DAVID is one of the well known gene enrichment analysis service provider(free for academic clients). Recently, they  provided new web service, which can give user more power to automatically do gene enrichment analysis through their SOAP or WSDL .

Current limitation for this service is:

”

A job with more than 3000 genes to generate gene or term cluster report will not be handled by DAVID due to resource limit.
No more than 200 jobs in a day from one user or computer.
DAVID Team reserves right to suspend any improper uses of the web service without notice.

”

Here is the ruby scripts to use this servie:

requirement: savon  (gem install savon)

#!/usr/bin/env ruby
# This content is released under MIT License
# copyright (c) 2012 Gangcai Xie <www.biodm.com>
require 'savon'
url="http://david.abcc.ncifcrf.gov/webservice/services/DAVIDWebService?wsdl"
client=Savon.client(url)
#get all possible WSDL actions
client.wsdl.soap_actions

#run the WSDL action request with parameters
response=client.request :authenticate do
	soap.body={
		:email=>'user@example.com' #your email address
	}
end

inputIds ='31741_at,31734_at,32696_at,37559_at,41400_at,35985_at,39304_g_at,41438_at,35067_at,32919_at,35429_at,36674_at,967_g_at,36669_at,39242_at,39573_at,39407_at,33346_r_at,40319_at,2043_s_at,1788_s_at,36651_at,41788_i_at,35595_at,36285_at,39586_at,35160_at,39424_at,36865_at,2004_at,36728_at,37218_at,40347_at,36226_r_at,33012_at,37906_at,32872_at,989_at,32718_at,36957_at,32645_at,37628_at,33825_at,35687_at,32779_s_at,34493_at,31564_at,887_at,34712_at,32897_at,34294_at,41365_at,41446_f_at,34375_at,875_g_at,41099_at,919_at,38970_s_at,39159_at,34184_at,1018_at,38032_at,35956_s_at,35536_at,34562_at,1867_at,35957_at,39519_at,41657_at,38491_at,652_g_at,35776_at,34989_at,33455_at,39950_at,37723_at,31977_at,38629_at,34581_s_at,36210_g_at,35120_at,41532_at,37889_at,1332_f_at,40540_at,41105_s_at,1919_at,37542_at,39698_at,36711_at,36809_at,1167_s_at,31648_at,32364_at,40792_s_at,38685_at,41358_at,32931_at,35294_at,39870_at,38654_at,257_at,39071_at,35606_at,41726_at,33094_s_at,32405_at,1432_s_at,33698_at,408_at,39748_at,1953_at,36100_at,36101_s_at,1372_at,35314_at,40790_at,2030_at,179_at,1852_at,259_s_at,38024_at,35376_f_at,41779_at,39232_at,41159_at,40365_at,31626_i_at,40385_at,35613_at,37506_at,38207_at,887_at,600_at,1461_at,38691_s_at,1267_at,1177_at,1125_s_at,2036_s_at,31615_i_at,37283_at,40954_at,31758_at,36960_at,33143_s_at,37048_at,38538_at,1005_at,34963_at,39408_at,32464_at,706_at,1276_g_at,164_at,41445_at,40735_at,1891_at,1258_s_at,40856_at,1911_s_at,31562_at,32359_at,274_at,1804_at,41387_r_at,848_at,41499_at,39448_r_at,34537_at,36459_at,35500_at,37139_at,612_s_at,32133_at,39757_at,37629_at,38463_s_at,568_at,749_at,1939_at,38018_g_at,1857_at,32699_s_at,40661_at,1994_at,38373_g_at,33893_r_at,1388_g_at,35345_at,1385_at,36615_at,1263_at,37385_at,1774_at,37233_at,39753_at,32626_at,35915_at,35714_at,31669_s_at,36519_at,40473_at,1750_at,33751_at,37831_at,35472_at,41825_at,34666_at,35471_g_at,31888_s_at,37722_s_at,35414_s_at,39750_at,35726_at,37662_at,33802_at,352_at,31737_at,37938_at,36161_at,31558_at,34475_at,37223_at,38953_at,37857_at,189_s_at,41169_at,33092_at,38660_at,40895_g_at,37146_at,1936_s_at,38860_at,40210_at,41180_i_at,31586_f_at,33366_at,31521_f_at,762_f_at,1124_at,36009_at,41111_at,36749_at,37310_at,31522_f_at,35768_at,39421_at,39967_at,35992_at,38356_at,39331_at,34145_at,35378_at,199_s_at,35966_at,1866_g_at,37377_i_at,37378_r_at,833_at,31586_f_at,38062_at,34981_at,1569_r_at,1548_s_at,41446_f_at,36999_at,34226_at,33385_g_at,36173_r_at,1007_s_at,35149_at,38671_at,1973_s_at,37724_at,37317_at,33829_at,36532_at,39372_at,41717_at,38221_at,37418_at,33120_at,136_at,33492_at,1602_at,41505_r_at,41736_g_at,37862_at,31859_at,40913_at,35956_s_at,32193_at,1148_s_at,1244_at,38684_at,37440_at,32186_at,1242_at,39503_s_at,224_at,38374_at,36018_at,36603_at,33288_i_at,33662_at,33555_at,33539_at,430_at,471_f_at,1369_s_at,35372_r_at,38089_at,40310_at,41106_at,41216_r_at,32815_at,37463_r_at,33470_at,40522_at,1463_at,1743_s_at,1895_at,32583_at,35440_g_at,1091_at'
idType = 'AFFYMETRIX_3PRIME_IVT_ID'
listName = 'make_up'
listType = 0

response=client.request :addList do
   soap.body={
   :inputid=>inputIds,
   :idtype=>idType,
   :listname=>listName,
   :listtype=>listType
   }
end

response=client.request :getDefaultCategoryNames
#response.body[:get_default_category_names_response][:return]

thd=0.1 #threshold
count = 2
chart=client.request :getChartReport do
  soap.body={
    :pvalue=>thd,
    :count=>count
  }
end

#chart_return=chart.body[:get_chart_report_response][:return] #old way

chart_return=chart.to_hash[:get_chart_report_response][:return] # return is an array



#each item is a hash with keys: [:ease_bonferroni, :afdr, :benjamini, :bonferroni, 
# :category_name, :ease, :fisher, :fold_enrichment, :gene_ids, :id, :list_hits, 
# :list_name, :list_totals, :percent, :pop_hits, :pop_totals, :rfdr, :scores, :term_name, :"@xmlns:xsi", :"@xsi:type"]

choose_types=[:term_name,:category_name,:list_hits,:fold_enrichment,:ease,:bonferroni,:gene_ids]
type_new_names=%w(Term_Name Category Hits EnrichFold Pvalue Bonferroni Hits_Genes)
#output the result

outfile=File.new("test.tsv","w")
outfile.puts type_new_names.join("\t")
chart_return.each do |item|
  values=choose_types.collect{|type| item[type]}
  outfile.puts values.join("\t")
end
outfile.close