parse

 Usage - $UniProtParser->parse ( $uniprot_file_path, $uniprot_map ) 
 Returns - ref to a hash { UniProtAC => SWISS::Entry object }
 Args - 
        1. UniProt data file path, 
        2. ref to a hash { UniProtAC => UniProtID } to filter by, optional
 Function - parses UniProt data file 
 

work

 Usage - $UniProtParser->work ( $onto, $data, $parent_protein_name, $parent_gene_name )
 Returns - a hash with terms for added genes { NCBI GeneID => OBO::Core::Term object } 
 Args - 
        1. OBO::Core::Ontology object, 
        2. ref to a hash { UniProtAC => SWISS::Entry object }
        3. parent term name for proteins ( string ), # to link added modified proteins to, e.g. 'modified gene regulation protein'
        4. parent term name for genes ( string ), # to link added genes to, e.g. 'gene regulation gene'
 Function - adds gene and modified protein terms to the input ontology along with appropriate relations
 

NAME

OBO::Parser::UniProtParser - A UniProt to OBO translator.

DESCRIPTION

Includes methods for adding information from UniProt files to ontologies

UniProt files can be obtained from: ftp://ftp.expasy.org/databases/uniprot/knowledgebase/

The method 'parse' parses imput UniProt file and filters the data by map (optioanally) The method 'work' transfers selected data from the ouput parse() into the input ontology. This method assumes: - the input ontology contains the NCBI taxonomy. - the input ontology contains the relationship types 'is_a', 'encoded_by', 'codes_for', 'has_source', 'tranformation_of', 'source_of'

AUTHOR

Vladimir Mironov <vladimir.n.mironov@gmail.com>

COPYRIGHT AND LICENSE

Copyright ( C ) 2006 by Vladimir Mironov

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.