[Bioc-devel] biocViews vocabulary expansion proposal: RFC

Seth Falcon sfalcon at fhcrc.org
Fri Mar 31 02:39:52 CEST 2006

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.


+ seth

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