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

EBI::FGPT::FuzzyRecogniser module finds the best match for the supplied term in the given ontology.

Copyright [2011] EMBL - European Bioinformatics Institute

Licensed free of charge for academic, non-commercial purposes under the EMBL Standard academic license; and for a fee to commercial users and/or commercial purposes under a commercial license. For download please follow: http://www.embl-em.de/login.php

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.