NAME

OBO::CCO::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.

This method assumes:

- the input ontology contains already the term 'gene', 'protein', 'cell cycle modified protein'

- the input ontology already contains relevant protein terms.

- the input ontology already contains the NCBI taxonomy.

- the input ontology already contains the relationship types 'is_a', 'encoded_by', 'codes_for', 'originates_from', 'tranformation_of', 'source_of'

- 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.

work

Usage    - $UniProtParser->work($ref_file_names, 'Arabidopsis thaliana organism')
Returns  - updated OBO::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,
              - CCO_id/gene_name map file one taxon only, 
              - CCO_id/gene_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