MHC function terms

[gocentral]

We need to add some function terms for annotating MHC gene products. Possible ideas are 'antigen presenter' and 'MHC/antigen complex binding'.

There are also a few problems in this area that need sorting out. e.g. we have 'MHC receptor' terms, meaning a receptor of the class MHC, and not a receptor FOR MHC as it might imply.

Also, check over process terms in this area.

Reported by: nobody

Original Ticket: "geneontology/ontology-requests/288":https://sourceforge.net/p/geneontology/ontology-requests/288

[gocentral]

Logged In: YES user_id=451873

We actually have quite a few process terms already:

antigen presentation ; GO:0019882 antigen processing ; GO:0030333

both with lots of children. For function, I think we can just use 'peptide binding ; GO:0042277' - perhaps add a child 'antigen peptide binding ; GO:new' and give it the second parent 'antigen binding ; GO:0003823'?

Original comment by: nobody

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: nobody

[gocentral]

Logged In: YES user_id=451873

I also think we should have a component term as part_of 'integral to plasma membrane':

'MHC protein complex ; GO:new'

definition: A transmembrane protein complex usually composed of an alpha and a beta chain. Functions in the presentation of antigen to the immune system.

NB: I think we'll have to call it MHC protein complex or something like that (even though it sounds a bit weird) to distinguish it from the DNA (called just MHC).

Original comment by: nobody

[gocentral]

Logged In: YES user_id=451873

After some discussion with the immunology interest group (i.e. Evelyn!) about SourceForge item [582758 ] MHC function terms we've come up with the following proposed improvements:

in function, new terms:

peptide binding activity ; GO:0042277 ---%peptide antigen binding ; GO: new ------%endogenous peptide antigen binding ; GO:new ------%exogenous peptide antigen binding ; GO:new

receptor binding activity ---%T-cell receptor binding activity; GO:new ---%CD4 receptor binding activity ; GO:new ---%CD8 receptor binding activity ; GO:new ---%CD70 receptor binding activity ; GO:new ---%CD154 receptor binding activity ; GO:new

and in component:

MHC protein complex ; GO:new ---%MHC class I protein complex ; GO:new ---%MHC class II protein complex ; GO:new

terms to obsolete -> replaced by: CD27 receptor activity ; GO:0005029 -> CD70 receptor binding activity ; GO:new CD40 receptor activity ; GO:0005028 -> CD154 receptor binding activity ; GO:new B-cell receptor activity ; GO:0004892 -> antigen binding activity ; GO:0003823 (and others) T-cell receptor activity ; GO:0004894 -> MHC class II molecule binding activity ; GO:0042289 -> exogenous peptide antigen binding ; GO:new

terms to change the name of: CD27 receptor ligand activity ; GO:0005175 -> CD27 receptor binding activity ; GO:0005175 CD40 receptor ligand activity ; GO:0005174 -> CD40 receptor binding activity ; GO:0005174

The logic behind these obsoletions and name changes is that 'xxx receptor activity' terms are not informative where xxx is the receptor type. For instance, if I were to annotate my TCR protein to the function term 'T-cell receptor activity ; GO:0004894', I'm not getting any functional information about the protein, I just know it's called a T-cell receptor. But if you replace this annotation with 'MHC class II molecule binding activity ; GO:0042289', 'exogenous peptide antigen binding ; GO:new' and 'T-cell receptor complex ; GO:0042101' we have info about its true function.

So now, an MHC class II protein might be annotated to the functions:

CD4 receptor binding ; GO:new exogenous peptide antigen binding ; GO:new and in component: MHC class II protein complex ; GO:new

an MHC class I protein could be annotated to:

T-cell receptor binding activity; GO:new CD8 receptor binding activity ; GO:new endogenous peptide antigen binding ; GO:new and in component: MHC class I protein complex ; GO:new

and a T-cell receptor protein to:

MHC class II molecule binding activity ; GO:0042289 exogenous peptide antigen binding ; GO:new and in component: T-cell receptor complex ; GO:0042101

The only thing I'm not completely sure about is whether to have a term 'MHC/peptide complex binding' or whether to just capture this in the annotation using 'peptide antigen binding ; GO: new' and 'MHC molecule binding activity ; GO:0042287'? I think I prefer the latter.

Original comment by: nobody

[gocentral]

Logged In: YES user_id=451873

Made changes described below. New ids:

GO:0042605 JL peptide antigen binding GO:0042606 JL endogenous peptide antigen binding GO:0042607 JL exogenous peptide antigen binding GO:0042608 JL T-cell receptor binding activity GO:0042609 JL CD4 receptor binding activity GO:0042610 JL CD8 receptor binding activity GO:0042611 JL MHC protein complex GO:0042612 JL MHC class I protein complex GO:0042613 JL MHC class II protein complex GO:0042614 JL CD70 receptor binding activity GO:0042615 JL CD154 receptor binding activity

Original comment by: nobody

[gocentral]

• status: open --> closed-fixed

Original comment by: nobody