mirror of
https://github.com/krislamo/puppet-pubcrawler
synced 2024-11-10 01:40:35 +00:00
491 lines
16 KiB
Puppet
491 lines
16 KiB
Puppet
# Default parameters for Pubcrawler
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class pubcrawler::params {
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$bgcolor = '#fff'
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$header_icon = ''
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$viewdays = '14'
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$relentrezdate = '90'
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$getmax = '800'
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$fullmax = '500'
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$include_config = 'no'
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$search_URL = ''
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$neighbour_URL = ''
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$retrieve_URL = ''
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$extra_range = '1000'
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$check = '0'
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$prompt = '1'
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$verbose = '0'
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$mute = '0'
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$log_file = ''
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$base_URL = 'local_file'
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$mail_features = 'all'
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$lynx = ''
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$prefix = ''
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$system = ''
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$proxy_port = ''
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$proxy_auth = ''
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$proxy_pass = ''
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$time_out = '180'
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$test_URL = 'http://www.ncbi.nlm.nih.gov/'
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$no_test = '0'
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$indent = '125'
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$no_decap = ''
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$spacer = ''
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$searches = undef
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# override some of the above defaults in hash form to make
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# configurations specific for a site.
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$site_specific_params = {
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'AmoebaDB' => {
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bgcolor => '#C8C5A2',
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header_icon => '/a/images/AmoebaDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Acanthamoeba',
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term => 'Acanthamoeba [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Acanthamoeba',
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term => 'Acanthamoeba [ALL]',
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},
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],
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},
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'CryptoDB' => {
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bgcolor => '#ffcccc',
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header_icon => '/a/images/CryptoDB/title_s.png',
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searches => [
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. parvum',
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term => 'Cryptosporidium parvum [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. hominis',
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term => 'Cryptosporidium hominis [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. muris',
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term => 'Cryptosporidium muris [ORGN]',
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},
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],
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},
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'EuPathDB' => {
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bgcolor => '#507494',
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header_icon => '/a/images/EuPathDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Cryptosporidium',
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term => 'Cryptosporidium [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Encephalitozoon or Enterocytozoon',
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term => 'Enterocytozoon [ALL] or Encephalitozoon [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Giardia',
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term => 'Giardia [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Microsporidia',
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term => 'Edhazardia [ALL] OR Encephalitozoon [ALL] OR Enterocytozoon [ALL] OR Hamiltosporidium [ALL] OR Nematocida [ALL] OR Nosema [ALL] OR Vavraia [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Piroplasma genera',
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term => 'Anthemosoma [ALL] OR Babesia [ALL] OR Cristalloidophora [ALL] OR Dactylosoma [ALL] OR Echinozoon [ALL] OR Haemohormidium [ALL] OR Sauroplasma [ALL] OR Theileria [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Plasmodium',
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term => 'Plasmodium [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Toxoplasma or Eimeria or Neospora',
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term => 'Toxoplasma [ALL] or Eimeria [ALL] or Neospora [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Trichomonas',
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term => 'Trichomonas [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on other Apicomplexan organisms',
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term => 'Apicomplexa OR Apicomplexan OR Eimeria OR Gregarina OR Neospora OR Sarcocystis OR Theileria NOT Cryptosporidium NOT Plasmodium NOT Toxoplasma [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Leishmania or Trypanosoma or Crithidia',
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term => 'Trypanosoma [ALL] or Leishmania [ALL] or Crithidia [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Cryptosporidium',
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term => 'Cryptosporidium [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Giardia',
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term => 'Giardia [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Microsporidia',
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term => 'Edhazardia [ORGN] OR Encephalitozoon [ORGN] OR Enterocytozoon [ORGN] OR Hamiltosporidium [ORGN] OR Nematocida [ORGN] OR Nosema [ORGN] OR Vavraia [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Piroplasma genera',
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term => 'Anthemosoma OR Babesia OR Cristalloidophora OR Dactylosoma OR Echinozoon OR Haemohormidium OR Sauroplasma OR Theileria [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Plasmodium',
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term => 'Plasmodium [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Toxoplasma',
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term => 'Toxoplasma [ORGN] or Eimeria [ORGN] or Neospora [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Trichomonas',
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term => 'Trichomonas [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for other Apicomplexan organisms',
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term => 'Apicomplexa NOT Toxoplasma NOT Plasmodium NOT Cryptosporidium [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Leishmania or Trypanosoma or Crithidia',
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term => 'Leishmania [ORGN] or Trypanosoma [ORGN] or Crithidia [ORGN]',
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},
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],
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},
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'FungiDB' => {
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bgcolor => '#cd919e',
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header_icon => '/a/images/FungiDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Aspergillus or Candida or Coccidioides or Cryptococcus or Fusarium or Gibberella or Magnaporthe or Neurospora or Puccinia or Rhizopus or Saccharomyces',
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term => 'Aspergillus [ALL] or Candida [ALL] or Coccidioides [ALL] or Cryptococcus [ALL] or Fusarium [ALL] or Gibberella [ALL] or Magnaporthe [ALL] or Neurospora [ALL] or Puccinia [ALL] or Rhizopus [ALL] or Saccharomyces [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Aspergillus or Candida or Coccidioides or Cryptococcus or Fusarium or Gibberella or Magnaporthe or Neurospora or Puccinia or Rhizopus or Saccharomyces',
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term => 'Aspergillus [ORGN] or Candida [ORGN] or Coccidioides [ORGN] or Cryptococcus [ORGN] or Fusarium [ORGN] or Gibberella [ORGN] or Magnaporthe [ORGN] or Neurospora [ORGN] or Puccinia [ORGN] or Rhizopus [ORGN] or Saccharomyces [ORGN]',
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},
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],
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},
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'GiardiaDB' => {
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bgcolor => '#993333',
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header_icon => '/a/images/GiardiaDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Giardia',
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term => 'Giardia [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Giardia',
