Approaches to Web Development for Bioinformatics

Medical Computing > Web Development for Bioinformatics > Public Databases > NCBI Databases, Gene Information

NCBI Databases

Data from the Entrez Gene database can be downloaded in bulk using FTP. It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq.

Gene Information

The file gene_info contains

NCBI Taxonomy unique identifier
the unique identifier for the gene
the default symbol for the gene
the LocusTag value
a bar-delimited set of unofficial symbols for the gene
a bar-delimited set of identifiers in other databases
the chromosome on which this gene is placed
the map location for this gene
a descriptive name for this gene
the type assigned to the gene
other nomenclature information

The file is large. The file from 5/11/2006 was 171 MB uncompressed. It contains gene data for all organisms where genetic data has been submitted to the NCBI. A small section of the file is here. To extract the human genetic data from this file this Perl script may be used.

Perl

#!/usr/bin/perl -w
# A Perl script to extract human gene data from the gene_info file
# param 1 file to extract data from
my $i = 0;
while (<>) {

if ($_ =~ /^9606.*/) {

print($_);
$i++;

}

}
print "Lines written $i.\n";

The program works by copying any line starting with the taxonomic id for Homo sapiens (9606). The output should be redirected to a file, as in

Program output

>extract_human.pl gene_info > output.txt

The file downloaded on 5/11/2006 there were 39,256 entries and the output file size was over 5 MB, easily small enough to open in a text editor such as emacs.

The genes in the file are named by registration with Human Genome Organization (HUGO) Gene Nomenclature Committee²⁶, which has a similar download file.

The Perl program below looks for a regular expression on the command line and parses the different fields for matching lines in the gene_info file.

Perl

#!/usr/bin/perl -w
# A Perl script to query human gene_info data file
# param 0 is the name of the file to search
# param 1 is the expression to search for

$file = $ARGV[0];
print "Searching for $ARGV[1] in file $file.\n";
my $exp = $ARGV[1];

# open file for reading and iterate over lines
open GENE_FILE, "<", $file;
while (<GENE_FILE>) {

if (/$exp/) {

print;

# Parse individual fields
my @fields = split "\t";
print

"Fields: \n",
"\tTaxonmoic ID: $fields[0]\n",
"\tGene ID: $fields[1]\n",
"\tGene Symbol: $fields[2]\n",
"\tLocus Tag: $fields[3]\n",
"\tSynonyms: $fields[4]\n",
"\tdbXrefs: $fields[5]\n",
"\tchromosome: $fields[6]\n",
"\tmapLocation: $fields[7]\n",
"\tdescription: $fields[8]\n";

}

When run on the file extracted from gene_info with the target expression SCN3A the result is

Program output

>query_gene_info.pl human_gene_info.txt SCN3A
Searching for SCN3A in file human_gene_info.txt.
9606 6328 SCN3A - NAC3 HGNC:10590|MIM:182391|HPRD:01671 2 2q24 sodium channel, voltage-gated, type III, alpha protein-coding SCN3A sodium channel, voltage-gated, type III, alpha O
Fields:

Taxonmoic ID: 9606
Gene ID: 6328
Gene Symbol: SCN3A
Locus Tag: -
Synonyms: NAC3
dbXrefs: HGNC:10590|MIM:182391|HPRD:01671
chromosome: 2
mapLocation: 2q24
description: sodium channel, voltage-gated, type III, alpha protein-coding SCN3A sodium channel, voltage-gated, type III, alpha

where query_gene_info.pl is the name of the script.

The web page for searching the gene information database on this site - Search Human Gene Information Database - was constructed based on these principles.

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