Erick Antezana
and 1 contributors


 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


 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


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


Includes methods for adding information from GOA association files to ontologies GOA associations files can be obtained from

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'


Vladimir Mironov <>


Copyright (c) 2006-2014 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.