[Bioperl-l] Proposal for Meta data

Chris Fields cjfields at uiuc.edu
Wed Dec 13 13:02:14 EST 2006


I am working on a few RNA-related things related to structure and  
have a few questions, specifically about Meta data.  This is sort of  
a proposal, but I would like to get everybody's thoughts about this  
to gauge what everyone thinks.  Jason, sorry to bug you but I thought  
it might be something that would be of use phylohackathon-wise.

Heikki has several modules present which adds meta data to sequences  
(Bio::Seq::Meta).  In this case, the meta data is stored as a string  
(Bio::Seq::Meta) or an array (Bio::Seq::Meta::Array).  In both cases  
you can have multiple types of meta data for a sequence based on a  
particular tag.  However, this also assumes that the meta data is  
somehow attached strictly to sequence data of some type.  It also  
doesn't allow for having mixed meta data types for a single sequence,  
such as attaching array data and string data to the same sequence.

Hence, I was thinking of a having a simple, generic meta data type  
(Bio::Meta), one which could encompass simple strings  
(Bio::Meta::Simple), arrays (Bio::Meta::Array), or any other  
structured type of data.  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?

Flames and jibes welcome; I'm wearing my asbestos suit today....

chris







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