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Shuraski · 04-19-2010, 11:37 PM

Hi there,

Anyone have a preferred way to query a website like NCBI/Pubmed using CGI?

For example, using the gene_query.html form given in the book:

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>
Basic Web Form
</title>
</head>
<body>
<h1>
Basic Web Form Example
</h1>
<p>
Please enter a gene name and click 'Search' to get a report of information for a gene.
</p>
<form action="/cgi-bin/gene_query.pl" method="get">
<p>
Gene:
<input type="text" name="gene" size="15" />
<input type="submit" value="Search" />
<input type="reset" value="Clear" />
</p>
</form>
</body>
</html>

In gene_query.pl what is the best technique to search Pubmed for all articles involving this gene?

Thanks,
Shuraski

***Daz*** · 04-20-2010, 10:35 AM

Hi,

I would suggest looking into the 'Entres Utilities'. That's probably the best approach for automated queries against anything within the NCBI (such as pubmed).

Cheers,

Daz

LorenzoNuniz · 08-20-2011, 11:42 AM

A query string is the part of a URL which is attached to the end, after the file name. It begins with a question mark and usually includes information in pairs. The format is parameter=value.
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