[Bioperl-l] XML blast parsing (was parsing tblastn using BPlite)

Wiepert, Mathieu Wiepert.Mathieu@mayo.edu
Mon, 29 Oct 2001 09:01:03 -0600

I think the notion of having DTD's be different for each report is good,
though I think it might be better if there were schemas created instead.  I
tried the simple case of letting a tool automatically map the blast dtd to a
schema awhile back, but an invalid XML doc was created (complex DTD to start
I guess).  I gave up quickly, but it would be better to have schemas at this
point, the theory being that the schemas are just XML docs, so if you want
to use transforms from one to another it should be much easier than using
the DTD's.  I give both of you kudos for attacking this problem though, when
you feel it is good enough for some alpha testing I might be able to do it

It would be a nice contribution if schemas were donated to bioXXX, I know we
could use them in biojava easily.  Another nice thing about XML is that it
will work in any implementation of parsers, java, perl , python, whatever.