Bioperl: XML/BioPerl

[David J. States]

Paul Gordon wrote:
... I am current working on a piece of software written in Java that 
facilitates
linear data (such as a piece of DNA) encoded in XML to be displayed
graphically.  ...

Anyway, since my application is starting with a BIOML module I'm going to
need BIOML documents.

I have a sequence/classification server that delivers a slightly extended 
version of BIOML. The server is accessible by the URLs

http://www.ibc.wustl.edu/bioXML/dtd/mcxml.cgi?DS=sp&LOC=xxx
or
http://www.ibc.wustl.edu/bioXML/dtd/mcxml.cgi?DS=sp&ACC=yyy

where xxx is a SwissProt locus or yyy is a SwissProt accession.  Actually, 
ds can be 'gi', or 'pir' although these datasets are not fully up to date. 
 The server will return a sequence object in XML/BIOML annotated with 
database cross-references and domain definitions as defined in PFAM, 
BLOCKS, PRINTS and some of our own classifications.

The dtd is accessible at http://www.ibc.wustl.edu/bioXML/dtd/bioml.dtd. The 
extensions to BIOML consist of definition of a couple of entities to 
describe names, species etc. and a structured database entry element.  The 
data served by the server and this dtd do validate.

We also have a first pass viewer applet at 
http://www.ibc.wustl.edu/~trevor/megaclass/megaclass.html.  You have to 
click in the text box and hit "enter" to fire the applet off, but then it 
gives you a graphical interactive view of the classifications applied to a 
sequence.

Please note that this is an experimental server.  We plan to continue 
serving XML views of our data, but the server URL and details of the dtd 
will change in future.

David

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