/
ontology_search.pl
executable file
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/
ontology_search.pl
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use Bio::OntologyIO;
use strict;
use Pod::Usage;
use Getopt::Long;
our $VERSION = '1.00';
our $LAST_CHANGED_DATE = '$LastChangedDate: 2014-04-022 (22nd, April, 2014) $';
our ($help, $man, $is_phenotype, $ontology_file, $format, $if_exact_match);
GetOptions('help|h'=>\$help, 'man|m' => \$man, 'phenotype|p' => \$is_phenotype,
'ontology_file|o=s'=>\$ontology_file, 'format|f=s' => \$format,
'exact'=>\$if_exact_match);
$help and pod2usage (-verbose=>1, -exitval=>1, -output=>\*STDOUT);
$man and pod2usage (-verbose=>2, -exitval=>1, -output=>\*STDOUT);
@ARGV or pod2usage (" ERROR: Please enter disease names!!");
@ARGV == 1 or pod2usage (" ERROR: too many input arguments");
$ontology_file||="./lib/hpo.obo" if ($is_phenotype); #Phenotype input
$ontology_file||="./lib/doid.obo" if (not $is_phenotype); #Disease input
$format ||= "name";
my $parser = Bio::OntologyIO->new ( -format => "obo",
-file => $ontology_file );
#Enter the input term
my $input_term = $ARGV[0];
my $query_term = $input_term;
$query_term =~ s/'s\b//g;
$query_term =~ s/\W+/ /g;
my $ont = $parser->next_ontology();
my $is_a = Bio::Ontology::RelationshipType->get_instance("IS_A");
my @roots = $ont->get_root_terms();
my @all_terms = $ont->get_descendant_terms($roots[0], $is_a);
unshift @all_terms, @roots;
my %found_terms = ();
for my $term ( @all_terms )
{
my $id = $term -> identifier();
next if $found_terms{$id};
my $name = $term-> name();
my @synonyms = $term -> get_synonyms();
my @search_list = ($name, @synonyms);
my $id_num = $id;
$id_num=~s/HP://;
if("hpo $id_num" eq $input_term or "hp $id_num" eq $input_term) {
$found_terms{$id} = $term;
}
else{
for my $each_name (@search_list){
my $each_name_change = $each_name;
$each_name_change =~ s/'s\b//g;
$each_name_change =~ s/\W+/ /g;
if( $each_name_change =~ /\b$query_term\b/i )
{
next if($if_exact_match and $each_name !~ /^$input_term$/i);
$found_terms{$id} = $term;
last;
}
}
}
if ($found_terms{$id}) #If the term is matched in this turn, then find its descendants
{
$format=~ /\bid\b/ and print $id."\n";
if($format=~/\bname\b/)
{
for (@search_list)
{
s/^(.*?)\s[A-Z]{4,}.*$/\1/;
print $_."\n" ;
}
}
my @descendant_terms = $ont->get_descendant_terms($found_terms{$id}, $is_a);
for my $descendant (@descendant_terms)
{
my $descendant_id = $descendant -> identifier();
next if ($found_terms{$descendant_id});
$name = $descendant -> name();
@synonyms = $descendant -> get_synonyms();
@search_list = ($name, @synonyms);
$found_terms{$descendant_id} = $descendant;
$format=~ /\bid\b/ and print $descendant_id."\n";
if($format=~/\bname\b/)
{
for (@search_list)
{
s/^(.*?)\s[A-Z]{4,}.*$/\1/;
print $_."\n" ;
}
}
}
}
}
=head1 SYNOPSIS
ontology_search.pl [arguments] <disease_term or phenotype_term>
Optional arguments:
-h, --help print help message
-m, --man print complete documentation
-p, --phenotype the term is a phenotype term
-o, --ontology_file <string> the ontology file (default:disease_ontology,
./lib/hpo.obo for phenotype and ./lib/doid.obo for disease)
-f, --format <string> the output format, 'name' or 'id' (default:name)
Function:
automatically match the term into a disease or phenotype term in the HPO or DO Database, then found
their descendants and then print all the names and synonyms, and ids.
Example:
perl ontology_search.pl alzheimer -format name,id