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term => 'Giardia [ORGN]',
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},
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],
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},
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'HostDB' => {
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bgcolor => '#e08265',
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header_icon => '/a/images/HostDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on host parasite interaction',
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term => 'host parasite interaction [ALL]',
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},
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],
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},
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'MicrosporidiaDB' => {
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bgcolor => '#C4BAD3',
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header_icon => '/a/images/MicrosporidiaDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Microsporidia',
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term => 'Edhazardia [ALL] OR Encephalitozoon [ALL] OR Enterocytozoon [ALL] OR Hamiltosporidium [ALL] OR Nematocida [ALL] OR Nosema [ALL] OR Vavraia [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Microsporidia',
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term => 'Edhazardia [ORGN] OR Encephalitozoon [ORGN] OR Enterocytozoon [ORGN] OR Hamiltosporidium [ORGN] OR Nematocida [ORGN] OR Nosema [ORGN] OR Vavraia [ORGN] or Anncaliia [ORGN] or Vittaforma [ORGN]',
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},
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],
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},
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'PiroplasmaDB' => {
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bgcolor => '#e08265',
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header_icon => '/a/images/PiroplasmaDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Piroplasma genera',
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term => 'Anthemosoma [ALL] OR Babesia [ALL] OR Cristalloidophora [ALL] OR Dactylosoma [ALL] OR Echinozoon [ALL] OR Haemohormidium [ALL] OR Sauroplasma [ALL] OR Theileria [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Piroplasma genera',
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term => 'Anthemosoma [ORGN] OR [ORGN] Babesia [ORGN] OR Cristalloidophora [ORGN] OR Dactylosoma [ORGN] OR Echinozoon [ORGN] OR Haemohormidium [ORGN] OR Sauroplasma [ORGN] OR Theileria [ORGN]',
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},
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],
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},
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'PlasmoDB' => {
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bgcolor => '#bbaacc',
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header_icon => '/a/images/PlasmoDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Plasmodium',
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term => 'Plasmodium [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Plasmodium',
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term => 'Plasmodium [ORGN]',
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},
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],
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},
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'SchistoDB' => {
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bgcolor => '#cd919e',
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header_icon => '/a/images/SchistoDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles related to Schistosoma',
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term => 'Schistosoma [ALL] or schistosoma [ALL] or blood-fluke [ALL] or Schistosomatidae [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Schistosoma',
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term => 'Schistosoma [ORGN]',
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},
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],
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},
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'ToxoDB' => {
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bgcolor => '#cd919e',
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header_icon => '/a/images/ToxoDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Toxoplasma',
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term => 'Toxoplasma [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Eimeria',
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term => 'Eimeria [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Eimeria',
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term => 'Gregarina [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Neospora',
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term => 'Neospora [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Toxoplasma, Eimeria, or Neospora',
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term => 'Toxoplasma [ORGN] or Eimeria [ORGN] or Neospora [ORGN] or Gregarina [ORGN]',
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},
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],
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},
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'TrichDB' => {
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bgcolor => '#993333',
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header_icon => '/a/images/TrichDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Trichomonas',
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term => 'Trichomonas [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Trichomonas',
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term => 'Trichomonas [ORGN]',
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},
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],
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},
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'TriTrypDB' => {
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bgcolor => '#dfbba6',
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header_icon => '/a/images/TriTrypDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Trypanosoma',
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term => 'Trypanosoma [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Leishmania',
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term => 'Leishmania [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Crithidia',
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term => 'Crithidia [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Endotrypanum',
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term => 'Endotrypanum [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Trypanosoma',
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term => 'Trypanosoma [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Crithidia',
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term => 'Crithidia [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Endotrypanum',
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term => 'Endotrypanum [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Leishmania',
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term => 'Leishmania [ORGN]',
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},
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],
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},
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'VectorBase' => {
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bgcolor => '#6ea05f',
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header_icon => '/a/images/VEuPathDB/Logos-color-text-web/vectorbase.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Diptera',
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term => 'Diptera [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Gastropoda',
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term => 'Gastropoda [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Hemiptera',
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term => 'Hemiptera [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Ixodida',
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term => 'Ixodida [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Phthiraptera',
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term => 'Phthiraptera [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Sarcoptiformes',
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term => 'Sarcoptiformes [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Trombidiformes',
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term => 'Trombidiformes [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Diptera',
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term => 'Diptera [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Gastropoda',
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term => 'Gastropoda [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Hemiptera',
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term => 'Hemiptera [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Ixodida',
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term => 'Ixodida [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Phthiraptera',
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term => 'Phthiraptera [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Sarcoptiformes',
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term => 'Sarcoptiformes [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Trombidiformes',
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term => 'Trombidiformes [ORGN]',
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}
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],
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},
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}
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}
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