Bioperl: XML/BioPerl

[Paul Gordon]

I know I'm a little slow on the draw here, but here is my $0.02 worth.

On Thu, 31 Dec 1998, Lincoln Stein wrote:
> For what it's worth, I will be adding a BoulderIO <-> XML converter in
> the next week or so (thanks to Jaime Prilusky for the code).  Also a
> CGI <-> XML converter.  For those of us using Boulder as a biological
> data conversion format, the future is already here!

<snip>

>  > Of course, if the applet being developed is already huge for some other
>  > reason like a complication in the data display algorithms or is set for
>  > deployment on an intranet, then a 26k XML parser becomes less of a
>  > concern. But most people tend to want to keep their applets as thin as
>  > possible.

As was discussed earlier, XML itself it not that useful as a final data
type, but as a go between for particular XMLs (such as BIOML and BSML). 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.  The XML parsing is lightweight and SAX compliant, but not
quite complete.  I traded off some functionality for simplicity.  I had
started with implementing BSML display, but it is definitely kitchen
sink-ish.  I know BIOML isn't perfect, but it is simple, and any
"standard" that is eventually adopted will likely be an easily mapped  
superset of BIOML.

Anyway, since my application is starting with a BIOML module I'm going to
need BIOML documents.  My plan (at least for now) is to write a BIOML
proxy (a la Lincoln's mod_perl Apache::AdBlocker), so that one can fetch a
genbank/swissprot/etc. page and display it seemlessly.  This will require
Genbank -> BIOML and other converters.  This seems to me to be a better
idea than waiting for the sources to standardize, if they ever do.

Of course, a better way to do it would probably be GenBank -> XML, XML ->
BIOML, but I believe that the XML -> BIOML module would become quite
complicated.  Before I embark on this escapade (which won't be for a
couple of weeks, as I'm still working on the Java) I'd appreciate
feedback on which approach to take, and more specifically, if anyone
else is working on  xxx -> XML converters which would make it worthwhile
to write XML -> BIOML right off the bat.

Regards,
	Paul Gordon
	Institute for Marine Biosciences
	National Research Council of Canada

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