Classes for OMP

[jimhu-tamu]

After thinking about this for several years, including conversations with @pbuttigieg at various meetings, I'd like to stimulate some discussion of instantiating ENVO classes to support OMP annotation, starting with very basic lab environments.

ENVO has children of tissue culture I wasn't sure what the plans are for #613
I also looked at OBI, which has OBI:0000079 culture medium, but is surprisingly lacking in useful children.

cc:@dsiegele

[cmungall]

How would this be used in an OMP annotation? I assume the lab environment is part of the evidence and not part of the phenotype?

[jimhu-tamu]

Phenotype is a manifestation of genotype + environment. So in OMP annotation environment is part of a composed equivalent of an annotation object in GO in combination with an identifier for genotype.

What stimulated me to post is that we have a ms deadline tomorrow for a special issue od J Biomed Semantics.

[pbuttigieg]

Hi @jimhu-tamu

We just added laboratory environment to support a Vampire Moth set up:seltmann/vampire-moth-globi#2

We could diversify that quite a bit. What sort of subclasses do you have in mind?

[pbuttigieg]

PS: You may want to ping EO, as they list lab conditions used in plant research which often simulate environments listed ENVO. It's plant focused, but they may have a set up you can use.

If you do want to list different kinds of lab environments in ENVO, we can talk co-editing.