[Bioc-devel] biocViews vocabulary expansion proposal: RFC

[James W. MacDonald]

Seth Falcon wrote:
> Hi all,
> 
> This request for comment regards adding terms the vocabulary
> understood by biocViews.
> 
> We propose to add terms under the AnnotationData node to help 
> organize HTML listings of annotation packages.
> 
> At the top-lvel, the biocViews vocabulary has three main nodes:
> 
> /* Root */
> TaskViews -> Software;
> TaskViews -> AnnotationData;
> TaskViews -> ExperimentData;
> 
> Under the AnnotationData node, we plan to add:
> 
> 1. A term for each chip.  For example, hgu95av2 would be added as a
>    term under AnnotationData.  This will allow us to construct an
>    alphabetic listing of chips such that each is a link to a page
>    listing all annotation packages related to that chip.
> 
> 2. A term for organisms that we have annotation data for.  The
>    proposed scheme is to use CamelCaps on the organism's Latin name.
>    This will allow a by-organism listing.

Does this mean that e.g., for human we would have 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.

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?


Best,

Jim


> 
> 3. For the annotation packages that deal with data across species and
>    across chips, we will add SequenceAnnotation for genome-wide
>    package, and FunctionalAnnotation for packages like GO, KEGG, PFAM,
>    and cMAP.  This will make finding these packages easier because we
>    will be able to produce listing that are separate from the bulk of
>    chip-specific annotation packages.
> 
> We welcome comments and suggestions on this plan.  Unless significant
> debate ensues, we will implement this plan next Thursday, April 6.
> 
> Best,
> 
> + seth
> 
> _______________________________________________
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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