the phylum apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera cryptosporidium , plasmodium and toxoplasma . multiple species of plasmodium are capable of causing malaria in humans , a leading cause of morbidity and mortality in developing countries ( 1 ) . cryptosporidium causes a severe and chronic diarrheal disease that may be life threatening in immunocompromised patients ( 2 ) . toxoplasma gondii infections , although typically asymptomatic in healthy individuals , may lead to congenital birth defects and encephalitis in hiv / aids patients ( 3 ) . human infections with t.gondii may be acquired from food or soil contamination and infections with cryptosporidium parvum from soil and water contamination . due to the potential threat to public health from intentional dispersal into the population , t.gondii and the research communities for cryptosporidium , plasmodium and toxoplasma have benefited from the bioinformatics resources provided by the distinct online genome databases cryptodb ( 4 ) , plasmodb ( 5 ) and toxodb ( 6 ) , respectively ( see supplementary material ) . because of the phylogenetic relationship of these human pathogens , ( all are included in the phylum apicomplexa , along with the prominent animal pathogens , babesia , theileria and eimeria ) comparative genomic and proteomic studies across these species is critical for expediting discovery of therapeutic targets , increasing understanding of parasite biology and enhancing other areas of research on the biology of these organisms . however , the researcher 's ability to perform comparative studies utilizing multiple data sources has been tempered by the difficulty of managing and collating the data from the existing disparate resource databases . here we describe the online apicomplexan bioinformatics resource center ( brc ) , apidb ( ) , which has been established to provide researchers centralized , integrated access to experimental and computational data , as well as tools to facilitate comparative research . database integration is accomplished via a combination of federation and link integration technologies ( 7 ) . link integration allows researchers to begin their query with one data source and then follow hypertext links to related information in other data sources . database federation is achieved by decomposing distributed queries into component queries and executing these queries in the source databases , delivering the results into a uniform format . it leaves the information in its source databases but builds an environment around the databases that makes them all seem part of one large system . in apidb 2.0 the federation has been implemented using oracle dblink technology . in order to handle heterogeneous data sources in the future we are studying other federation approaches , such as java database connectivity ( jdbc ) ( ) and web services ( ws ) ( ) . genome data from other apicomplexan parasites are also integrated . in its current release , apidb 2.0 offers an initial set of queries that enable gene searches of the three component databases by a variety of criteria such as text keywords , enzyme commission ( ec ) number gene ontology ( 8) assignments , and pfam ( 9 ) terms . in addition , apidb offers tools to blast ( 10 ) all public apicomplexan data , access to the multi - species gene orthology database orthomcl db ( 11 ) and access to kegg ( 12 ) metabolic pathway maps with the datasets available in apidb include the component databases ( cryptodb , plasmodb and toxodb ) , apicomplexan genomic sequences for other species ( theileria annulata and theileria parva ) obtained from the ncbi genbank ( 13 ) and genedb ( 14 ) , a collection of clustered apicomplexan ests including : eimeria , gregarina , neospora , sarcocystis and theileria called apidots [ a newer version of apiest - db ( 15 ) ] and unclustered ests from the ncbi genbank division , dbest . the apidb web interface shares its architecture and  look and feel with the component sites ( cryptodb , plasmodb and toxodb ) . the user can interact with four areas on the main page : the sidebar , a tools section , a query section and a menu bar ( figure 1a ) . the sidebar gives the user access to apicomplexan community resources , from our project 's most recent news to pubcrawler ( 16 ) and external resources , as well as information on the annual apidb training workshop ( see supplementary material ) . the tools section provides access to a blast search of apicomplexa genomic , est and gene model sequences ( figure 1d ) and to orthomcl db and kegg maps with apicomplexan and human enzymes highlighted . the query section provides queries for gene and protein features that span cryptodb , plasmodb and toxodb and may include searches of all or a subset of the component species genomes ( figure 1b ) . finally , the menu bar appears on every page and gives access to the user 's query history and the information on the datasets used in the database . database functionality ( a ) searches are initiated via tools or queries provided on the web site 's front page . ( b ) query forms allow user - defined refinement for the queries , e.g. which species would you like to search ? ( c ) query searches return a table with results from the component databases sites . the result summary states the number of records found at each site ( circled ) . ( d ) the blast tool integrates searches of all publicly available apicomplexan genomic data , including species not hosted by a component database . ( e ) query results can be downloaded in a customized tab - delimited file . apidb 's query architecture provides a set of pages where users can easily execute and manage queries . on the front page , six federated queries are currently available that span the component databases : search genes by gene i d , by annotated keyword in product description ( figure 1b ) , by pfam domain , by ec number , by go term , and by blast similarity . upon query selection , the user is presented with a question page where they can refine their search ( figure 1b ) . when the query is executed , a summary page offers the number of hits for each organism and the list of genes that meet the requirements ( figure 1c ) . gene pages , acquired from the appropriate component database provide a detailed view of annotation and analysis for the given gene record in the database . for a detailed description of the gene record page we refer to the component databases ( 46 ) . the query history page , linked in the menu bar , permits users to track their searches and combine them into more complex queries across data types , e.g. find all genes in cryptosporidium , plasmodium and toxoplasma that have a signal peptide and no transmembrane domains . summaries of the number of hits for each organism are provided when queries are executed ( figure 1c ) . as in the component sites , the web interface includes a mechanism to allow users to readily download the sequences and other attributes associated with their query result set ( e.g. gene name , product description , coordinates , length ) in a versatile tab - delimited file ( figure 1e ) that can be viewed in the spreadsheet programs , or , if only sequences are desired , may be downloaded in fasta format . examples of inquiries that can be performed on apidb are located in the supplementary material . apidb will be guided in large part by input from the user communities of apidb , the component databases and the objectives of the brcs . an annual workshop on the usage of apicomplexan database resources is not only a valuable opportunity for users to obtain hands - on instruction , but it also provides a forum for feedback used to further drive development of this site . as the autonomous component databases evolve with new data and features , apidb will respond to integrate these elements as appropriate . as data from phylogenetically related species becomes increasingly available , e.g. ciliates and perkinsus , and perhaps , some day a dinoflagellate , orthologous genes will be determined and links will be provided , via orthology to these resources when possible . the apidb website currently excludes queries of datasets not found in all three component databases . for example , plasmodb contains microarray - based gene expression data whereas cryptodb and toxodb presently do not . we will investigate permitting the querying of a subset of the component databases through apidb . feature enhancements that will be available by early 2007 include persistent history to allow users to save their search results and corresponding results and a  sort tool to allow users to sort the results they obtain from individual queries ( figure 1c ) by species , gene i d or feature description . combinations of existing tools , pre - formed queries and query history can be leveraged in powerful ways to mine the apicomplexan data but do not lend themselves well to high - throughput explorations . to facilitate large - scale database utilization , we will be providing programmatic access to our facilities through the use of standard web service technologies . modular web service tasks will serve as building blocks for creating a user - defined workflow . as a single example , linking a series of tasks would enable a researcher with a collection of putative gene regulatory motifs to perform a bulk series of blast searches of chromosomal sequences , extract hit coordinates from the report , then query for gene models downstream of each hit . as our web services capabilities expand , we will use them to permit workflows that include clustalw ( 17 ) for multiple sequence alignments . web services may also be used to collaborate with additional databases , including other brcs ( ) , to offer users integrated access to additional pathogen data .
apidb ( ) represents a unified entry point for the nih - funded apicomplexan bioinformatics resource center ( brc ) that integrates numerous database resources and multiple data types . 
 the phylum apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera cryptosporidium , plasmodium and toxoplasma . 
 apidb serves not only as a database in its own right , but as a single web - based point of entry that unifies access to three major existing individual organism databases ( ,   and cryptodb.org ) , and integrates these databases with data available from additional sources . through the apidb site 
 , users may pose queries and search all available apicomplexan data and tools , or they may visit individual component organism databases .