[Bioperl-l] Proposal for Meta data

Chris Fields cjfields at uiuc.edu
Mon Dec 18 18:15:56 EST 2006

On Dec 18, 2006, at 3:50 PM, Chris Mungall wrote:

> I agree with everything Heikki is saying, I just wanted to highlight
> one paragraph:
>> The problem I see with undefined, totally open meta annotation, is
>> that if you
>> can put anything in there, it is also totally confusing to a user.
>> If you can
>> put anything in, how do you know what to get get out and know that
>> it is
>> there?
> One solution is to give your annotation/metadata-model formal
> computational semantics and use ontologies to give additional
> semantics to your metadata tags. This provides both user information
> in the form of documentation, and a means of specifying to the
> computer exactly what should be done with the tags.
> This is probably overkill for bioperl; but if the use cases being
> proposed do lean in the direction of a new metadata system that is
> not necessarily backwards compatible with the existing one, then I'd
> recommend checking out what's already out there before re-inventing
> the wheel. Perl RDF libraries are getting a little better.
> If anyone is interested in pursuing this sort of thing (probably on a
> branch), let me know

I like the idea of of using ontologies (although that's one of my  
many weak points!).  I'll likely start off with simple examples using  
meta data initially, then progress from there.  It is a developer  
series, after all!

Thanks everybody!  I think I have an idea on how to at least get  


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