Rutger Vos > Bio-Phylo-0.55 > Bio::Phylo::PhyloWS::Service::UbioClassificationBank

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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

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