parse

Usage    - $GoaParser->parse()
Returns  - An CCO::Util::GoaAssociationSet object
Args     - GOA associations file
Function - converts a GOA associations file into a CCO::Util::GoaAssociationSet object

work

Usage    - $GoaParser->work($ref_file_names, $ref_taxa)
Returns  - updated OBO ontology object 
Args     - reference to a list of filenames(input OBO file, output OBO file, GOA associations file, input CCO_id/Uniprot_id map file), referece to a hash NCBI_id =>taxon_name
Function - filters GOA associations file by TAXON and GO_ID, adds relevant information to the input  ontology 

NAME

CCO::Parser::GoaParser - A GOA associations to OBO translator.

DESCRIPTION

The function 'work' converts selected parts of GOA associations into an OBO file. GOA assiciations files can be obtained from http://www.ebi.ac.uk/GOA/proteomes.html

Comments: Currently only OBJ_SRC, OBJ_ID, OBJ_SYMB, SYNONYM, DESCRIPTION are transfered into ontology. Synonyms will be eventually parsed out of the description.

Assumptions: 1. the ontology contains already the term 'protein' 2. the ontology already contains all and only the necessary GO process terms. 3. the ontology already contains the NCBI taxonomy. 4. the ontology already contains the relationship types 'is_a', 'participates_in', "derives_from"

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.