work

Usage    - $GoaParser->work()
Returns  - the new OBO ontology object 
Args     - input OBO file, output OBO file, GOA associations file, list of NCBI taxon IDs
Function - adds information from a GOA associations file to an existing 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. The function 'work' generates dummy protein IDs, will be fixed soon. Synonyms will be eventually parsed out of the description.

Assumptions: 1. the ontology contains already the term 'protein' 2. there are yet no subclasses of it corresponding to individual proteins. 3. the ontology already contains all and only the necessary GO process terms. 4. the ontology already contains the NCBI taxonomy. 5. 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.