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 [2011] EMBL - European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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.