[Bioperl-l] Proposal for Meta data
dmessina at wustl.edu
Thu Dec 14 20:45:24 EST 2006
My thoughts below.
> This could be used to annotate any
> PrimarySeq, LocatableSeq, SimpleAlign, SeqFeature, or what-have-you,
> maybe in a collection (similar to AnnotationCollection). I thought
> something like this may be of general use for any PrimarySeq
> (quality, structure), alignments like NEXUS and Stockholm,
> SeqFeatures where structure could be stored (tRNA or riboswitches),
> However, this also seems to fall into the category of sequence
> annotation. So, would it be better to have a set of Bio::Annotation
> classes used for this purpose?
To me, all meta data is equal. That is, your classic Genbank feature
annotation and a user's arbitrary meta-tag like "Bob thinks this is a
kinase domain" aren't different in kind even if they are different in
As resequencing projects multiply, the ability to create arbitrary
meta tags, attach them to different types of objects, and use those
tags to link them together will become desirable, if not essential.
Keeping a common interface to all of these meta data types would be
advantageous, plus new users won't have to determine whether they
need to use Bio::Meta objects or Bio::Annotation objects.
So I would argue for all of the meta data types to live "under one
roof". Which roof isn't as important. Bio::Annotation, since it
already exists for today's meta data, seems like a reasonable choice.
(assuming Annotation objects are flexible enough to be extended as
There, and no flames or jibes even. :)
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