Abstract
Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists’ needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself – the strategy followed – differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies.
Availability: http://www.lri.fr/~cohen/bioguide/bioguide.html
This work was supported in part by the European Project HKIS IST-2001-38153, the Fulbright Program as well as a Hitachi Chair at INRIA.
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References
Buneman, P., Khanna, S., Tan, W.: Why and Where: A Characterization of Data Provenance. In: Van den Bussche, J., Vianu, V. (eds.) ICDT 2001. LNCS, vol. 1973, pp. 316–330. Springer, Heidelberg (2000)
Cohen-Boulakia, S., Lair, S., Stransky, N., Graziani, S., Radvanyi, F., Barillot, E., Froidevaux, C.: Selecting biomedical data sources according to user preferences. In: Bioinformatics, Proc. ISMB/ECCB 2004, vol. 20, pp. i86–i93 (2004)
Davidson, S., Crabtree, J., Brunk, B., Schug, J., Tannen, V., Overton, C., Stoeckert, C.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal (2001)
De Santis, L., Scannapieco, M., Catarci, T.: Trusting Data Quality in Cooperative Information Systems. In: Proc. of CoopIS/DOA/ODBASE 2003, pp. 354–369 (2003)
Donelson, L., Tarczy-Hornoch, P., Mork, P., Dolan, C., Mitchell, J., Barrier, M., Mei, H.: The BioMediator System as a Data Integration Tool to Answer Diverse Biologic Queries. In: Proc. of MedInfo, IMIA, in CDROM (2004)
Ely, J.W., Osheroff, J.A., Gorman, P.N., Ebell, M.H., Chambliss, M.L., Pifer, E.A., Stavri, P.Z.: A taxonomy of generic clinical questions: classification study. British Medical Journal BMJ 321 (7258), 429–432 (2000)
Etzold, T., Ulyanov, A., Argos, P.: SRS: information retrieval system for molecular biology data banks. Methods Enzymol 266, 114–128 (1996)
Lacroix, Z., Parekh, K., Raschid, L., Vidal, M.: Navigating through the Biological Maze. In: Proc. Int. IEEE Computational Systems Bioinformatics (CSB), pp. 594–595 (2004)
Lacroix, Z., Raschid, L., Vidal, M.: Efficient Techniques to Explore and Rank Paths in Life Science Data Sources. In: Proc. Data Integration in the Life Sciences, pp. 187–202 (2004)
Levy, A.Y.: Combining Artificial Intelligent and Databases for Data Integration. Artificial Intelligence Today, 249–268 (1999)
Lord, P., Bechhofer, S., Wilkinson, M.D., Schiltz, G., Gessler, D., Hull, D., Goble, C., Stein, L.: Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 350–364. Springer, Heidelberg (2004)
Mork, P., Halevy, A., Tarczy-Hornoch, P.: A model for data integration systems of biomedical data applied to online genetic databases. In: AMIA Symp, pp. 473–477 (2001)
Mork, P., Shaker, A., Halevy, A., Tarczy-Hornoch, P.: PQL: A declarative query language over dynamic biological schemata. In: Proc. AMIA Symp, pp. 533–537 (2002)
Muller, H., Naumann, F.: Data Quality in Genome Databases. In: Proc. Int. Conf. on Information Quality, pp. 269–284 (2003)
Naumann, F., Leser, U., Freytag, J.C.: Quality-driven Integration of Heterogenous Information Systems. In: Proc. Int. Conf. Very Large DataBases (VLDB), pp. 447–458 (1999)
Samsonova, M., Pisarev, A., Blagov, M.: Processing of natural language queries to a relational database. Bioinformatics 19, i241–i249 (2003)
Schallehn, E., Sattler, K.-U., Saake, G.: Efficient similarity-based operations for data integration. Data and Knowledge Engineering 48, 361–387 (2003)
Stevens, R.D., Goble, A.C., Baker, P.G., Brass, A.: A classification of tasks in bioinformatics. Bioinformatics 17(1), 180–188 (2001)
Zhao, J., Wroe, C., Goble, C., Stevens, R., Quan, D., Greenwood, M.: Using Semantic Web Technologies for Representing e-Science Provenance. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 92–106. Springer, Heidelberg (2004)
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Cohen-Boulakia, S., Davidson, S., Froidevaux, C. (2005). A User-Centric Framework for Accessing Biological Sources and Tools. In: Ludäscher, B., Raschid, L. (eds) Data Integration in the Life Sciences. DILS 2005. Lecture Notes in Computer Science(), vol 3615. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11530084_3
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DOI: https://doi.org/10.1007/11530084_3
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