[Bioperl-l] Proposal for Meta data

Chris Fields cjfields at uiuc.edu
Thu Dec 14 21:21:10 EST 2006

On Dec 14, 2006, at 7:45 PM, David Messina wrote:

> Hey Chris,
> My thoughts below.
>> [Chris]
>> 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),
>> etc.
>> 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
> content.
> 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
> you propose)
> There, and no flames or jibes even. :)

I guess what I want to know is whether there should to be a  
distinction between 'normal' sequence annotation (comments,  
references, and so on) and annotation that could be best described as  
position-specific (like RNA or protein structural annotation).  The  
current meta implementation is for sequence data only; I felt it  
would be nice to have a generic implementation that would be  
applicable to any object data.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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