cell surface binding mismash

[gocentral]

As was brought up (again) at the April GOC meeting, 'cell surface binding ; GO:0043498' is causing confusion.

The InterPro mappings have just been updated: https://sourceforge.net/tracker/?func=detail&atid=605890&aid=3611547&group\_id=36855

There are a mixture of proteins annotated to GO:0043498 and its children, including growth factors for cell surface receptors, cell adhesion proteins, immunoglobulins and scavenger receptors. It doesn't make sense to group all of these, so after discussion with Cambridge GO-Eds, we would like to obsolete the cell surface binding terms, and suggest GPs be reannotated to any of the following terms:

host cell surface binding ; GO:0046812 receptor binding ; GO:0005102 cell surface ; GO:0009986 cell adhesion ; GO:0007155 antigen binding ; GO:0003823 immune response ; GO:0006955 defense response to bacterium ; GO:0042742 defense response to Gram-negative bacterium ; GO:0050829 defense response to Gram-positive bacterium ; GO:0050830

I'll send out an obsoletion notice. Comments can be collected in this SF item.

Becky

Reported by: rebeccafoulger

Original Ticket: geneontology/ontology-requests/10140

[gocentral]

Some of the terms proposed for obsoletion look like they might actually be useful in sorting out the mishmash, like"cell adhesion" and "antigen binding". Then again, perhaps better alternatives already exist. Is the GOC discussion summarized someplace, and is there a list of alternative suggested terms? (And what is the impact on existing annotations?) Thanks. Peter

Original comment by: deustp01

[gocentral]

Hi Peter,

I'm proposing obsoletion of the cell surface binding terms (obsoletion email to be sent out next week). The terms listed above (antigen binding, cell adhesion etc) are the terms I suggest annotations are transferred to.

Annotation impact: (manual IMP,IGI,IPI,IDA,IEP,EXP annotations) cell surface binding ; 32 annotations eukaryotic cell surface binding ; 53 annotations regulation of eukaryotic cell surface binding ; 5 negative regulation of eukaryotic cell surface binding ; 1 positive regulation of eukaryotic cell surface binding ; 2 bacterial cell surface binding ; 84 annotations Gram-negative bacterial cell surface binding ; 18 annotations Gram-positive bacterial cell surface binding ; 17 annotations

Most annotations are from FlyBase, MGI, UniProt and BHF.

The 'eukaryotic cell surface binding ' and 'bacterial cell surface binding' are especially unclear. They have been used for inter-species binding (e.g. when a mammalian Toll receptor binds a bacterial antigen), and for binding within a species.

Hope that's a bit clearer. Becky

Original comment by: rebeccafoulger

[gocentral]

Hi Becky, Yes, that helps a lot - looks fine to me, Thanks. Peter

Original comment by: deustp01

[gocentral]

Sent obsoletion mail to GO list. Obsoletions planned for May 23rd 2013.

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-accepted
• Group: --> None

Original comment by: rebeccafoulger

[gocentral]

Obsoletions done. Horray.

Original comment by: rebeccafoulger