Bioperl: XML/BioPerl

[Steven E. Brenner]

[Note to Readers on cc list: there has recently been considerable
discussion of XML on the bioperl mailing list (see footer for details),
and the following issue is coming up.]

> 
> PDB is moving to San Diego, and the people involved have been quite devoted 
> to CIF, but again, I have not heard anything specific.  There is a real 
> need for a biological entities (as opposed to crystallographic unit cells) 
> view of PDB, and XML would be a great place to start.
> 
> David States
> 

I have spoken with Helen Berman and John Westbrook (of the new PDB)
regarding using XML for biological macromolecules.  I cannot speak for
them; however, they seem very open to the possibility of providing XML
versions of the data.

As they point out, the hard problem is to define the data structures and
collect data which reliably conforms to it.  Once that's done, producing
reports in different formats is comparatively easy.  While I think they
are currently taking a wait-and-see attitude to XML (perhaps because they
are heavily overburdened with other projects right now -- they are trying
to do an immense amount of work with a limited staff), I think that if XML
does become established, we will see PDB providing data (in the
crystallographic view) in that format.

I do not know of any plans to provide a "biological" view.  However, my
impression is that the PDB is very open to suggestions from the community.


Steven Brenner


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