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.
#!/usr/bin/ruby
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}"
end
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....
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!
cjfields
May 27, 2009 at 11:39 pm
Very nice write-up. BioRuby doesn’t handle EInfo too well yet, but does a good job with the rest of the EUtils.
nsaunders
May 27, 2009 at 11:50 pm
Nice tip – thanks!
I’ve written up a example using EInfo in Biopython,
http://news.open-bio.org/news/2009/06/ncbi-einfo-biopython/
Peter
June 22, 2009 at 8:37 pm