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

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ONTO-PERL/ONTO-PERL-1.41.tar.gz

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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.

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