NAME

EBI::FGPT::FuzzyRecogniser

DESCRIPTION

The module EBI::FGPT::FuzzyRecogniser takes in the constructor an ontology file (OWL/OBO/OMIM/MeSH) and parses it into an internal table of ontology terms (type of EBI::FGPT::FuzzyRecogniser::OntologyTerm). The module contains the find_match method which finds the best match for the supplied term in the given ontology. This can be then queried for ->match_similarity(), ->matched_value(), ->matched_label(), and ->matched_accession(). The best match is based on the n-grams similarity metric.

SYNOPSIS

    use EBI::FGPT::FuzzyRecogniser;
        
        # instantiate and pass ontology file
        
    my $fuzzy = EBI::FGPT::FuzzyRecogniser->new( obofile => 'obo.txt' );
    
    # call find_match on a supplied term
    # finds the best match for the supplied term in the ontology.
    
    my $x = $fuzzy->find_match('submitter');

AUTHOR

Emma Hastings , <ehastings@cpan.org>

ACKNOWLEDGEMENTS

Tomasz Adamusiak <tomasz@cpan.org>

COPYRIGHT AND LICENSE

Copyright (c) 2010 European Bioinformatics Institute. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under GPLv3.

This software is provided "as is" without warranty of any kind.

find_match()

Finds the best match for the supplied term in the ontology.

createOntologyTerm()

Creates an OntologyTerm object given its accession and annotations

parseMeSH()

Custom MeSH parser for the MeSH ASCII format.

parseMeSH()

Custom OMIM parser.

parseOBO()

Custom OBO parser.

parseOWL()

Custom OWL parser.