[Bioc-devel] biocViews vocabulary expansion proposal: RFC

James W. MacDonald jmacdon at med.umich.edu
Fri Mar 31 19:10:15 CEST 2006

Seth Falcon wrote:
> "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.

OK. Looks good to me then.



> + seth
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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