in the last few years , major advances have been made in the sequencing of genomes of the blood flukes of the genus schistosoma which causes chronic diseases in 200 million people globally ( 1 ) .
thus far , the focus has been on schistosoma 
  haematobium , schistosoma 
  japonicum and schistosoma 
  mansoni .
recently , s. haematobium had its genome sequenced ( 2 ) and published as well as a new and improved assembly of the first - sequenced schistosome genome , s. mansoni , was made available ( 3 ) .
the initial version of schistodb ( http://schistodb.net ) ( 4 ) was implemented to provide easy access and visualization of the s. mansoni genome and features ( 5 ) , integrated to other data types such as expressed sequence tags ( ests ) , proteins and metabolic pathways . in order to interrogate datasets from multiple genomes in a comprehensive manner ,
a new version of schistodb was developed as a resource for genomic data across the genus schistosoma .
this was done in partnership with the niaid - funded eukaryotic pathogen bioinformatics resource center ( http://eupathdb.org ) ( 6 ) .
this enhanced database uses the same database structural framework and uses the graphical strategies web development kit ( wdk ) search interface ( 7 ) .
it also provides a data - mining interface for the comparative and functional genomic data of three species of schistsomes and an integrated query system as part of the wdk and genomics unified schema database structure .
schistodb differs from other resources such as the wellcome trust sanger institute genedb ( http://genedb.org ) which has complementary data query or visualization tools but do not have the data - mining capabilities and broad cross - species comparisons which are possible using the wdk search interface .
data are currently obtained directly from providers at sequencing centers , genbank and associated functional data repositories .
the current release of schistodb contains the latest release of the genome sequence and annotation from s. haematobium ( 2 ) , s. japonicum ( 8) and s. mansoni ( 3 ) provided by the faculty of veterinary science at the university of melbourne , the chinese national human genome center and the wellcome trust sanger institute , respectively .
table 1.species in the current release of schistodbspeciesstraingenome size ( mb)number of genesreference 
 schistosoma haematobium 
 egypt38513  073(2 ) 
 schistosoma japonicum 
 anhui39712 
669(8 ) 
 schistosoma mansoni 
 puerto rico38012  871(3 ) 
  species in the current release of schistodb genomes and annotation in schistodb are processed through the same analysis pipeline , which provides additional data , including interpro domains ( 9 ) , gene ontology term association ( 10 ) , signal peptide predictions ( 11 ) , transmembrane domain predictions , open reading frame predictions , blast against the non - redundant genome database at the national center for bioinformatics , orthology prediction based on orthomcl ( 12 ) and synteny prediction .
the schistodb home page is virtually the same as all eupathdb pages , with differences only in color , logo and data content .
a visitor to these sites will first notice the home page layout , which has been designed to provide the user with convenient and immediate access to data and tools .
( i ) a top banner section , providing quick access back to the home page , gene i d and text searches , ( ii )  contact and login / registration links and ( iii ) mouse over menus ( figure 1a ) . the information and help menus on the left ( figure 1b ) .
the central section provides links to all searches ( figure 1c ) , and links to tools , such as blast ( 13 ) , the sequence retrieval tool and the generic model organism database genome browser ( 14 ) .
creating an account and logging in allows search strategies to be saved and shared , and gene associated annotation comments to be created which are linked to the author . 

( a ) the banner section present on all schistodb webpages provides links to registration , login , and contact us forms , i d and text searches , information and help , and all available searches and tools .
( b ) the side panel on the homepage provides expandable tabs that reveal links to a data summary table , community news items , links to community resources , web tutorials and additional information and help links .
( c ) the central portion of the home page includes all available searches and tools  gene - specific searches , searches against other data types such as genomic sequence , open reading frames and ests and tools , such as blast , sequence retrieval and the genome browser . 
 
( a ) the banner section present on all schistodb webpages provides links to registration , login , and contact us forms , i d and text searches , information and help , and all available searches and tools .
( b ) the side panel on the homepage provides expandable tabs that reveal links to a data summary table , community news items , links to community resources , web tutorials and additional information and help links .
( c ) the central portion of the home page includes all available searches and tools  gene - specific searches , searches against other data types such as genomic sequence , open reading frames and ests and tools , such as blast , sequence retrieval and the genome browser .
the search strategy system allows users to filter the results list based on a combined set of criteria and also add or sort columns . after running the first search ( figure 2 ) ,
steps in a strategy may be viewed , revised , renamed and developed further by nesting or deleted .
entire search strategies may be renamed , copied , saved and shared with a unique strategy url or deleted .
an example of a complex multi - step search strategy can be seen in figure 2 . using this strategy , for example , all secretory genes expressed in eggs
this is achieved by finding all genes with predicted secretory signal peptides and/or transmembrane domains ( steps 1 and 2 , figure 2 ) , and that have egg est libraries mapping evidence ( step 3 , figure 2 ) . as a final step ,
a transformation is applied on the results to identify all schistosoma orthologs of the results in step 3 ( step 4 , figure 2 ) since there are only egg est libraries for s. mansoni .
several options can be applied to a whole strategy including renaming , copying , saving , deleting and sharing .
the latter allows users to email colleagues a unique url of a strategy of interest , which enables the receiver to open and modify the strategy in their own workspace ( for example , the strategy in figure 2 can be accessed here : http://schistodb.net/schisto/im.do?s=ea7002f6e5b2996d ) . 

figure 2.screen shot of a search strategy with the first step being the results of running the search shown in figure 1c ( inset ) .
the results of any search are displayed in a dynamic table that allows removing , adding and moving columns , downloading results and adding results to the basket . 
 
