Just in case anyone is interested, here are two implementations using XML::Rules. The first one prints the reactions as it parses through the XML, the other builds a more simplified data structure.

use strict;
use warnings;

use XML::Rules;
use Data::Dumper;

my $parser = XML::Rules->new(
    rules => [
        substrate => sub {return '@substrates' => $_[1]->{name}},
        product => sub {return '@products' => $_[1]->{name}},
        reaction => sub {
            print "$_[1]->{name} ($_[1]->{type}):\n";
            print "\tSubstrates: ", join(", ", @{$_[1]->{substrates}})
+, "\n";
            print "\tProducts:   ", join(", ", @{$_[1]->{products}}), 
+"\n\n";
            return;
        },
    ],
);

$parser->parse(\*DATA);

__DATA__
<root>
    <reaction name="rn:R00710" type="reversible">
        <substrate name="cpd:C00084"/>
        <product name="cpd:C00033"/>
    </reaction>
    <reaction name="rn:R00014" type="irreversible">
        <substrate name="cpd:C00068"/>
        <substrate name="cpd:C00022"/>
        <product name="cpd:C05125"/>
    </reaction>
</root>
[download]

and

use strict;
use warnings;

use XML::Rules;
use Data::Dumper;

my $parser = XML::Rules->new(
    rules => [
        substrate => sub {return '@substrates' => $_[1]->{name}},
        product => sub {return '@products' => $_[1]->{name}},
        reaction => sub {
            my $name = delete($_[1]->{name});
            delete($_[1]->{_content});
            return $name => $_[1];
        },
        root => 'pass no content',
    ],
);

my $result = $parser->parse(\*DATA);
print Dumper($result);

while (my ($reaction, $data) = each(%$result)) {
    print "$reaction ($data->{type})\n";
    print "\tSubstrates: ", join(", ", @{$data->{substrates}}), "\n";
    print "\tProducts:   ", join(", ", @{$data->{products}}), "\n\n";
}

__DATA__
<root>
    <reaction name="rn:R00710" type="reversible">
        <substrate name="cpd:C00084"/>
        <product name="cpd:C00033"/>
    </reaction>
    <reaction name="rn:R00014" type="irreversible">
        <substrate name="cpd:C00068"/>
        <substrate name="cpd:C00022"/>
        <product name="cpd:C05125"/>
    </reaction>
</root>
[download]

The substrate and product rules could be rewriten like this:

 'substrate,product' => sub {return '@'.$_[0].'s' => $_[1]->{name}},
[download]

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.