Querying NCBI Entrez database fields using Ruby

Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example:

“9606”[Taxonomy ID]

to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query.

EInfo can return an XML file with this information. Ruby + Hpricot eats XML for breakfast. Here’s an example using the GEO Datasets (gds) database.


require 'rubygems'
require 'hpricot'
require 'open-uri'

doc = Hpricot(open("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gds"))

(doc/'//fieldlist/field').each do |f|
  puts "#{(f/'/name').inner_html},#{(f/'/fullname').inner_html},#{(f/'description').inner_html}"

And the first few lines of output:

ALL,All Fields,All terms from all searchable fields
UID,UID,Unique number assigned to publication
FILT,Filter,Limits the records
ORGN,Organism,exploded organism names
....24 more lines....

3 thoughts on “Querying NCBI Entrez database fields using Ruby

  1. Going the Ruby route I see! I wrote up the BioPerl EUtilities tools (Bio::DB::EUtilities, Bio::Tools::EUtilities) to run and parse this stuff (it doesn’t dive into Seq objects, you get raw data for now).

    Got a small HOWTO on it as well!

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