[Bioperl-l] Proposal for Meta data

[Jason Stajich]

On Dec 14, 2006, at 9:21 PM, Chris Fields wrote:

>
> 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.

my stream-of-consciousness for right now:

I was thinking Bio::Annotation is where this should go - that system  
doesn't have anything about it that makes it explicitly sequence  
related. What we're trying to hammer out here on the Alignment side -  
which fits with your RNA example - is have features, basically  
SeqFeatures - associated with alignments so columns can be annotated  
to cover things like character sets and partitions for phylogenetic  
analyses.  As for data which annotates non-contiguous things like  
RNAstems we may have  to be more creative about that or model it with  
a splitLocation.

So currently we've added code so that an Alignment is-a  
Bio::AnnotableI and is-a Bio::FeatureHolderI to move towards this  
end, with the goal of being able to capture more of the data that can  
be represented in a NEXUS file.

It feels more like a hack than an elegant Meta-data solution, but I  
am totally sure whether the data you are thinking about doing at this  
point, perhaps I need to spend more time thinking about it.
Or are you worried about the idea of whether the semantic mapping of  
the data into features or annotations is confusing users?