edit definition of regulation of DNA binding

[gocentral]

Hi

Please could you look at the definitions for GO:0051101 regulation of DNA binding, and it's positive and negative children.

Regulation of binding has the definition: Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.

So this statement has the target and the interacting molecule listed in the definition.

Whereas the definition of GO:0051101 regulation of DNA binding is: Any process that modulates the frequency, rate or extent of DNA binding, selective interaction with deoxyribonucleic acid.

This definition only lists the target, based on the child terms the interacting molecule is a protein. Please could this definition clarify that there is an interacting molecule which can be a protein (or is a protein if this is what was meant to be covered here).

Thanks

Ruth

Reported by: RLovering

Original Ticket: "geneontology/ontology-requests/6038":https://sourceforge.net/p/geneontology/ontology-requests/6038

[gocentral]

I'm turning this over to David & Tanya as part of their all-things-regulation remit, but I'll admit I don't really understand the question myself. The 'regulation of binding' term definitions follow the standard phrasing, as does the definition of 'DNA binding' itself. DNA binding excludes base pairing (a sibling term under nucleic acid binding), and we could easily add a comment to this effect, but otherwise I don't see a problem with the definitions. If there's no "interacting molecule" there's no binding.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

OK maybe I am being pedantic, I am sorry, but although 'base pairing with DNA' exists, you have to really pay attention to notice that this sibling is there. And as I was looking at regulation terms and these aren't linked I didn't venture into the actual binding terms, but stuck to the regulation of binding terms.

Having said that I think the binding terms are a bit too vague, GO:0003676 nucleic acid binding has a very similar name and description to 'DNA binding' and yet one includes base pairing and one doesn't. From the definitions it would have been possible to construct the ontology with GO:0000497 base pairing with DNA as a child of 'DNA binding'. Oh have just noticed that DNA binding does have the child 'GO:0000497 base pairing with DNA' which is a DNA-DNA interaction, maybe this shouldn't be here?

But back to regulation of DNA binding.

If possible could the definition of this term and it's child terms be written as: Any process that modulates the frequency, rate or extent at which a protein binds DNA.

Or would this mean that the term would need to be changed to regulation of protein/DNA binding? Or is this term supposed to cover regulation of base pairing?

Thanks

Ruth

Original comment by: RLovering

[gocentral]

We are not really clear about the issue here either. All GO terms describe the action of gene products, whether they are proteins or nucleic acids. It seems clear that both proteins and nucleic acids can bind nucleic acids, but only nucleic acids can be involved in base pairing functions. To make it perfectly clear, we will add the gene product phrasing to the definitions of the binding terms and their regulation terms.

Original comment by: ukemi

[gocentral]

• status: open --> closed-fixed

Original comment by: ukemi