Abstract
In information retrieval, named entity recognition gives the opportunity to apply semantic search in domain specific corpora. Recently, more full text patents and journal articles became freely available. As the information distribution amongst the different sections is unknown, an analysis of the diversity is of interest.
This paper discovers the density and variety of relevant life science terminologies in Medline abstracts, PubMedCentral journal articles and patents from the TREC Chemistry Track. For this purpose named entity recognition for various bio, pharmaceutical, and chemical entity classes has been conducted and the frequencies and distributions in the different text zones analyzed.
The full texts from PubMedCentral comprise information to a greater extent than their abstracts while containing almost all given content from their abstracts. In the patents from the TREC Chemistry Track, it is even more extrem. Especially the description section includes almost all entities mentioned in a patent and contains in comparison to the claim section at least 79 % of all entities exclusively.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Fluck, J., Mevissen, H.T., Dach, H., Oster, M., Hofmann-Apitius, M.: ProMiner: recognition of human gene and protein names using regularly updated dictionaries. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop, pp. 149–151 (2007) (last accessed August 2009)
Friedrich, C.M., Dach, H., Gattermayer, T., Engelbrecht, G., Benkner, S., Hofmann-Apitius, M.: @neuLink: A service-oriented application for biomedical knowledge discovery. In: Proceedings of the HealthGrid 2008, pp. 165–172 (2008) (last accessed August 2009)
Gospodnetic, O., Hatcher, E.: Lucene In Action. Action Series. Manning Publications Co., Greenwich (2005)
Guha, R., McCool, R., Miller, E.: Semantic search. In: WWW 2003: Proceedings of the 12th international conference on World Wide Web, pp. 700–709. ACM, New York (2003)
Gurulingappa, H., Müller, B., Klinger, R., Mevissen, H.-T., Hofmann-Apitius, M., Fluck, J., Friedrich, C.M.: Patent retrieval in chemistry based on semantically tagged named entities. In: Voorhees, E.M., Buckland, L.P. (eds.) The Eighteenth Text RETrieval Conference (TREC 2009) Proceedings, Gaithersburg, Maryland, USA (November 2009)
Hanisch, D., Fundel, K., Mevissen, H.-T., Zimmer, R., Fluck, J.: Prominer: rule-based protein and gene entity recognition. BMC Bioinformatics 6(suppl. 1), S14 (2005)
Hirschman, L., Colosimo, M., Morgan, A., Yeh, A.: Overview of biocreative task 1b: normalized gene lists. BMC Bioinformatics 6(suppl. 1), S11 (2005)
Hofmann-Apitius, M., Fluck, J., Furlong, L., Fornes, O., Kolářik, C., Hanser, S., Boeker, M., Schulz, S., Sanz, F., Klinger, R., Mevissen, T., Gattermayer, T., Oliva, B., Friedrich, C.M.: Knowledge environments representing molecular entities for the virtual physiological human. Philos. Transact. A Math. Phys. Eng. Sci. 366(1878), 3091–3110 (2008)
Kanehisa, M., Goto, S.: Kegg: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30 (2000)
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: new developments in kegg. Nucleic Acids Res. 34(Database issue), D354–D357 (2006)
Klinger, R., Friedrich, C.M., Fluck, J., Hofmann-Apitius, M.: Named Entity Recognition with Combinations of Conditional Random Fields. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 2007, pp. 89–91 (2007)
Klinger, R., Friedrich, C.M., Mevissen, H.T., Fluck, J., Hofmann-Apitius, M., Furlong, L.I., Sanz, F.: Identifying gene-specific variations in biomedical text. J. Bioinform. Comput. Biol. 5(6), 1277–1296 (2007)
Klinger, R., Kolářik, C., Fluck, J., Hofmann-Apitius, M., Friedrich, C.M.: Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics 24(13), i268–i276 (2008); Proceedings of the International Conference Intelligent Systems for Molecular Biology (ISMB)
Kolářik, C., Klinger, R., Friedrich, C.M., Hofmann-Apitius, M., Fluck, J.: Chemical names: Terminological resources and corpora annotation. In: Workshop on Building and evaluating resources for biomedical text mining, volume 6th edition of the Language Resources and Evaluation Conference, Marrakech, Morocco (2008)
Schuemie, M.J., Weeber, M., Schijvenaars, B.J.A., van Mulligen, E.M., van der Eijk, C.C., Jelier, R., Mons, B., Kors, J.A.: Distribution of information in biomedical abstracts and full-text publications. Bioinformatics 20(16), 2597–2604 (2004)
Shah, P.K., Perez-Iratxeta, C., Bork, P., Andrade, M.A.: Information extraction from full text scientific articles: where are the keywords? BMC Bioinformatics 4, 20 (2003)
Verspoor, K., Bretonnel Cohen, K., Hunter, L.: The textual characteristics of traditional and open access scientific journals are similar. BMC Bioinformatics 10(1), 183 (2009)
White, M.J.: Espacenet, europe’s network of patent databases. Issues in Science & Technology Librarianship 47 (2006)
Wishart, D.S., Knox, C., Guo, A.C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., Hassanali, M.: Drugbank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36(Database issue), D901–D906 (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Müller, B. et al. (2010). Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities. In: Cunningham, H., Hanbury, A., Rüger, S. (eds) Advances in Multidisciplinary Retrieval. IRFC 2010. Lecture Notes in Computer Science, vol 6107. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13084-7_12
Download citation
DOI: https://doi.org/10.1007/978-3-642-13084-7_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-13083-0
Online ISBN: 978-3-642-13084-7
eBook Packages: Computer ScienceComputer Science (R0)