[Bioc-devel] biocViews vocabulary expansion proposal: RFC

"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