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"Extensible Markup Language (XML) is a simple, very flexible
text format derived from SGML (ISO 8879). Originally designed
to meet the challenges of large-scale electronic publishing,
XML is also playing an increasingly important role in the
exchange of a wide variety of data on the Web and elsewhere."
--- W3C XML Web Site 2003/08/20
The proteomics community (and the more general bioinformatics community) is
beginning to standardize data and information exchange, around the general ideas
embodied in XML. The GPM is an XML application from the ground up: all of the
GPM input and output data is specified through XML. The Biopolymer Markup
Language (BIOML), originally specified by David Fenyo in 1999 was selected
as the basic language for GPM input and output, with the General Analytical
Markup Language (GAML) used as a namespace extension for parts of the
information that require the use of histogram data sets that cannot be
easily rendered in BIOML.
While the GPM does not use the Proteomics Experiment Markup Language
at the moment, a link to this relatively new language project is included below
for interest. As that language improves and extends, it may be possible to
create XSLT stylesheets to make GPM input and output transparently compatible
with this language.
The data-centric BIOML:GAML files are rendered into text and graphics
using XHTML and the Scalable Vector Graphics language, using either XSLT or
simple PERL scripts, providing the user interface that is the GPM.
Below is a list of scientific XML languages. Click the links to
view details about individual specifications.
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