Thursday, November 22, 2007

A more complex LSID client

This one merges metadata from multiple endpoints, and then parses it using RDF::Core.

use strict;
use LS::ID;
use LS::Locator;
use RDF::Core::Model::Parser;
use RDF::Core::Storage::Memory;
use RDF::Core::Model;
use RDF::Core::Resource;
use RDF::Core::Literal;
use RDF::Core::Statement;

my $storage = new RDF::Core::Storage::Memory;
my $model = new RDF::Core::Model (Storage => $storage);
my $id = ',FASTA2HighestGenericSequenceObject:2006-04-12T18-27-15Z';

# the lines below convert the LSID into a URL since that's what BioMoby
# currently returns in its metadata... sorry!
my $r = '';
$id =~ /[^:]+)/;
$r .= $1;

my $lsid = LS::ID->new($id);

my $locator = LS::Locator->new();
my $authority = $locator->resolveAuthority($lsid);
my $resource = $authority->getResource($lsid);
my $locations = $resource->getMetadataLocations;

foreach my $locs(keys %$locations){
foreach my $loc(@{$locations->{$locs}}){

my $data;
eval{$data = $resource->getMetadata(location => $loc);};
next if $@;

my $response_filehandle = $data->response;
my $RDF = join "", <$response_filehandle>;

my %options = (Model => $model,
Source => $RDF,
SourceType => 'string',
BaseURI => "",
BNodePrefix => "genid"
my $parser = new RDF::Core::Model::Parser(%options);

print "model contains ", $model->countStmts, " statements\n\n";
my $resource = RDF::Core::Resource->new($r);
my $enumerator = $model->getStmts($resource);
my $statement = $enumerator->getFirst;
while (defined $statement) {
my $s= $statement->getSubject->getLocalValue;
my $o= $statement->getObject;
my $p= $statement->getPredicate->getLocalValue;
print "$s $p $o\n" unless $o =~ /genid/;
$statement = $enumerator->getNext

Wednesday, November 14, 2007

LSID Perl libraries submitted to CPAN

Just a quick note to announce that my lead developer, Eddie Kawas, has recently uploaded the Perl LSID stack to CPAN. As such, it is no longer necessary to get the code from the sourceforge Subversion repository. Just start-up CPAN and say "install LS".

Google Gadgets for BioMoby

I love it when a bunch of open APIs come together into something greater than the sum of the parts :-)

Thanks to the good folks at Google and their Google Gadgets for making things so darn simple! It only took an hour or so to write a script that wrapped every BioMoby Web service (more than 1400 of them!) with a Google Gadget. Now it is an absolute a no-brainer to create an amazing mashup of bioinformatics data by simply selecting the various services you are interested in and dropping their Gadgets on your iGoogle page. You might even make a variety of different Gadget tabs with different combinations of services to provide different views.

I'm still working on getting the rendering to be more size-appropriate (currently I am using the same rendering engine as I used in Gbrowse_moby) but I think it's pretty good for a first-pass!

Try them for yourself: