Abstract
We present an architecture aimed at semantic search and synthesis of information acquired from the document repositories. The proposed framework is expected to provide domain knowledge interfaces enabling the internally implemented algorithms to identify relationships between documents, researchers, institutions, as well as concepts extracted from various types of knowledge bases. The framework should be scalable with respect to data volumes, diversity of analytic processes, and the speed of search. In this paper, we investigate these requirements for the case of medical publications gathered in PubMed.
Keywords
This work was supported by the grant N N516 077837 from the Ministry of Science and Higher Education of the Republic of Poland and by the National Centre for Research and Development (NCBiR) under the grant SP/I/1/77065/10 by the Strategic scientific research and experimental development program “Interdisciplinary System for Interactive Scientific and Scientific-Technical Information (SYNAT)”. We would like to acknowledge the whole SYNAT team, in particular: Marek Grzegorowski, Michał Kijowski, Marcin Kowalski, Adam Krasuski, and Krzysztof Stencel (co-creators of database model; Section ?), Kamil Herba, Grzegorz Jaśkiewicz, Michał Meina, Sinh Hoa Nguyen, and Marcin Szczuka (co-creators of experimental framework; Section ?), as well as Przemysław Pardel and Sebastian Stawicki (responsible for loading and parsing PubMed data). Special thanks go to Stanisława Bazan-Socha for her remarks on possible future usage of SONCA by biomedical experts.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Agrawal, R., Gollapudi, S., Kannan, A., Kenthapadi, K.: Enriching Education through Data Mining. In: Kuznetsov, S.O., Mandal, D.P., Kundu, M.K., Pal, S.K. (eds.) PReMI 2011. LNCS, vol. 6744, pp. 1–2. Springer, Heidelberg (2011)
Badr, Y., Chbeir, R., Abraham, A., Hassanien, A.: Emergent Web Intelligence: Advanced Semantic Technologies. Springer, Heidelberg (2010)
Baldi, P., Hatfield, G.W.: DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. Cambridge University Press (2002)
Barwise, J., Seligman, J.: Information Flow: The Logic of Distributed Systems. Cambridge University Press (1997)
Bazan, J.G.: Hierarchical Classifiers for Complex Spatio-temporal Concepts. Transactions on Rough Sets 9, 474–750 (2008)
Bembenik, R., Skonieczny, Ł., Rybiński, H., Niezgódka, M. (eds.): Intelligent Tools for Building a Scientific Information Platform. Springer, Heidelberg (2011)
Butcher, S., Clarke, C.L.A., Cormack, G.: Information Retrieval: Implementing and Evaluating Search Engines. MIT Press (2010)
Chodorow, K., Dirolf, M.: MongoDB: The Definitive Guide: Powerful and Scalable Data Storage. O’Reilly Media (2010)
Davies, J., Grobelnik, M., Mladenic, D.: Semantic Knowledge Management: Integrating Ontology Management, Knowledge Discovery, and Human Language Technologies. Springer, Heidelberg (2009)
Gabrilovich, E., Markovitch, S.: Computing Semantic Relatedness using Wikipedia-based Explicit Semantic Analysis. In: Proc. of the 20th Int. Joint Conf. on Artificial Intelligence (IJCAI), pp. 6–12 (2007)
Góra, G., Kruczek, P., Skowron, A., Bazan, J.G., Bazan-Socha, S., Pietrzyk, J.J.: Case-based Planning of Treatment of Infants with Respiratory Failure. Fundamenta Informaticae 85(1-4), 155–172 (2008)