screen shot of a search strategy with the first step being the results of running the search shown in figure 1c ( inset ) .
the results of any search are displayed in a dynamic table that allows removing , adding and moving columns , downloading results and adding results to the basket .
there is a range of features that allows users to bookmark their favorite genes for quick future access ; add genes to a basket in order to combine such gene set in later search ; add arbitrary weights to steps to obtain a ranked list or write comments to genes to improve its annotation .
data in schistodb are conveniently available for bulk download from the  data files section accessible from the 
the sequence retrieval tool , accessible from the tools section ( figure 1c ) , allows users to specify exact coordinates or lists of genes or proteins to be downloaded .
the schistodb home page is virtually the same as all eupathdb pages , with differences only in color , logo and data content .
a visitor to these sites will first notice the home page layout , which has been designed to provide the user with convenient and immediate access to data and tools .
( i ) a top banner section , providing quick access back to the home page , gene i d and text searches , ( ii )  contact and login / registration links and ( iii ) mouse over menus ( figure 1a ) . the information and help menus on the left ( figure 1b ) .
the central section provides links to all searches ( figure 1c ) , and links to tools , such as blast ( 13 ) , the sequence retrieval tool and the generic model organism database genome browser ( 14 ) .
creating an account and logging in allows search strategies to be saved and shared , and gene associated annotation comments to be created which are linked to the author . 

( a ) the banner section present on all schistodb webpages provides links to registration , login , and contact us forms , i d and text searches , information and help , and all available searches and tools .
( b ) the side panel on the homepage provides expandable tabs that reveal links to a data summary table , community news items , links to community resources , web tutorials and additional information and help links .
( c ) the central portion of the home page includes all available searches and tools  gene - specific searches , searches against other data types such as genomic sequence , open reading frames and ests and tools , such as blast , sequence retrieval and the genome browser . 
 
( a ) the banner section present on all schistodb webpages provides links to registration , login , and contact us forms , i d and text searches , information and help , and all available searches and tools .
( b ) the side panel on the homepage provides expandable tabs that reveal links to a data summary table , community news items , links to community resources , web tutorials and additional information and help links .
( c ) the central portion of the home page includes all available searches and tools  gene - specific searches , searches against other data types such as genomic sequence , open reading frames and ests and tools , such as blast , sequence retrieval and the genome browser .
the search strategy system allows users to filter the results list based on a combined set of criteria and also add or sort columns . after running the first search ( figure 2 ) ,
steps in a strategy may be viewed , revised , renamed and developed further by nesting or deleted .
entire search strategies may be renamed , copied , saved and shared with a unique strategy url or deleted .
an example of a complex multi - step search strategy can be seen in figure 2 . using this strategy , for example , all secretory genes expressed in eggs
this is achieved by finding all genes with predicted secretory signal peptides and/or transmembrane domains ( steps 1 and 2 , figure 2 ) , and that have egg est libraries mapping evidence ( step 3 , figure 2 ) . as a final step ,
a transformation is applied on the results to identify all schistosoma orthologs of the results in step 3 ( step 4 , figure 2 ) since there are only egg est libraries for s. mansoni .
several options can be applied to a whole strategy including renaming , copying , saving , deleting and sharing .
the latter allows users to email colleagues a unique url of a strategy of interest , which enables the receiver to open and modify the strategy in their own workspace ( for example , the strategy in figure 2 can be accessed here : http://schistodb.net/schisto/im.do?s=ea7002f6e5b2996d ) . 

figure 2.screen shot of a search strategy with the first step being the results of running the search shown in figure 1c ( inset ) .
the results of any search are displayed in a dynamic table that allows removing , adding and moving columns , downloading results and adding results to the basket . 
 
screen shot of a search strategy with the first step being the results of running the search shown in figure 1c ( inset ) .
the results of any search are displayed in a dynamic table that allows removing , adding and moving columns , downloading results and adding results to the basket .
there is a range of features that allows users to bookmark their favorite genes for quick future access ; add genes to a basket in order to combine such gene set in later search ; add arbitrary weights to steps to obtain a ranked list or write comments to genes to improve its annotation .
data in schistodb are conveniently available for bulk download from the  data files section accessible from the 
the sequence retrieval tool , accessible from the tools section ( figure 1c ) , allows users to specify exact coordinates or lists of genes or proteins to be downloaded .
national institutes of health ( nih)fogarty international center [ tw007012 - 03 ] ; the burroughs wellcome fund ( bwf ) ; cnpq [ 573839/2008 - 5 ] ; fapemig [ cbb-1181/08485/2009 , rede-56/11 ] and ec fp7 . funding for open access charge :
 the new release of schistodb ( http://schistodb.net ) provides a rich resource of genomic data for key blood flukes ( genus schistosoma ) which cause disease in hundreds of millions of people worldwide . 
 schistodb integrates whole - genome sequence and annotation of three species of the genus and provides enhanced bioinformatics analyses and data - mining tools . a simple , yet comprehensive web interface provided through the strategies web development kit is available for the mining and visualization of the data . 
 genomic scale data can be queried based on blast searches , annotation keywords and gene i d searches , gene ontology terms , sequence motifs , protein characteristics and phylogenetic relationships . 
 search strategies can be saved within a user s profile for future retrieval and may also be shared with other researchers using a unique web address . 
INTRODUCTION
CONTENTS OF THE CURRENT RELEASE
HOW TO USE SCHISTODB
The home page
Building a search strategy
Additional features
FUNDING