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Approaches in Integrative Bioinformatics pp 73–109Cite as

Information Retrieval in Life Sciences: A Programmatic Survey

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Abstract

Biomedical databases are a major resource of knowledge for research in the life sciences. The biomedical knowledge is stored in a network of thousands of databases, repositories and ontologies. These data repositories differ substantially in granularity of data, storage formats, database systems, supported data models and interfaces. In order to make full use of available data resources, the high number of heterogeneous query methods and frontends requires high bioinformatic skills. Consequently, the manual inspection of database entries and citations is a time-consuming task for which methods from computer science should be applied.Concepts and algorithms from information retrieval (IR) play a central role in facing those challenges. While originally developed to manage and query less structured data, information retrieval techniques become increasingly important for the integration of life science data repositories and associated information. This chapter provides an overview of IR concepts and their current applications in life sciences. Enriched by a high number of selected references to pursuing literature, the following sections will successively build a practical guide for biologists and bioinformaticians.

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Notes

  1. 1.

    http://www.ncbi.nlm.nih.gov/pubmed/

  2. 2.

    http://dblp.uni-trier.de/

  3. 3.

    http://www.ics.uci.edu/~fielding/pubs/dissertation/rest_arch_style.htm

  4. 4.

    http://www.w3.org/TR/soap/

  5. 5.

    http://www.kegg.jp/kegg/xml/

  6. 6.

    http://www.mged.org/Workgroups/MAGE/

  7. 7.

    The computational modelling in biology network, COMBINE, http://co.mbine.org/.

  8. 8.

    http://www.uniprot.org/uniprot/Q8W413

  9. 9.

    http://www.expasy.org/enzyme/3.2.1.26

  10. 10.

    http://www.arabidopsis.org/servlets/TairObject?type=locus&name=AT2G36190

  11. 11.

    http://www.uniprot.org/?tab=mapping

  12. 12.

    http://dublincore.org/documents/dces

  13. 13.

    http://schema.datacite.org/meta/kernel-2.2/index.html

  14. 14.

    http://en.wikipedia.org/wiki/List_of_search_engines#Desktop_search_engines

  15. 15.

    http://lucene.apache.org/solr/

  16. 16.

    http://lucene.apache.org

  17. 17.

    http://flamenco.berkeley.edu/demos.html

  18. 18.

    https://www.ebi.ac.uk/chembl/malaria/target/browser/classification

  19. 19.

    http://sabio.h-its.org

  20. 20.

    http://gbis.ipk-gatersleben.de/gbis_i/home.jsf

  21. 21.

    http://www.ensembl.org

  22. 22.

    http://urgi.versailles.inra.fr/gnpis

  23. 23.

    http://www.ncbi.nlm.nih.gov/Taxonomy/

  24. 24.

    http://www.ebi.ac.uk/miriam/main/mdb?section=qualifiers

  25. 25.

    Twenty-fourth release of BioModels Database, December 2012.

  26. 26.

    http://code.google.com/p/path2models/

  27. 27.

    http://www.ebi.ac.uk/biomodels-main/BIOMD0000000241

  28. 28.

    http://bio2rdf.org/

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Acknowledgements

This work was supported by the European Commission within its 7th Framework Programme, under the thematic area “Infrastructures”, contract number 283496, by the BMBF e:bio programme (University of Rostock) and the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

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  1. Leibniz Institute of Plant Genetics and Crop Plant Research, Bioinformatics and Information Technology, OT Gatersleben, Corrensstraße 3, 06466, Stadt Seeland, Germany

    Matthias Lange & Stephan Weise

  2. Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstraße 69, 18057, Rostock, Germany

    Ron Henkel & Dagmar Waltemath

  3. HITS gGmbH, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany

    Wolfgang Müller

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    Ming Chen

  2. Department of Bioinformatics and Medical Informatics, Bielefeld University, Bielefeld, Germany

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Lange, M., Henkel, R., Müller, W., Waltemath, D., Weise, S. (2014). Information Retrieval in Life Sciences: A Programmatic Survey. In: Chen, M., Hofestädt, R. (eds) Approaches in Integrative Bioinformatics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41281-3_3

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