File Coverage

blib/lib/OBO/APO/NCBIToRDF.pm

Criterion	Covered	Total	%
statement	78	78	100.0
branch	8	12	66.6
condition			n/a
subroutine	8	8	100.0
pod	2	3	66.6
total	96	101	95.0

package OBO::APO::NCBIToRDF;

=head1 NAME

OBO::APO::NCBIToRDF - A NCBI taxonomy dump to RDF converter.

=head1 DESCRIPTION

Converts NCBI taxonomy dump files (names and nodes) to a RDF graph.

NCBI taxonomy dump files files can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/

The method 'work' gets the nodes file, the names file, and file handler for the RDF graph.

=head1 AUTHOR

Mikel Egana Aranguren
[e-mail]

=head1 COPYRIGHT AND LICENSE

Copyright (c) 2008 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.

=cut

use strict;
use warnings;
use Carp;

use open qw(:std :utf8); # Make All I/O Default to UTF-8

sub new {
	my $class                   = shift;
	my $self                    = {};

	bless ($self, $class);
	return $self;
}

=head2 work

  Usage    - $NCBIToRDF->work($NCBINodesFilePath,$NCBINamesFilePath,$RDF_file_handler)
  Returns  - RDF file handler
  Args     - The paths to the NCBI nodes and names files and a file handler for the new RDF file
  Function - Converts NCBI nodes and NCBI names to an RDF graph.

=cut
#vlmir
# Argumenents
# 1. Full path to the names.dmp file
# 2. Full path to the nodes.dmp file
# 3. File handle for writing RDF
# 4. base URI (e.g. 'http://www.semantic-systems-biology.org/')
# 5. name space (e.g. 'SSB')
#vlmir

sub work {


	my $self = shift;

# 	TODO: have a thorough look into: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt

	# Get the arguments
	# my ($NCBInodesFileName,$NCBInamesFileName,$file_handle ) = @_;
	my ($NCBInamesFileName,$NCBInodesFileName, $file_handle, $base, $namespace ) = @_; #vlmir

	# For the ID
# 	$path_to_assoc_file =~ /.*\/(.*)/; # get what is after the slash in the path...
# 	my $f_name = $1;
# 	(my $prefix_id = $f_name) =~ s/\.goa//;
# 	$prefix_id =~ s/\./_/g;

	# TODO: set all the NS and URI via arguments
	# my $default_URL = "http://www.semantic-systems-biology.org/";
	my $default_URL = $base; #vlmir
	my $NS = $namespace; #vlmir
	my $ns = lc ($NS);
	my $rdf_subnamespace = "taxon";

	my $obo_ns     = $default_URL.$NS."#"; #$default_URL."OBO#";
	my $ncbi_ns    = $default_URL.$NS."#"; #$default_URL."NCBI#";

	# Preamble of RDF file
	print $file_handle "\n";
	print $file_handle "
	print $file_handle "\txmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n";
	print $file_handle "\txmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n";
	print $file_handle "\txmlns:".$ns."=\"".$ncbi_ns."\">\n";
	#print $file_handle "\txmlns:obo=\"".$obo_ns."\">\n";

	my %nodes = ();
	my %names = ();

	# Open and parse names file (we want groups 1 and 2 only if group 4 is scientific name)
	open(NCBInamesFile, $NCBInamesFileName) || croak("can't open file: $!");
	my @mynamelines = ;
	foreach my $theline (@mynamelines){
		if ($theline =~ /(.+)\|(.+)\|(.+)\|(.+)\|/){
			my $childid = $1;
			my $childname = $2;
			my $nametype = $4;
			$childid =~ s/\s//g;
			$nametype =~ s/\s//g;
			if($nametype eq 'scientificname'){
				$childname =~ s/^\s+//;
				$childname =~ s/\s+$//;
				$names{$childid} = $childname;
			}
		}
	}
	close(NCBInamesFile);

	# Open and parse the nodes file
	open(NCBInodesFile, $NCBInodesFileName) || croak("can't open file: $!");
	my @mynodelines =;
	foreach my $theline (@mynodelines){
		if ($theline =~ /(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|(.+)\|/){
			my $child = $1;
			my $parent = $2;
			my $rank = $3;
			$child =~ s/\s//g;
			$parent =~ s/\s//g;
			$rank =~ s/\s//g;
			$nodes{$child} = $parent;
			print $file_handle "\t<",$ns,":".$rdf_subnamespace." rdf:about=\"#"."NCBI"."_".$child."\">\n";
			print $file_handle "\t\t".&char_hex_http($names{$child})."\n";
			print $file_handle "\t\t<".$ns.":name xml:lang=\"en\">".&char_hex_http($names{$child})."\n";
			print $file_handle "\t\t<".$ns.":rank>".&char_hex_http($rank)."\n";

			unless ($child eq "1"){
				print $file_handle "\t\t<".$ns.":is_a rdf:resource=\"#"."NCBI"."_".$parent."\"/>\n";
			}

			print $file_handle "\t\n";
		}
	}
	close(NCBInodesFile);

	print $file_handle "\n\n";
	print $file_handle "";

	return $file_handle;
}

sub __date {
	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
	my $result = sprintf "%02d:%02d:%4d %02d:%02d", $mday,$mon+1,$year+1900,$hour,$min; # e.g. 11:05:2008 12:52
}

=head2 char_hex_http

  Usage    - $ontology->char_hex_http($seq)
  Returns  - the sequence with the hexadecimal representation for the http special characters
  Args     - the sequence of characters
  Function - Transforms a http character to its equivalent one in hexadecimal. E.g. : -> %3A

=cut


sub char_hex_http {
	$_[0] =~ s/:/%3A/g;
	$_[0] =~ s/;/%3B/g;
	$_[0] =~ s/
	$_[0] =~ s/=/%3D/g;
	$_[0] =~ s/>/%3E/g;
	$_[0] =~ s/\?/%3F/g;

#number sign                    #     23   # --> #   #      --> #
#dollar sign                    $     24   $ --> $   $   --> $
#percent sign                   %     25   % --> %   %   --> %

	$_[0] =~ s/\//%2F/g;
	$_[0] =~ s/&/%26/g;

	return $_[0];
}
1;