Best Predicate For Association With Go Terms?

Question

[Marcin Cieslik]

I am struggling to find any documentation about the correct predicate to use the Gene Ontology (for annotation) in a RDF setting i.e.

<gene_id> < ???? > <go_term>

go2rdf.pl (from ONTO-Perl) uses located_in, participates_in, has_function (presumably from the OBO_REL). On the other hand the GO has go:association that "represents the gene associations of each term.". Is this an explicitly symmetric property is this even of rdf:Property type?

Answer 1

[biobot 0.0.77.a.1099]

This relation is not formally defined by the GO, as I understand it. GO annotations are associations between a GO term (a type) and another class of biological entity e.g. a particular gene product (also a type, representing all instances of that gene product, rather than a specific individual), which makes things a bit tricky.

There is a discussion of the problem on the bioontology wiki where the author contrasts a more ontologically correct, but complex model, with a simpler approach that appears to be the one you describe for ONTO-Perl.

[Marcin Cieslik]

Thanks, this is what I was looking for.