Abstract
In the last decade, many projects have tried to deal with the integration of biological resources. Web portals have flourished online, each providing data from a public provider. Although these online resources are available with a set of manipulation tools, scientists, researchers, and students often have to shift from one resource to another to accomplish a particular task. Making a rich tool set available along with a variety of databases, data formats, and computational capabilities is a complex task. It requires building a versatile environment for data integration, data manipulation, and data storage. In this paper, we study the requirements and report the architectural design of a web application, code named SWAMI, which aims at integrating a rich tool set and a variety of biological databases. The suggested architecture is highly scalable in terms of adding databases and new manipulation tools.
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References
Scientific Data Management Center (2005), http://sdm.lbl.gov/sdmcenter/
Abiteboul, S., Agrawal, R., Bernstein, P., Carey, M., Ceri, S., Croft, B., DeWitt, D., et al.: The Lowell database research self-assessment. Commun. ACM 48(5), 111–118 (2005)
Subramaniam, S.: The Biology Workbench (1998), http://workbench.sdsc.edu/
Etzold, T., Argos, P.: SRS – An Indexing And Retrieval Tool For Flat File Data Libraries. CABIOS 9, 49–57 (1993)
Documentation, S.: SRS at the European Bioinformatics Institute (2006), http://srs.ebi.ac.uk/srs/doc/index.html
Entigen. Bionavigator - BioNode & BioNodeSA: Overview (2001), http://www.entigen.com/library
National Library of Medicine (2005), http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed
Michalickova, K., Bader, G.D., Dumontier, M., Lieu, H., Betel, D., Isserlin, R., Hogue, C.W.: Seqhound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics 3(1), 32 (2002)
GMOD, LuceGene: Document/Object Search and Retrieval (2007), http://www.gmod.org/?q=node/83
Subramaniam, S.: The biology workbench - A seamless database and analysis environment for the biologist. Proteins-Structure Function and Genetics 32(1), 1–2 (1998)
Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., Stoeckert, C.J.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. Ibm. Systems Journal 40(2), 512–531 (2001)
Shah, S.P., Huang, Y., Xu, T., Yuen, M.M.S., Ling, J., Ouellette, B.F.F.: Atlas - a data warehouse for integrative bioinformatics. Bmc Bioinformatics 6 (2005)
Lapp, H.: BioSQL (2006), http://www.biosql.org/wiki/Main_Page
Haider, S., Holland, R., Smedley, D., Kasprzyk, A.: BioMART Project (2007), http://www.biomart.org/index.html
Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W.-J., Tenenbaum, J.D., Karp, P.D.: BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics 7, 170–184 (2006)
GMOD, Getting Started with Chado and GMOD (2007), http://www.gmod.org/getting_started
Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., Brass, A.: TAMBIS: Transparent access to multiple bioinformatics information sources. Bioinformatics 16(2), 184–185 (2000)
Haas, L., Schwartz, P., Kodali, P., Kotlar, E., Rice, J., Swope, W.: DiscoveryLink: A System for Integrated Access to Life Sciences Data Sources. Ibm. Systems Journal 40(2), 489–511 (2001)
Kohler, J.: Integration of Life Sciences Databases. BIOSILICO 2, 61–69 (2004)
Letondal, C.: A Web interface generator for molecular biology programs in Unix. Bioinformatics 17(1), 73–82 (2001)
RENCI, The NC BioPortal Project (2007), http://www.ncbioportal.org/
Rampp, M., Soddemann, T., Lederer, H.: The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Research 34(Web Server issue), W15–W19 (2006)
Badidi, E., De Sousa, C., Lang, B.F., Burger, G.: AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis. BMC informatics 4, 63–72 (2003)
Badidi, E., De Sousa, C., Lang, B.F., Burger, G.: FLOSYS–a web-accessible workflow system for protocol-driven biomolecular sequence analysis. Cell. Mol. Biol (Noisy-le-grand) 50(7), 785–793 (2004)
Lee, S., Wang, T.D., Hashmi, N., Cummings, M.P.: Bio-STEER: a Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Computer Systems 23, 497–509 (2007)
Shah, S.P., He, D.Y.M., Sawkins, J.N., Druce, J.C., Quon, G., Lett, D., Zheng, G.X.Y., Xu, T., Ouellette, B.F.: Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 5, 40–48 (2004)
Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., Mock, S.: Kepler: An Extensible System for Design and Execution of Scientific Workflows. In: 16th Intl. Conf. on Scientific and Statistical Database Management (SSDBM’04), Santorini Island, Greece (2004)
Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A., Li, P.: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20(17), 3045–3054 (2003)
Baldridge, K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., Sudholt, W., Krishnan, S., Bowen, A., Amoreira, C., Potier, Y.: GEMSTONE: Grid Enabled Molecular Science Through Online Networked Environments. In: Life Sciences Grid 2005, LSGrid, Singapore (2005)
McGuinness, D.L., van Harmelen, F.: OWL Web Ontology Language (2007), http://www.w3.org/TR/owl-features/
Parsia, B., Sirin, E.: Pellet: An OWL DL Reasoner. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, Springer, Heidelberg (2004)
Nambiar, U., Ludaescher, B., Lin, K., Baru, C.: The GEON portal: accelerating knowledge discovery in the geosciences. In: Eighth ACM international Workshop on Web information and Data Management (WIDM ’06), Arlington, Virginia, USA, pp. 83–90. ACM Press, New York (2006)
Buzko, O.: SIRIUS: An Extensible Molecular Graphics and Analysis Environment (2007), http://sirius.sdsc.edu
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Rifaieh, R., Unwin, R., Carver, J., Miller, M.A. (2007). SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment. In: Cohen-Boulakia, S., Tannen, V. (eds) Data Integration in the Life Sciences. DILS 2007. Lecture Notes in Computer Science(), vol 4544. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73255-6_7
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DOI: https://doi.org/10.1007/978-3-540-73255-6_7
Publisher Name: Springer, Berlin, Heidelberg
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