/ 
onto-perl-0.31
/ CCO::Parser::UniProtParser

work

Usage    - $UniProtParser->work($ref_file_names, 'Arabidopsis thaliana organism')
Returns  - updated CCO::Core::Ontology object 
Args     - 1. reference to a list of filenames(input OBO file, output OBO file, UniProt file, CCO_id/protein_name map file one taxon only, CCO_id/protein_name map file all taxa), 2. taxon_name
Function - parses a Uniprot file, adds relevant information to the input  ontology, writes OBO and map files

NAME

CCO::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 'work' incorporates relevant data from a UniProt file into the input ontology, writes the ontology into an OBO file, writes map files.

Assumptions:

- the ontology contains already the term 'gene'

- the ontology already contains relevant protein terms.

- the ontology already contains the NCBI taxonomy.

- the ontology already contains the relationship types 'is_a', 'encoded_by', "derives_from"

- the input UniProt file contains entries for one species only and for protein terms present in the input ontology only

- the full map file ($long_file_name, the UNION of the species specific map files ($short_file_name)) contains all the proteins to be processed by the UniProtParser

AUTHOR

Vladimir Mironov vlmir@psb.ugent.be

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.