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BION2SEL: An Ontology-Based Approach for the Selection of Molecular Biology Databases

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Advances in Bioinformatics and Computational Biology (BSB 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8826))

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Abstract

The catalogs of molecular biology databases does not provide a full description of databases, so the user should select databases using limited information available. Taking into account this fact, in the context of an initiative called BioDBCore, a group of experts proposes core metadata definitions to describe the molecular biology databases. However, how to use these metadata to infer the quality of a database is a clear open issue. In the present work, we propose an ontology-based approach aiming to guide the database selection process from molecular biology database catalogs using these metadata.

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References

  1. Galperin, M.Y., Rigden, D.J., Fernndez-Surez, X.M.: The, nucleic acids research database issue and an updated nar online molecular biology database collection. Nucleic Acids Research 42(D1), D1–D6 (2014)

    Google Scholar 

  2. Gaudet, P., Bairoch, A., Field, D., Sansone, S., Taylor, C., Attwood, T., Bateman, A., Blake, J., Bult, C., Cherry, J., et al.: Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research 39(suppl 1),  D7 (2011)

    Google Scholar 

  3. Smedley, D., Schofield, P., Chen, C., Aidinis, V., Ainali, C., Bard, J., Balling, R., Birney, E., Blake, A., Bongcam-Rudloff, E.: et al.: Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database: The Journal of Biological Databases and Curation 2010 (2010)

    Google Scholar 

  4. Naumann, F., Rolker, C.: Do metadata models meet iq requirements. In: Proceedings of the International Conference on Information Quality (IQ), pp. 99–114 (1999)

    Google Scholar 

  5. Wang, R.Y., Strong, D.M.: Beyond accuracy: what data quality means to data consumers. J. Manage. Inf. Syst. 12(4), 5–33 (1996)

    MATH  Google Scholar 

  6. Naumann, F., Leser, U., Freytag, J.C.: Quality-driven integration of heterogenous information systems. In: VLDB 1999: Proceedings of the 25th International Conference on Very Large Data Bases, San Francisco, CA, USA, pp. 447–458. Morgan Kaufmann Publishers Inc. (1999)

    Google Scholar 

  7. Lichtnow, D., Levin, A., Alves, R., Castello, I.M., Dopazo, J., Pastor, O., de Oliveira, J.P.M.: Using metadata and web metrics to create a ranking of genomic databases. In: White, B., Isaas, P., Santoro, F.M. (eds.) WWW/Internet 2011 Conference, IADIS,, pp. 253–260. IADIS Press (2011)

    Google Scholar 

  8. Lichtnow, D., Alves, R., de Oliveira, J.P.M., Levin, A., Pastor, O., Castello, I.M., Dopazo, J.: Using papers citations for selecting the best genomic databases. In: Proceedings of the 2011 30th International Conference of the Chilean Computer Science Society, SCCC 2011, pp. 33–42. IEEE Computer Society, Washington, DC (2011)

    Google Scholar 

  9. Cohen-Boulakia, S., Lair, S., Stransky, N., Graziani, S., Radvanyi, F., Barillot, E., Froidevaux, C.: Selecting biomedical data sources according to user preferences. Bioinformatics 20(1), 86–93 (2004)

    Article  Google Scholar 

  10. O’Connor, M.F., Knublauch, H., Tu, S., Grosof, B.N., Dean, M., Grosso, W., Musen, M.A.: Supporting rule system interoperability on the semantic web with SWRL. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 974–986. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  11. Martello, C.L., Alves, R.: Explorando marcadores gênicos em estudos transcriptomicos relacionados ao alzheimer. Technical report, Instituto de Biociências - UFRGS (2011)

    Google Scholar 

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Lichtnow, D., Alves, R., Pastor, O., Burriel, V., de Oliveira, J.P.M. (2014). BION2SEL: An Ontology-Based Approach for the Selection of Molecular Biology Databases. In: Campos, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2014. Lecture Notes in Computer Science(), vol 8826. Springer, Cham. https://doi.org/10.1007/978-3-319-12418-6_11

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  • DOI: https://doi.org/10.1007/978-3-319-12418-6_11

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-12417-9

  • Online ISBN: 978-3-319-12418-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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