NAME

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

DESCRIPTION

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.

AUTHOR

Mikel Egana Aranguren

http://www.mikeleganaranguren.com

eganaarm@cs.man.ac.uk

COPYRIGHT AND LICENSE

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.

work

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

To install OBO::Core::Def, copy and paste the appropriate command in to your terminal.

cpanm

cpanm OBO::Core::Def

CPAN shell

perl -MCPAN -e shell
install OBO::Core::Def

For more information on module installation, please visit the detailed CPAN module installation guide.

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NAME

DESCRIPTION

AUTHOR

COPYRIGHT AND LICENSE

work

Module Install Instructions