parse

 Usage - $GoaParser->parse ( $FH, $map )
 Returns - OBO::APO::GoaAssociationSet object
 Args - 
        1. indirect filehandle to a GOA associations file
        2. ref to a hash { UniProtAC => UniProtID } or { GO ID => GO term name } to filter by, optional
 Function - converts a GOA associations file into a OBO::APO::GoaAssociationSet object
 

work

 Usage - $GoaParser->work ( $ontology, $data, $up_map, $parent_protein_name ) # the last arg is optional
 Returns - a data structure with added proteins ( { NCBI_ID => {UP_AC => OBO::Core::Term object}} )
 Args - 
         1. OBO::Core::Ontology object, 
         2. OBO::APO::GoaAssociationSet object,
         3. parent term name for proteins ( string ), # to link new proteins to, e.g. 'gene regulation protein'
 Function - adds GO associations ( and optionally protein terms ) to ontology
 

NAME

OBO::Parser::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 optioanlly filters data by a map

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: - the ontology contains all and only the necessary GO terms. - the ontology contains the relationship types 'is_a', 'participates_in', 'has_participant'

AUTHOR

Vladimir Mironov <vladimir.n.mironov@gmail.com>

COPYRIGHT AND LICENSE

Copyright (c) 2006-2015 by Vladimir Mironov. All rights reserved.

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.