OBO::CCO::NCBIParser - A NCBI taxonomy to OBO translator.

This parser converts chosen parts of the NCBI taxonomy-tree into an OBO file. Some taxa are given to the parser and the whole tree till the root is reconstructed in a given OBO ontology, using scientific names.

The dump files (nodes.dmp and names.dmp) should be obtained from:

	ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

TODO: include ranks and disjoints only in correlating ranks.

Mikel Egana Aranguren

http://www.mikeleganaranguren.com

eganaarm@cs.man.ac.uk

Copyright (C) 2006 by Mikel Egana Aranguren

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    - $NCBIParser->work()
  Returns  - the parsed OBO ontology
  Args     - old OBO file, new OBO file, cco ids file, nodes dump file, names dump file, taxon 1, taxon 2, ...
  Function - converts NCBI taxonomy into an OBO file