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

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

Vladimir Mironov <vladimir.mironov@bio.ntnu.no>

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.

  Usage    - $intact_parser->parse($intact_file)
  Returns  - XML::XPath object
  Args     - IntAct data file path
  Function - parses IntAct data file 

  Usage - $IntActParser->work($ontology, $xpath, $up_map, $up_core_map, $adding_new_terms)
  Returns - OBO::Core::Ontology object 
  Args - OBO::Core::Ontology object, XML::XPath object, \( map UniProt AC=>ID, \( map UniProt AC=>ID), 
  \(
	  indirect file handle, # for writing a UniProt map for added proteins (AC=>ID)
	  parent term name for proteins (string), # to link new proteins to, e.g. 'cell cycle protein'
	  taxon id (string), # e.g. '3702'
  )
  Function - adds OBO::Core::Term objects for interactions and proteins to ontology