Bioperl: XML

[Peter Murray-Rust]

At 16:12 06/05/99 -0300, [Paul Gordon and others] wrote:
>> The BioPerl list hasn't mentioned XML since January... The message below
>> was forwarded to me.  What is the current view/status in the BioPerl
>> community as regards XML?  There was talk of a BoulderIO <-> XML convertros
>> as well as a CGI <-> XML converter.

Greetings,
	We (Adam Moore and myself)  have been working on XML for biomolecular
science for some time and have been funded for a year to develop resources
(BIODOM a biomolecular DocumentObjectModel) - these are freely available at:
http://www.vsms.nottingham.ac.uk/biodom

Among the things we hope to release shortly are a Swissprot->CML converter.
One of the exciting things about XML is that tools such as XSL make it easy
to interconvert between different *MLs, so our conversion should be
algorithmically translatable to other XML formats without much difficulty.
[We stick very closely to the Swissprot structure and vocabulary.) We are
also doing the same for "PDB".

The outstanding collection of XML resources is from Robin Cover of OASIS
(the "XML Open" association) - see http://www.oasis-open.org/cover. Robin
picks up almost everything of note that is going on and if he misses
something will include it on request. The current relevant examples are:

http://www.oasis-open.org/cover/xml.html#xml-bsml (BSML)
http://www.oasis-open.org/cover/xml.html#bioml (BIOML)
http://www.oasis-open.org/cover/xml.html#xml-cml (CML)

I can't speak for the others at the current moment (though I am in touch
with Joe Spitzner of BSML).

A new draft of CML should be out very shortly. CML designed to interoperate
with other languages such as BIOML and BSML. 

I have just come back from XML Europe. Very exciting as it is clear that
XML will be universal in the next generation of software. The only downside
is that most of the impetus is coming from commercial companies (to be fair
- many of them are offering high-quality freeware). I think the Perl
community - with its traditional of OpenSource is in a good position to
help develop the innovations that XML now makes possible.

	PeterMR



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