[Bioc-devel] biocViews vocabulary expansion proposal: RFC

Aedin Culhane aedin at jimmy.harvard.edu
Fri Mar 31 20:29:34 CEST 2006

Hi Seth
This will be very welcome.  Will there is a manufacturer term also?
So one can sort by a commerical Agilent/Affymetrix or
Institute/Academic/submitter term.

The other thing that might help (if its not lots of work), would be the nrow or
number of ID's. When I can't recall the extact annotation package, its a quick
compare I use.


> Date: Thu, 30 Mar 2006 16:39:52 -0800
> From: Seth Falcon <sfalcon at fhcrc.org>
> Subject: [Bioc-devel] biocViews vocabulary expansion proposal: RFC
> To: bioc-devel at stat.math.ethz.ch
> Message-ID: <m2zmj78n1j.fsf at ziti.local>
> Content-Type: text/plain; charset=us-ascii
> 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.
> 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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