Approaches to Web Development for Bioinformatics

Medical Computing > Web Development for Bioinformatics > Public Databases > NCBI > Web Services

Web Services

NCBI also provides programmatic access to its databases via web services. The Entrez EUtilities service² is included within in this. Here is an example of a Perl program that performs a query from the NCBI PubMed database for terms matching 'Huntington'.

#!/usr/bin/perl
# CGI Program to test searching PubMed with NCBI Entrez EUtilities
use LWP::Simple;

# Print header
print "Content-type: text/plain\n\n";

# Perform query
my $url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/$utils/esearch.fcgi?db=Pubmed&retmax=1&usehistory=y&term=Huntington";
my $esearch_result = get($url);

# Print result
print "\nESEARCH RESULT: $esearch_result\n";

The program makes use of the LWP::simple module, which makes HTTP requests in the same way a browser does. The program uses the get() function to query PubMed for the term 'Huntingon' and prints out the results. The output of the program is

ESEARCH RESULT:
<?xml version="1.0"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN"

"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">

<Count>9201</Count>
<RetMax>1</RetMax>
<RetStart>0</RetStart>
<QueryKey>1</QueryKey>
<WebEnv>0Va6QU_UfRhO7-lRqJepWjj701QentQrMpyEGfWUCE2C-Uf_xmzOAQ@vJV1gIIOFpQAAFj-QskAAAAI</WebEnv>
<IdList>

</IdList>
<TranslationSet> </TranslationSet>
<TranslationStack>

<Term>Huntington[All Fields]</Term>
<Field>All Fields</Field>
<Count>9212</Count>
<Explode>Y</Explode>

</TermSet>
<OP>GROUP</OP>

</TranslationStack>

</eSearchResult>

This XML response can be parsed with an XML parser. See CPAN for details on Perl XML parsing or Introduction to Extensible Markup Language for Chemistry and Biosciences for details on working with XML in Java.

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