parse

 Usage    : $ncbi_parser->parse ( $ncbi_nodes_path )
 Returns  : ref to a hash { child_id => parent_id }
 Args     : nodes.dmp path ( string )
 
 Usage    : $ncbi_parser->parse ( $ncbi_names_path, $name_type )
 Returns  : ref to a hash { ncbi_id => ncbi_name }
 Args     : 
            1. names.dmp path or nodes.dmp path, string 
            2. ncbi name type ( string, e.g. 'scientific name' ) if the first arg is names.dmp otherwise none                           
 Function : parses the complete NCBI taxonomy
 

work

 Usage   : $NCBIParser->work ( $onto, $nodes, $names, $ncbi_ids )
 Returns : map of added terms { NCBI ID => OBO::Core::Term object }
 Args    :
           1. input ontology, OBO::Core::Ontology object
           2. ref to a hash { child_id => parent_id }
           3. ref to a hash { ncbi_id => scientific_name }
           4. parental ontology term for the root of the taxonomy, OBO::Core::Term object
           5. ref to a list of NCBI taxon ids ( \d+ )
                                        
 Function : adds NCBI taxonomy to the input ontology for the specified taxa
 

NAME

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

DESCRIPTION

This parser converts chosen parts of the NCBI taxonomy-tree into an OBO file. A taxon ID is given to the parser and the whole tree up to the root is reconstructed in the 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.

AUTHOR

Mikel Egana Aranguren and Vladimir Mironov

http://www.mikeleganaranguren.com, vladimir.n.mironov@gmail.com

COPYRIGHT AND LICENSE

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.