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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0019538 protein metabolic process #13988

Closed ValWood closed 6 years ago

ValWood commented 6 years ago

is defined as The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.

What does the phrase "involving a specific protein, rather than of proteins in general" mean? What is excluded by this clause, it isn't clear to me.

(comes via a collaborator question how to describe protein related processes)

hdrabkin commented 6 years ago

We THINK that the term and its children was meant to be used to describe things that happen to a specific protein rather than "things that can happen to any/all proteins".

ValWood commented 6 years ago

What does that mean though- I don't understand? Everything protein related is underneath it (translation etc).

Can you provide an example of something that happens to a single protein vs. something that happens to many proteins? Please explain to me in small words :)

hdrabkin commented 6 years ago

@ukemi , to you want to take a crack at this? It comes from the mind of MA!

ukemi commented 6 years ago

I suspect that the clause was added to the definition back when were were thinking a lot about instances of the terms in the ontology. If you think about this term with respect to a single process that is made up of molecular functions, you should think about it with respect to a process that happens to a single type of protein, not a process that happens to a population of different proteins.

pgaudet commented 6 years ago

Hi,

So does that mean that this part of the definition should be removed ? Otherwise some clarification would be nice !

hdrabkin commented 6 years ago

Changed def to The chemical reactions and pathways involving a protein. Includes protein modification

pgaudet commented 6 years ago

Hi @hdrabkin ,

I wonder if this definition may not be mistakenly taken to also include the enzymatic activities of proteins themselves.

How about: The chemical reactions in which a protein is the substrate, including synthesis, degradation, maturation and modification.

What do you think ? @ukemi @ValWood

hdrabkin commented 6 years ago

I don't think a protein is a substrate of its synthesis; it's a product. It's a substrate for maturation and modification and a substrate for its degradation? I think of the enzymatic activity is something the protein does, not what's done to it.

ValWood commented 6 years ago

That sounds much clearer to me!

Maybe based on H. comment

The chemical reactions in which a protein is synthesized, or is the substrate.