[Biodevelopers] XML schema/API for BLAST?

[David Huen]

On Mon, 28 Jul 2003, Abhik Shah wrote:

> I know for sure that NCBI's Blast supports XML output. The XML Schema is
> here:
> 
> http://www.kaiseryang.com/bio/db/NCBI_XSD.html
> 
> BioPerl, BioJava and others have parsers (and possibly example code)  for
> the XML output. As for input, I don't think NCBI's Blast supports XML-RPC
> or SOAP.  IBM has some free SOAP wrappers for common bioinformatics
> services (including BLAST) here:
> 
I don't know about the rest but Biojava has some Blast XML support
although it needs updating to work with the latest format (i.e. I hear the
latest doesn't concat the outputs together from multiple queries forming a
unparsable mess).  There is example code in the demos in the package. That
will be done eventually.  However, use of the Biojava parser does require
some understanding of its parsing framework as the parser parses blast XML
and generates SAX calls to simulate the parsing of an equivalent file in
our standard internal XML format.  That way, we share a common downstream
parser framework for all our parsers (Blast/FASTA/etc).

Rgds,
David Huen