[Bioperl-l] Proposal for Meta data

David Messina dmessina at wustl.edu
Thu Dec 14 20:45:24 EST 2006


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. :)

Dave


More information about the Bioperl-l mailing list