NAME

Bio::Phylo::PhyloWS::Service::UbioClassificationBank - PhyloWS service wrapper for uBio ClassificationBank records

SYNOPSIS

# inside a CGI script:
use CGI;
use Bio::Phylo::PhyloWS::Service::UbioClassificationBank;

# obtain a key code from http://www.ubio.org/index.php?pagename=form
# and define it as an environment variable:
$ENV{'UBIO_KEYCODE'} = '******';
my $cgi = CGI->new;
my $service = Bio::Phylo::PhyloWS::Service::UbioClassificationBank->new(
   '-base_uri' => $url
);
$service->handle_request($cgi);

DESCRIPTION

This is an example implementation of a PhyloWS service. The service wraps around some of the uBio XML services described at http://www.ubio.org/index.php?pagename=xml_services.

Record lookups for this service return project objects that capture the RDF metadata for a single ClassficationBank record as semantic annotations to a taxon object. An example of the sort of metadata that can be expected is shown here: http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:classificationbank:11168417

METHODS

ACCESSORS

get_record()

Gets a uBio classification bank record by its id

Type    : Accessor
Title   : get_record
Usage   : my $record = $obj->get_record( -guid => $guid );
Function: Gets a uBio classification bank record by its id
Returns : Bio::Phylo::Project
Args    : Required: -guid => $guid
Comments: For the $guid argument, this method only cares
          whether the last part of the argument is a series
          of integers, which are understood to be classification
          bank identifiers

get_supported_formats()

Gets an array ref of supported formats

Type    : Accessor
Title   : get_supported_formats
Usage   : my @formats = @{ $obj->get_supported_formats };
Function: Gets an array ref of supported formats
Returns : [ 'nexml', 'json', 'nexus', 'rss1' ]
Args    : NONE

get_authority()

Gets the authority prefix (e.g. TB2) for the implementing service

Type    : Authority
Title   : get_authority
Usage   : my $auth = $obj->get_authority;
Function: Gets authority prefix
Returns : 'uBioCB'
Args    : None

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63