left/right symmetry/asymmetry

[gocentral]

Hi,

We have a term for determination of left/right symmetry:

term: determination of left/right symmetry goid: GO:0007368 definition: The establishment of an organism's body plan or part of an organism such that the left and right halves are mirror images. definition_reference: GO:jic

I have a gene product involved in generating l/r asymmetry in the Drosophila gut (PMID:11245582). I found a discussion in the GO email archive about symmetry and assymetry and clumping them together in the same term so I just want to know- should I use GO:0007368 to annotate my gene, or should I create a new term:

determination of left/right asymmetry ; GO:NEW parent: unsure..... def: The establishment of an organism's body plan or part of an organism such that the left and right sides of the body or body part exhibit a stable lack of symmetry. For example, in humans, organs like the heart and the spleen are normally displaced to the left hand side of the body, while the liver is normally displaced to the right. PMID:11245582

My problem with using GO:0007368 is that the definition of GO:0007368 doesn't really describe the role of my gene since its role is to make the left and the right so they are NOT mirror images. But the emails in the archive suggest that asymmetry and symmetry terms should be grouped together/synonymous- have i understood this right?

Maybe the definition of GO:0007368 should be tweaked if this is so? Also GO:0009855, since I think the current definition creates a TPV for GO:0048262.

determination of bilateral symmetry ; GO:0009855 --%determination of dorsoventral asymmetry ; GO:0048262

Apologies if I've misunderstood completely!

while I'm here:

determination of symmetry is a child of pattern specification in process.

Therefore should:

determination of dorsoventral asymmetry ; GO:0048262 have the additional parent: dorsal/ventral pattern formation ; GO:0009953 ?

(does this work ok with the adaxial/abaxial exact synonyms for GO:0048262?)

and

determination of radial symmetry ; GO:0009879 have the additional parent: radial pattern formation ; GO:0009956

And I'd like to add the synonym 'determination of dorsal/ventral asymmetry' to GO:0048262 , for searching purposes.

thanks, Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/2001":https://sourceforge.net/p/geneontology/ontology-requests/2001

[gocentral]

Logged In: YES user_id=631592

Hi Becky,

I have been using the symmetry/asymmetry terms to annotate anything that has to do with the concept of symmetry. By that I mean gene products that either make things symmetric or asymmetric. I remember that we had a discussion about this before, and it seemed that this would be o.k. Chris suggested that we include symmetry/asymmetry in the terms somehow. I don't know if this was ever done.

suggested def:The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or deviate from this symmetry.

I would say go for it and add the missing parents where applicable for the subterms.

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=835115

This is my recollection as well. ditto what David said.

-Doug

Original comment by: doughowe

[gocentral]

Logged In: YES user_id=482748

ok- thanks for your comments!

I've changed the definiton of determination of left/right symmetry ; GO:0007368 to make it clearer that it includes l/r symmetry and l/r asymmetry to: The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.

and have similarly tweaked the definition of determination of bilateral symmetry; GO:0009855 to: The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.

And have added in the following relationships:

dorsal/ventral pattern formation ; GO:0009953 --<determination of dorsoventral asymmetry ; GO:0048262

radial pattern formation ; GO:0009956 --<determination of radial symmetry ; GO:0009879

And added the exact synonym etermination of dorsal/ventral asymmetry. to 'determination of dorsoventral asymmetry ; GO:0048262'.

Becky

Original comment by: beckyfoulger

[gocentral]

• assigned_to: nobody --> beckyfoulger
• status: open --> closed-fixed

Original comment by: beckyfoulger

[gocentral]

• assigned_to: Becky Foulger --> nobody
• Group: Plant Ontology --> None

Original comment by: cooperl09