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Nucleic Acids ResNucleic Acids ResnarNucleic Acids ResearchNucleic Acids Research0305-10481362-4962Oxford University Press 1709893010.1093/nar/gkl880ArticlesApiDB: integrated resources for the apicomplexan bioinformatics resource center Aurrecoechea Cristina 1Heiges Mark 1Wang Haiming 1Wang Zhiming 2Fischer Steve 3Rhodes Philippa 2Miller John 2Kraemer Eileen 2Stoeckert Christian J. Jr.3Roos David S. 4Kissinger Jessica C. 15*1Center for Tropical and Emerging Global DiseasesAthens GA, USA2Department of Computer Science, University of GeorgiaAthens GA, USA3Department of Genetics, Center for Bioinformatics423 Guardian Dr, Philadelphia, PA, USA4Penn Genomics Institute, University of PennsylvaniaPhiladelphia, PA, USA5Department of Genetics, University of GeorgiaAthens GA, USA*To whom correspondence should be addressed. Tel: +1 706 542 6562; Fax: +1 706 542 3582; Email: jkissing@uga.edu1 2007 10 11 2006 10 11 2006 35 Database issue D427 D430 15 8 2006 10 10 2006 11 10 2006 © 2006 The Author(s)2006This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.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.
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INTRODUCTION
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 C.parvum are listed as Category B Biodefense Pathogens by the National Institutes of Health.

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.

ApiDB integrates the existing CryptoDB, ToxoDB and PlasmoDB component resources. 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) ().

ApiDB serves as a web portal for cross-species comparison. 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 ‘painted’ comparative highlights of apicomplexan and human enzymes.

FUNCTIONALITY OF CURRENT RELEASE
ApiDB 2.0 was released in April 2006. 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.

Figure 1 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? Descriptions and help are provided for the queries. (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). Individual results are linked to a detailed record page at its component database site. (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 ID, 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). Hyperlinks connect the user to the gene page in the component sites. 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 (4–6).

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.

FUTURE DIRECTIONS
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 ID 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.

SUPPLEMENTARY DATA
Supplementary Data are available at NAR Online.

The ApiDB project is co-administered by David S. Roos, Christian J. Stoeckert Jr and Jessica C. Kissinger. We thank our database development collaborators: Aaron J. Mackey, Bindu Gajria, Thomas Gan, Jerric Gao, John Iodice and the entire development team for the component database sites. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400037C. Funding to pay the Open Access publication charges for this article was provided by National Institute of Allergy and Infectious 215 Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN26620040 0037C.

Conflict of interest statement. None declared.
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REFERENCES
1 Lopéz-Antuñano F.J.  Schmunis G.A.   Parasitic Protozoa 1993 Vol. 5 San Deigo, CA Academic Press Inc. 135 265 
2 Fayer R.   Cryptosporidium and Cryptosporidiosis 1997 Boca Raton, FL CRC Press Inc. 
3 Dubey J.P.  Beattie C.P.   Toxoplasmosis of Animals and Man. 1988 Boca Raton, FL CRC Press Inc. 
4 Heiges M.  Wang H.  Robinson E.  Aurrecoechea C.  Gao X.  Kaluskar N.  Rhodes P.  Wang S.  He C.-Z.  Su Y.    CryptoDB: a Cryptosporidium  bioinformatics resource update Nucleic Acids Res. 2006 34 D419 D422 16381902 
5 Bahl A.  Brunk B.  Crabtree J.  Fraunholz M.J.  Gajria B.  Grant G.R.  Ginsburg H.  Gupta D.  Kissinger J.C.  Labo P.    PlasmoDB: the Plasmodium  genome resource. A database integrating experimental and computational data Nucleic Acids Res. 2003 31 212 215 12519984 
6 Kissinger J.C.  Gajria B.  Li L.  Paulsen I.T.  Roos D.S.   ToxoDB: accessing the Toxoplasma gondii  genome Nucleic Acids Res. 2003 31 234 236 12519989 
7 Stein L.D.   Integrating biological databases Nature Rev. Genet. 2003 4 337 345 12728276 
8 Ashburner M.  Ball C.A.  Blake J.A.  Botstein D.  Butler H.  Cherry J.M.  Davis A.P.  Dolinski K.  Dwight S.S.  Eppig J.T.    Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nature Genet. 2000 25 25 29 10802651 
9 Bateman A.  Birney E.  Durbin R.  Eddy S.R.  Howe K.L.  Sonnhammer E.L.   The Pfam protein families database Nucleic Acids Res. 2000 28 263 266 10592242 
10 Altschul S.F.  Madden T.L.  Schaffer A.A.  Zhang J.  Zhang Z.  Miller W.  Lipman D.J.   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997 25 3389 3402 9254694 
11 Chen F.  Mackey A.J.  Stoeckert C.J. Jr  Roos D.S.   OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Res. 2006 34 D363 D368 16381887 
12 Kanehisa M.  Goto S.  Hattori M.  Aoki-Kinoshita K.F.  Itoh M.  Kawashima S.  Katayama T.  Araki M.  Hirakawa M.   From genomics to chemical genomics: new developments in KEGG Nucleic Acids Res. 2006 34 D354 D357 16381885 
13 Benson D.A.  Karsch-Mizrachi I.  Lipman D.J.  Ostell J.  Wheeler D.L.   GenBank Nucleic Acids Res. 2003 31 23 27 12519940 
14 Hertz-Fowler C.  Peacock C.S.  Wood V.  Aslett M.  Kerhornou A.  Mooney P.  Tivey A.  Berriman M.  Hall N.  Rutherford K.    GeneDB: a resource for prokaryotic and eukaryotic organisms Nucleic Acids Res. 2004 32 D339 D343 14681429 
15 Li L.  Crabtree J.  Fischer S.  Pinney D.  Stoeckert C.J.  Sibley L.D.  Roos D.S.   ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites Nucleic Acids Res. 2004 32 D326 D328 14681425 
16 Hokamp K.  Wolfe K.H.   PubCrawler: keeping up comfortably with PubMed and GenBank Nucleic Acids Res. 2004 32 W16 W19 15215341 
17 Jeanmougin F.  Thompson J.D.  Gouy M.  Higgins D.G.  Gibson T.J.   Multiple sequence alignment with ClustalX Trends Biochem. Sci. 1998 23 403 405 9810230

