an annotation to P35555. The >> manual GO annotations for FBN1_HUMAN originate from Proteome Inc., which >> were incorporated into the GOA dataset from their last public release >> in 2001. One of GOA's priorities is to gradually update, improve and >> correct these annotations. >> >> I've looked at the paper that provides evidence for the 'visual >> perception' annotation and suspect that the annotation was made based on >> Table I which indicates that some of the EL patients have myopia. I >> did a PubMed search for Fibrillin-1 and myopia and came up with a couple >> of other articles which state that patients with a fibrillin-1 mutation >> also have myopia (e.g. PubMed ID:10486319). In GOA we would normally >> capture this information by using an evidence code Inferred from Mutant >> Phenotype (IMP) which indicates that the annotation should be read >> with caution because this process may not be a direct effect of the >> mutation. Do you think the 'visual perception' annotation would be >> acceptable with the updated evidence code? >> >> All of the annotations for FBN1_HUMAN originate from Proteome Inc. so I >> will update them as a priority. I will inform you when I have done >> this and if you have any other comments on the updated annotations, >> please feel free to contact me directly. >> >> Thanks again for your interest in GOA. >> >> >> Best wishes, >> >> >> Rachael.

UniProtKB/Swiss-Prot AC: P35555 >>>> >>>> >>>> >>>> The GO annotation "visual perception" for fibrillin-1 is wrong. >>>> Fibrillin-rich microfibrils are the main component of the ciliary >>>> zonules, which are responsible for holding the lens of the eye in >>>> place, and people with Marfan syndrome get ectopia lentis, meaning >>>> that the lens slips out of place (this is the reference used to >>>> support the "visual perception" annotation)- Therefore, I think that >>>> this annotation is a misinterpretation. >>>> >>>> Thanks for the incredibly useful resource you are providing!! >>>> >>>> >>>> Peter

Reported by: rachhuntley

Original Ticket: "geneontology/ontology-requests/3338":https://sourceforge.net/p/geneontology/ontology-requests/3338

[gocentral]

Logged In: YES user_id=631592

This is an excellent point. Visual perception should not include things like turning one's head. I like the idea of the process beginning in the retina. However how do we capture what the lens does before the light hits the retina. Perhaps we need to have a vision term that begins at the cornea.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=1375277

Forwarded comment from Peter Robinson;

The correct vision term for things that go on between cornea and retina is "refraction". This does not appear to be a term right now. The connection is probably a little indirect, but proteins such as the crystallins (in the lens of the eye) have developed to enable refraction, that is, bundling the light rays such that the focus on the macula (the "sweet spot" of the retina).

Original comment by: rachhuntley

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: mah11

[gocentral]

Logged In: YES user_id=631592 Originator: NO

As I read this again, I think this was just a simple misinterpretation of the data based on the mutant phenotype. Knowing that what causes this is the lens slipping out of place suggests that the defect is in eye development and not in th actual mechanism of visual perception per se. If at some point we do want to capture the refraction part of vision under this term, I think we might want to make it a 'regulation' term in some way where the thing being regulated is the light. But even in this case, I think that knowing what we know about this phenotype, the annotation is still not entirely accurate.

Original comment by: ukemi

[gocentral]

• status: open --> closed-works-for-me

Original comment by: ukemi