A Novel Search Engine Supporting Specific Drug Queries and Literature Management

  • Alberto G. Jácome
  • Florentino Fdez-Riverola
  • Anália Lourenço
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 375)

Abstract

The growing concern for acquired microbial resistance is promoting the publication of a large number of clinical and biological antimicrobial studies. Most of these publications can be obtained by searching the PubMed database, but the broad scope and huge size of this collection make the search challenging, and time consuming. This paper presents an advanced search engine for the screening of up-to-date information on drug-related experimental studies. The main contributions lay on the resource-oriented architecture and the semantic analysis of the documents. The RESTful API enables the use of the searchable collection by different user interfaces whereas text mining tools support domain-specific document labeling, scoring and indexing. A small search engine demo indexing articles on antimicrobial peptide research is available at http://sing.ei.uvigo.es/sds/. The source code is also accessible from the same homepage and freely available under MIT License.

Keywords

Drugs Experimental testing Vertical search engine Text mining Document annotation Web application 

References

  1. 1.
    Martin, C., Low, W.L., Gupta, A., Cairul, M., Amin, I.M., Radecka, I., Britland, S.T., Raj, P., Kenward, K.M.: Strategies for antimicrobial drug delivery to biofilm. Curr. Pharm, Des (2014)Google Scholar
  2. 2.
    Rennie, R.P.: Current and future challenges in the development of antimicrobial agents. Antibiot. Resist. 211, 45–65 (2012)CrossRefGoogle Scholar
  3. 3.
    Römling, U., Balsalobre, C.: Biofilm infections, their resilience to therapy and innovative treatment strategies. J. Intern. Med. 272, 541–561 (2012)CrossRefGoogle Scholar
  4. 4.
    Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., Djoumbou, Y., Eisner, R., Guo, A.C., Wishart, D.S.: DrugBank 3.0: a comprehensive resource for “omics” research on drugs. Nucleic Acids Res. 39, D1035–41 (2011)Google Scholar
  5. 5.
    Waghu, F.H., Gopi, L., Barai, R.S., Ramteke, P., Nizami, B., Idicula-Thomas, S.: CAMP: Collection of sequences and structures of antimicrobial peptides. Nucleic Acids Res. 1–5 (2013)Google Scholar
  6. 6.
    Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L.J., Bork, P.: STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 40, D876–D880 (2012)Google Scholar
  7. 7.
    Lu, Z.: PubMed and beyond: A survey of web tools for searching biomedical literature. Database 2011, 1–13 (2011)CrossRefGoogle Scholar
  8. 8.
    Pasche, E., Gobeill, J., Kreim, O., Oezdemir-Zaech, F., Vachon, T., Lovis, C., Ruch, P.: Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. 15(Suppl 1), S15 (2014)Google Scholar
  9. 9.
    Galperin, M.Y., Rigden, D.J., Fernández-Suárez, X.M.: The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. Nucleic Acids Res. 43(Database issue):D1–D5 (2015). doi:10.1093/nar/gku1241
  10. 10.
    Percha, B., Altman, R.B.: Informatics confronts drug-drug interactions. Trends Pharmacol. Sci. 34, 178–184 (2013)Google Scholar
  11. 11.
    Settles, B.: ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text. Bioinformatics 21(14), 3191–3192 (2005)CrossRefGoogle Scholar
  12. 12.
    Jessop, D.M., Adams, S.E., Willighagen, E.L., Hawizy, L., Murray-Rust, P.: OSCAR4: a flexible architecture for chemical text-mining. J. Cheminform. 3(1), 41 (2011). doi:10.1186/1758-2946-3-41 CrossRefGoogle Scholar
  13. 13.
    Gerner, M., Nenadic, G., Bergman, C.M.: LINNAEUS: a species name identification system for biomedical literature. BMC Bioinform. 11, 85 (2010). doi:10.1186/1471-2105-11-85 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Alberto G. Jácome
    • 1
  • Florentino Fdez-Riverola
    • 1
  • Anália Lourenço
    • 1
    • 2
  1. 1.ESEI - Escuela Superior de Ingeniería Informática Edificio PolitécnicoCampus Universitario as Lagoas S/NOurenseSpain
  2. 2.Centre of Biological EngineeringUniversity of MinhoBragaPortugal

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