/ 
ONTO-PERL-1.27
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/ OBO::CCO::GoaParser

NAME

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

DESCRIPTION

Includes methods for adding information from GOA association files to ontologies GOA associations files can be obtained from http://www.ebi.ac.uk/GOA/proteomes.html

The method 'parse' parses the GOA association file and returns a OBO::CCO::GoaAssociationSet object

The method 'work' incorporates OBJ_SRC, OBJ_ID, OBJ_SYMB, SYNONYM, DESCRIPTION into the input ontology, writes the ontology into an OBO file, writes map files. This method assumes: 1. the ontology contains already the term 'protein' 2. the ontology already contains all and only the necessary GO terms. 3. the ontology already contains the relationship types 'is_a', 'participates_in', 'has_participant' 4. the input GOA association file contains entries for one species only and for GO terms present in the input ontology only

AUTHOR

Vladimir Mironov <vladimir.mironov@bio.ntnu.no>

COPYRIGHT AND LICENSE

Copyright (C) 2006, 2007, 2008, 2009, 2010 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.

parse

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

work

Usage    - $GoaParser->work($ref_file_names)
Returns  - updated OBO::Core::Ontology object 
Args     - reference to a list of filenames(input OBO file, output OBO file, GOA associations file, CCO_id/Uniprot_id map file one taxon only, CCO_id/Uniprot_id map file all taxa)
Function - parses a GOA associations file, adds relevant information to the input  ontology, writes OBO and map files

work

Usage    - $GoaParser->add_goa_assocs($ref_file_names)
Returns  - updated OBO::Core::Ontology object
Args     - reference to a list of filenames(input OBO file, output OBO file, GOA associations file, UniProt map file 'AC'\t'ID', 'go_id'\t'cco_id' map file)
Function - parses a GOA associations file, adds new associations to the input  ontology, writes OBO