parse

            

              
              
Usage - $intact_parser->parse  (  $intact_files, $map  )
Returns - data structure  ( hash reference )
Args - 
 1. [ IntAct data file paths  ( fully qualified )]  (  array reference )
 2. { UniProtKB accession => UniProtKB id  ( strings )}  ( hash reference )
 3. { UniProtKB accession => UniProtKB id  ( strings )}  ( hash reference ), optional
Function - parses IntAct data file and optionally filters it by the map
            
          

work

            

              
              
Usage - $intact_parser->work ( $ontology, $data, $parent_protein_name )
Returns - { NCBI ID => { UP AC => OBO::Core::Term object }} ( data structure with all the proteins in the interactions )
Args - 
1. OBO::Core::Ontology object, 
2. data structure from parse ( )
3. parent term name for proteins ( string ) # to link new proteins to, e.g. 'cell cycle protein'
Function - adds to the input ontology OBO::Core::Term objects along with appropriate relations for interactions and proteins from IntAct data
            
          

NAME

OBO::Parser::IntActParser - An IntAct to OBO parser/filter.

DESCRIPTION

A parser for IntAct-to-OBO conversion. The conversion is filtered according to the proteins already existing in the input ontology.

AUTHOR

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

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.