Erick Antezana > ONTO-PERL > OBO::Parser::IntActParser

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ONTO-PERL/ONTO-PERL-1.44.tar.gz

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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.

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