Semantic resources project/PRO/Gene Annotations

= Annotating Proteins with Genes =

GDCs can be used in two ways to annotate proteins:
 * protein annotations directly, such as protein domains and regions.
 * gene annotations whose concretizations inhere in the DNA which produced a protein.

The PRO term for Psen1 is PRO:000013344, and the URL for the Entrez Gene record for (the human version of) Psen1 is http://www.ncbi.nlm.nih.gov/gene/5663 -- leaving aside the species-specificity issue for a moment, how could we represent that (all members of) this class of proteins are derived from (some member of) this class of genes?

First, let's talk about the gene itself. A "gene," at least the way that the Sequence Ontology defines it, is a generic dependent continuant (GDC). A piece of DNA bears a concretization of the GDC if it "is annotated with the gene" (for the common definition of "annotation").

The relationship 'denotes' is defined in RO as

g denotes r =def r is a portion of reality there is some c that is a concretization of g    every c that is a concretization of g specifically denotes r

I'm not sure that I get the difference between "materially denotes," "denotes," and "mentions," but this seems to me to be the right relationship to use.

In my conception, I want to treat the "gene record" (such as the record indicated by the GeneID 5663, above) as a kind of information artifact which denotes members of a class of genes. Turning this around, we could pick out a particular gene by talking about the GDC that is denoted by the gene record we have in hand.

So the OWL expression

bearer_of some (is_concretization_of value      (inv('specifically denotes') value http://www.ncbi.nlm.nih.gov/gene/5663))

might be the way to talk about the class of things which are annotated with the Psen1 gene.

Therefore, if we want to talk about the class of things which are derived from this class of Psen1-annotated things, we could write that as:

derives_from some (bearer_of some     (is_concretization_of value (inv('specifically denotes') value http://www.ncbi.nlm.nih.gov/gene/5663)))

Relationships from "the Central Dogma"
transcribes

translates

= Sequence Ontology =

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