Abstract
Data integration projects in the life sciences often gather data on a particular subject from multiple sources. Some of these sources overlap to a certain degree. Therefore, integrated search results may be supported by one, few, or all data sources. To reflect these differences, results should be ranked according to the number of data sources that support them. How such a ranking should look like is not clear per se. Either, results supported by only few sources are ranked high because this information is potentially new, or such results are ranked low because the strength of evidence supporting them is limited.
We present two scoring schemes to rank search results in the integrated protein annotation database Columba. We define a surprisingness score, preferring results supported by few sources, and a confidence score, preferring frequently encountered information. Unlike many other scoring schemes our proposal is purely data-driven and does not require users to specify preferences among sources. Both scores take the concrete overlaps of data sources into account and do not presume statistical independence. We show how our schemes have been implemented efficiently using SQL.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Berman, H., Westbrook, J., Feng, Z., Gilliland, G., et al.: The Protein Data Bank. Nucleic Acids Research 28(1), 235–242 (2000)
Bleiholder, J., Khuller, S., Naumann, F., Raschid, L., Wu, Y.: Query Planning in the Presence of Overlapping Sources. In: Ioannidis, Y., Scholl, M.H., Schmidt, J.W., Matthes, F., Hatzopoulos, M., Boehm, K., Kemper, A., Grust, T., Boehm, C. (eds.) EDBT 2006. LNCS, vol. 3896, pp. 811–828. Springer, Heidelberg (2006)
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31(1), 365–370 (2003)
Florescu, D., Koller, D., Levy, A.: Using Probabilistic Information in Data Integration.. In: Proceedings of the VLDB, pp. 216–225. Morgan Kaufmann, San Francisco (1997)
Huttenhower, C., Hibbs, M., Myers, C., Troyanskaya, O.: A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 22(23), 2890–2897 (2006)
Joshi-Tope, G., Gillespie, M., Vastrik, I., D’Eustachio, P., et al.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Research 33, D428–D432 (2005)
Kanehisa, M., Goto, S., Kawashima, S., Nakaya, A.: The KEGG databases at GenomeNet. Nucleic Acids Research 30, 42–46 (2002)
Lacroix, Z., Murthy, H., Naumann, F., Raschid, L.: Links and Paths through Life Sciences Data Sources. In: DILS 2004. LNCS (LNBI), vol. 2994, pp. 203–211 Springer, Heidelberg (2004)
Lemer, C., Antezana, E., Couche, F., Fays, F., et al.: The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Research 32, D443–D448 (2004)
Marcotte, E., Pellegrini, M., Ng, H., Rice, D., et al.: Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428), 751–753 (1999)
Martin, A.C.: Mapping PDB chains to UniProtKB entries. Bioinformatics 21(23), 4297–4301 (2005)
von Mering, C., Jensen, L., Snel, B., Hooper, S., et al.: STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research 33,D433–D437 (2005)
Naumann, F., Leser, U., Freytag, J.-C.: Quality-driven Integration of Heterogenous Information Systems. In: Proceedings of the VLDB, pp. 447–458. Morgan Kaufmann, San Francisco (1999)
Rother, K., Müller, H., Trissl, S., Koch, I., et al.: Columba: Multidimensional Data Integration of Protein Annotations. In: DILS 2004. LNCS (LNBI), vol. 2994, pp. 156–171. Springer, Heidelberg (2004)
Velankar, S., Mcneil, P., Mittard-Runte, V., Suarez, A., et al.: E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Research 33, D262+ (2005)
Via, A., Zanzoni, A., Helmer-Citterich, M.: Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics 21(4), 551–553 (2004)
Yanai, I., DeLisi, C.: The society of genes: networks of functional links between genes from comparative genomics. Genome Biology 3(11) : (research0064) (October 2002)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Hussels, P., Trißl, S., Leser, U. (2007). What’s New? What’s Certain? – Scoring Search Results in the Presence of Overlapping Data Sources. 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_19
Download citation
DOI: https://doi.org/10.1007/978-3-540-73255-6_19
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73254-9
Online ISBN: 978-3-540-73255-6
eBook Packages: Computer ScienceComputer Science (R0)