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

  • Daniel Lichtnow
  • Ronnie Alves
  • Oscar Pastor
  • Verónica Burriel
  • José Palazzo Moreira de Oliveira
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8826)


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.


molecular biology databases database catalog data quality ontology database selection 


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

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Daniel Lichtnow
    • 1
  • Ronnie Alves
    • 2
    • 5
    • 6
  • Oscar Pastor
    • 3
  • Verónica Burriel
    • 3
  • José Palazzo Moreira de Oliveira
    • 4
  1. 1.Universidade Federal de Santa Maria, UFSMSanta MariaBrazil
  2. 2.Institut de Biologie ComputationnelleMontpellierFrance
  3. 3.Universitat Politècnica de ValènciaValenciaSpain
  4. 4.Universidade Federal do Rio Grande do Sul, UFRGSPorto AlegreBrazil
  5. 5.Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506Université Montpellier 2, Centre National de la Recherche ScientifiqueMontpellierFrance
  6. 6.PPGCCUniversidade Federal do ParáBelémBrazil

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