Grużdź, A., Ihnatowicz, A., Ślęzak, D.: Interactive Gene Clustering - A Case Study of Breast Cancer Microarray Data. Information Systems Frontiers 8(1), 21–27 (2006)
Han, J.: Construction and Analysis of Web-Based Computer Science Information Networks. In: Kuznetsov, S.O., Ślęzak, D., Hepting, D.H., Mirkin, B.G. (eds.) RSFDGrC 2011. LNCS (LNAI), vol. 6743, pp. 1–2. Springer, Heidelberg (2011)
Jankowski, A., Skowron, A.: Wisdom Technology: A Rough-Granular Approach. In: Marciniak, M., Mykowiecka, A. (eds.) Bolc Festschrift, vol. 5070, pp. 3–41. Springer, Heidelberg (2009)
Jörg, B., Jeffery, K., van Grootel, G., Asserson, A., Dvorak, J., Rasmussen, H.: CERIF 2008 - 1.2 Full Data Model (FDM) Introduction and Specification (2008), http://www.eurocris.org/Index.php?page=CERIF2008&t=1
Kacprzyk, J., Zadrożny, S.: Computing With Words Is an Implementable Paradigm: Fuzzy Queries, Linguistic Data Summaries, and Natural-Language Generation. IEEE Transactions on Fuzzy Systems 18(3), 461–472 (2010)
McCandless, M., Hatcher, E., Gospodnetić, O.: Lucene in Action, 2nd edn. Manning Publications (2010)
Mika, P.: Social Networks and the Semantic Web. In: Proc. of the 2004 IEEE/WIC/ACM Int. Conf. on Web Intelligence (WI), pp. 285–291 (2004)
Nguyen, H.S.: Approximate Boolean Reasoning: Foundations and Applications in Data Mining. Transactions on Rough Sets 5, 334–506 (2006)
Nguyen, H.S., Ho, T.B.: Rough Document Clustering and the Internet. In: Pedrycz, W., Skowron, A., Kreinovich, V. (eds.) Handbook of Granular Computing, pp. 987–1003. John Wiley & Sons, Inc., New York (2008)
Roberts, R.J.: PubMed Central: The GenBank of the Published Literature. Proc. of the National Academy of Sciences of the United States of America 98(2), 381–382 (2001), http://www.pnas.org/content/98/2/381.abstract
Ślęzak, D., Wróblewski, J., Eastwood, V., Synak, P.: Brighthouse: An Analytic Data Warehouse for Ad-hoc Queries. Proc. of the VLDB Endowment (PVLDB) 1(2), 1337–1345 (2008)
Szczuka, M., Janusz, A., Herba, K.: Clustering of Rough Set Related Documents with use of Knowledge from DBpedia. In: Yao, J., Ramanna, S., Wang, G., Suraj, Z. (eds.) RSKT 2011. LNCS (LNAI), vol. 6954, pp. 394–403. Springer, Heidelberg (2011)
Tenenbaum, J.M., Shrager, J.: Cancer: A Computational Disease that AI Can Cure. AI Magazine 32(2), 14–26 (2011)
Ulam, S.: Analogies Between Analogies: The Mathematical Reports of S. M. Ulam and His Los Alamos Collaborators. University of California Press (1990)
United States National Library of Medicine: Introduction to MeSH - 2011 (2011), http://www.nlm.nih.gov/mesh/introduction.html
Valiant, L.G.: Robust Logics. Artif. Intell. 117(2), 231–253 (2000)
Vapnik, V.: Learning Has Just Started (An interview with Vladimir Vapnik by Ran Gilad-Bachrach) (2008), http://seed.ucsd.edu/joomla/index.php/articles/12-interviews/9-qlearning-has-just-startedq-an-interview-with-prof-vladimir-vapnik
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Ślęzak, D., Janusz, A., Świeboda, W., Nguyen, H.S., Bazan, J.G., Skowron, A. (2011). Semantic Analytics of PubMed Content. In: Holzinger, A., Simonic, KM. (eds) Information Quality in e-Health. USAB 2011. Lecture Notes in Computer Science, vol 7058. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25364-5_7
Download citation
DOI: https://doi.org/10.1007/978-3-642-25364-5_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-25363-8
Online ISBN: 978-3-642-25364-5
eBook Packages: Computer ScienceComputer Science (R0)