[Bioc-devel] biocViews vocabulary expansion proposal: RFC

[Seth Falcon]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:
> Does this mean that e.g., for human we would have homoSapiens? 

Yes, or perhaps HomoSapiens.

> I am not too keen on that idea, as we would be going against the
> established convention that genus is capitalized but species is
> not. Unless there is a compelling argument for this scheme, I would
> rather something like Homo_sapiens or better yet, Hsapiens, Ecoli,
> Mmusculus, etc.

That would be fine with me.  We considered using a TLA (three letter
acronymn) like HSA for Hsapiens, but we are not convinced that there
exists a real standard.

I like your underscore suggestion best: Homo_sapiens

> Am I correct in assuming that the organism node would simply contain
> chip specific nodes as well as whatever organism-level packages exist?
> For instance, the human node would contain the hgu133a, hgu133plus2,
> hgu95av2, etc. nodes plus the hshomology, humanCHRLOC, and
> humanLLmappings packages?

Yes, the idea would be that any annotation data packages having to do
with humans would list in their biocViews field (among other terms)
Homo_sapiens.  Then under the Homo_sapiens node/listing will be all
those packages.

+ seth