Abstract
Success in the life sciences depends on access to information in knowlegde bases and literature. Finding and extracting the relevant information depends on a user’s domain knowledge and the knowledge of the search technology. In this paper we present a system that helps users formulate queries and search the scientific literature. The system coordinates ontologies, knowledge representation, text mining and NLP techniques to generate relevant queries in response to keyword input from the user. Queries are presented in natural language, translated to formal query syntax and issued to a knowledge base of scientific literature, documents or aligned document segments. We describe the components of the system and exemplify using real-world examples.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Ang, W.T., Kanagasabai, R., Baker, C.J.O.: Knowledge translation: Computing the query potential of bioontologies. In: International Workshop on Semantic Web Applications and Tools for Life Sciences (2008)
Baker, C.J.O., Kanagasabai, R., Ang, W.T., Veeramani, A., Low, H.S., Wenk, M.R.: Towards ontology-driven navigation of the lipid bibliosphere. BMC Bioinformatics 9(suppl. 1), S5 (2008)
Bontcheva, K., Davis, B.: Natural language generation from ontologies. In: Davis, Grobelnik, Mladenic (eds.) Semantic Knowledge Management, Integrating Ontology Management, Knowledge Discovery, and Human Language Technologies, pp. 113–127. Springer, Heidelberg (2008)
Doms, A., Schroeder, M.: GoPubMed - exploring PubMed with the gene ontology. Nucleic Acids Research 33(web server issue), W783–W786 (2005)
Euzenat, J., Shvaiko, P.: Ontology Matching. Springer, Heidelberg (2007)
Fontelo, P., Liu, F., Ackerman, M.: askMEDLINE: a free-text, natural language query tool for MEDLINE/PubMed. BMC Medical Informatics and Decision Making 5(1) (2005)
Haarslev, V., Möller, R., Wessel, M.: Querying the semantic web with Racer + nRQL. In: Proceedings of the International Workshop on Applications of Description Logics (2004)
Harris, M.D.: Building a large-scale commercial nlg system for an EMR. In: Proceedings of the Fifth International Natural Language Generation Conference (2008)
Kalfoglou, Y., Schorlemmer, M.: Ontology mapping: the state of the art. The Knowledge Engineering Review 18(1), 1–31 (2003)
Kanagasabai, R., Low, H.-S., Ang, W.T., Wenk, M.R., Baker, C.J.O.: Ontology-centric navigation of pathway information mined from text. In: Knowledge in Biology - 11th Annual Bio-Ontologies Meeting colocated with Intelligent Systems for Molecular Biology, pp. 1–4 (2008)
Lambrix, P., Tan, H.: SAMBO - a system for aligning and merging biomedical ontologies. Journal of Web Semantics 4(3), 196–206 (2006)
Lambrix, P., Tan, H., Jakonienė, V., Strömbäck, L.: Biological ontologies. In: Baker, Cheung (eds.) Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, pp. 85–99. Springer, Heidelberg (2007)
Müller, H.-M., Kenny, E.E., Sternberg, P.W.: Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biology 2(11), e309 (2004)
Noy, N.F.: Semantic integration: A survey of ontology-based approaches. Sigmod Record 33(4), 65–70 (2004)
Noy, N.F., Griffith, N., Musen, M.: Collecting community-based mappings in an ontology repository. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 371–386. Springer, Heidelberg (2008)
Rebholz-Schuhmann, D., Kirsch, H., Arregui, M., Gaudan, S., Riethoven, M., Stoehr, P.: EBIMed - text crunching to gather facts for proteins from Medline. Bioinformatics 23, e237–e244 (2007)
Shvaiko, P., Euzenat, J.: A survey of schema-based matching approaches. In: Spaccapietra, S. (ed.) Journal on Data Semantics IV. LNCS, vol. 3730, pp. 146–171. Springer, Heidelberg (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Baker, C.J.O., Lambrix, P., Laurila Bergman, J., Kanagasabai, R., Ang, W.T. (2009). Slicing through the Scientific Literature. In: Paton, N.W., Missier, P., Hedeler, C. (eds) Data Integration in the Life Sciences. DILS 2009. Lecture Notes in Computer Science(), vol 5647. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02879-3_11
Download citation
DOI: https://doi.org/10.1007/978-3-642-02879-3_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02878-6
Online ISBN: 978-3-642-02879-3
eBook Packages: Computer ScienceComputer Science (R0)