Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Utils::BiotypeMapper Class Reference

List of all members.


Class Summary

Synopsis

use Bio::EnsEMBL::Utils::BiotypeMapper

my $ontology_adaptor = $registry-\>get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
my $biotype_mapper = new BiotypeMapper($ontology_adaptor);

print $biotype_mapper-\>translate_feature_to_SO_term($feature);

Description

BiotypeMapper provides a series of nearest matches between EnsEMBL biotypes and
the Sequence Ontology (http://www.sequenceontology.org)
Mappings are imperfect due to the inexact correspondance of biotypes to 
several SO terms. The a best guess has been chosen in each case.
Reverse mappings from SO to biotype are vague, due to many-to-one relationships.
In this case a list of possible terms is given.
 

Definition at line 28 of file BiotypeMapper.pm.

Available Methods

public Bio::EnsEMBL::BiotypeMapper new ()
public String translate_feature_to_SO_term ()
public String translate_SO_to_biotype ()

Method Documentation

public Bio::EnsEMBL::BiotypeMapper Bio::EnsEMBL::Utils::BiotypeMapper::new ( )
    Constructor
    Arg [1]    : OntologyAdaptor from the EnsEMBL registry
	Returntype : Bio::EnsEMBL::BiotypeMapper
 
Code:
click to view
public String Bio::EnsEMBL::Utils::BiotypeMapper::translate_feature_to_SO_term ( )
	Arg [0]    : Bio::EnsEMBL::Feature, subclass or related Storable
	Description: Translates a Feature type into an SO term. If the Feature is a
	             Gene or Transcript, then a further refinement of the type is made
				 via Biotype
	Returntype : String
 
Code:
click to view
public String Bio::EnsEMBL::Utils::BiotypeMapper::translate_SO_to_biotype ( )
	Arg [0]    : Sequence Ontology term, either in name or URI format
	Description: Returns the closest corresponding Ensembl biotypes to a given SO term
	Returntype : String containing a comma-separated list of biotypes
 
Code:
click to view

The documentation for this class was generated from the following file: