Abstract
Warehousing heterogeneous, dynamic biological data is a key technique for biological data integration as it greatly improves performance. However, it requires complex maintenance procedures to update the warehouse in light of the changes to the sources. Consequently, a key issue to address is how to detect changes to the underlying biological data sources. In this paper, we present an algorithm called BioDiff for detecting exact changes to biological annotations. In our approach we transform heterogeneous biological data to XML format and then detect changes between two versions of XML representation of biological data. Our algorithm extends X-Diff, a published XML change detection algorithm. X-Diff, being designed for any type of XML data, does not exploit the semantics of biological data to reduce the data set of bipartite mapping. We have implemented BioDiff in Java. We have conducted an extensive performance study using data from EMBL, GenBank, SwissProt and PDB. Our experimental results show that BioDiff runs 1.5 to 6 times faster than X-Diff.
Keywords: Biological Data, Matching Phase, Bipartite Match, Biological Annotation, Change Detection Algorithm
Contributor Information
Ramamohanarao Kotagiri, Email: kotagiri@unimelb.edu.au.
P. Radha Krishna, Email: prkrishna@idrbt.ac.in.
Mukesh Mohania, Email: mkmukesh@in.ibm.com.
Ekawit Nantajeewarawat, Email: ekawit@siit.tu.ac.th.
Sourav S. Bhowmick, Email: assourav@ntu.edu.sg
C. Forbes Dewey, Jr., Email: cfdewey@mit.edu
References
- 1.Bahl A. PlasmoDB: the Plasmodium genome resource. An integrated database that provides tools for accessing, analysing and mapping expression and sequence data (both finished and unfinished) Nucleic Acids Res. 2002;30:87–90. doi: 10.1093/nar/30.1.87. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Cobena, G., Abiteboul, S., Marian, A.: Detecting Changes in XML Documents. In: In Proc. of ICDE, pp. 41–52 (2002)
- 3.Davidson S.B., Crabtree J., Brunk B., et al. K2/Kleisli and GUS: Experiments in integrated Access to Genomic Data Sources. IBM Systems Journal. 2001;40(2):512–531. doi: 10.1147/sj.402.0512. [DOI] [Google Scholar]
- 4.Garofalakis, M.N., Gionis, A., Rastogi, R., Seshadri, S., Shim, K.: XTRACT: A System for Extracting Document Type Descriptors from XML Documents. In: Proc. of SIGMOD, pp. 165–176 (2000)
- 5.Hammer, J., Schneider, M.: Genomics Algebra: A New, Integrating Data Model, Language, and Tool for Processing and Querying Genomic Information. In: Proc. of Conference on Innovative Data Systems Research (CIDR) (2003)
- 6.Leser, U., Naumann, F. (Almost) Hands-Off Information Integration for the Life Sciences. In: Proc. of CIDR (2005)
- 7.Ritter O., Kocab P., Senger M., Wolf D., Suhai S. Prototype implementation of the integrated genomic database. Comput. Biomed. Res. 1994;27:97–115. doi: 10.1006/cbmr.1994.1011. [DOI] [PubMed] [Google Scholar]
- 8.Stein L.D. Integrating Biological Databases. Nature Rev. Genet. 2003;4(5):337–345. doi: 10.1038/nrg1065. [DOI] [PubMed] [Google Scholar]
- 9.Song, Y., Bhowmick, S.S.: BioDiff: An Effective Fast Change Detection Algorithm for Genomic and Proteomic Data. In: Proc. of ACM CIKM (Poster), pp. 146–147 (2004)
- 10.Song Y., Bhowmick S.S. Bio2X: A Rule-based Approach for Semi-automatic Transformation of Semistructured Biological Data to XML. Data and Knowledge Engineering Journal. 2005;52(2):249–271. [Google Scholar]
- 11.Wang, Y., DeWitt, D., Cai, J.-Y.: X-Diff: A Fast Change Detection Algorithm for XML Documents. In: Proc. of IEEE ICDE , pp. 519–530 (2003)
- 12.Zdobnov E.M., Lopez R., Apweiler R., Etzold T. The EBI SRS server-recent Developments. Bioinformatics. 2002;18(2):368–373. doi: 10.1093/bioinformatics/18.2.368. [DOI] [PubMed] [Google Scholar]