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Extracting Citation Metadata from Online Publication Lists Using BLAST

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Advances in Knowledge Discovery and Data Mining (PAKDD 2004)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3056))

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Abstract

Scientific research reports usually contain a list of citations on previous related works. Therefore an automatic citation tool is an essential component of a digital library of scientific literatures. Due to variations in formats, it is difficult to automatically transform semi-structured citation data into structured citations. Some digital library institutes, like ResearchIndex (CiteSeer) or OpCit, have attempted automatic citation parsing. In order to recognize metadata, e.g., authors, title, journal, etc., of a citation string, we present a new methodology based on protein sequence alignment tool. We also develop a template generating system to transform known semi-structured citation strings into protein sequences. These protein sequences are then saved as templates in a database. A new semi-structured citation string is also translated it into a protein sequence. We then use BLAST (Basic Local Alignment Search Tool), a sequence alignment tool, to match for the most similar template to the new protein sequence from the template database previously constructed. We then parse metadata of the citation string according to the template. In our experiment, 2,500 templates are generated by our template generating system. By parsing all of these 2,500 citations using our parsing system, we obtain 89% precision rate. However, using the same template database to train ParaTools, 79% precision rate is obtained. Note that the original ParaTools using its default template database, which contains about 400 templates, only obtains 30% precision rate.

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References

  1. Lee Giles, C., Bollacker, K.D., Lawrence, S.: CiteSeer: An Automatic Citation Indexing System. In: Digital Libraries 1998, Pittsburgh, PA, USA (1998)

    Google Scholar 

  2. Bollacker, K.D., Lawrence, S., Lee Giles, C.: CiteSeer: An Autonomous Web Agent for Automatic Retrieval and Identification of Interesting Publications. In: 2nd International ACM Conference on Autonomous Agents, May 1998, pp. 116–123. ACM Press, New York (1998)

    Chapter  Google Scholar 

  3. Lawrence, S., Lee Giles, C., Bollacker, K.D.: Autonomous Citation Matching. In: Proceedings of the Third International Conference on Autonomous Agents, Seattle, Washington, May 1-5, ACM Press, New York (1999)

    Google Scholar 

  4. Lawrence, S., Lee Giles, C., Bollacker, K.D.: Digital Libraries and Autonomous Citation Indexing. IEEE Computer 32(6), 67–71 (1999)

    Google Scholar 

  5. Harnad, S., Carr, L.: Integrating, Navigating and Analyzing Eprint Archives Through Open Citation Linking (the OpCit Project). Current Science (special issue honour of Eugene Garfield) 79, 629–638 (2000)

    Google Scholar 

  6. Bergmark, D.: Automatic Extraction of Reference Linking Information from Online Documents, Cornell University Technical Report, TR 2000-1821 (November 2000)

    Google Scholar 

  7. Bergmark, D., Lagoze, C.: An Architecture for Automatic Reference Linking, Cornell University Technical Report, TR 2000-1820 (October 2000)

    Google Scholar 

  8. Jewell, M.: ParaTools Reference Parsing Toolkit - Version 1.0 Released. D-Lib Magazine 9(2) (February 2003)

    Google Scholar 

  9. Altschul, S.F., Gish, W., Miller, W., Myers, E., Lipman, D.: A basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

    Google Scholar 

  10. http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html

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Author information

Authors and Affiliations

  1. Institute of Information Science, Academia Sinica, Taiwan

    I-Ane Huang, Jan-Ming Ho & Hung-Yu Kao

  2. Institute of Biomedical Sciences, Academia Sinica, Taiwan

    Wen-Chang Lin

Authors
  1. I-Ane Huang
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  2. Jan-Ming Ho
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  3. Hung-Yu Kao
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  4. Wen-Chang Lin
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Editor information

Editors and Affiliations

  1. School of Engineering and Information Technology, Deakin University, VIC 3125, Australia

    Honghua Dai

  2. University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA

    Ramakrishnan Srikant

  3. Faculty of Engineering and Information Technology, Centre for Quantum Computation and Intelligent Systems, and Australian ACS National Committee for Artificial Intelligence, University of Technology, Sydney, Australia

    Chengqi Zhang

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© 2004 Springer-Verlag Berlin Heidelberg

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Huang, IA., Ho, JM., Kao, HY., Lin, WC. (2004). Extracting Citation Metadata from Online Publication Lists Using BLAST. In: Dai, H., Srikant, R., Zhang, C. (eds) Advances in Knowledge Discovery and Data Mining. PAKDD 2004. Lecture Notes in Computer Science(), vol 3056. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24775-3_64

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  • DOI: https://doi.org/10.1007/978-3-540-24775-3_64

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-22064-0

  • Online ISBN: 978-3-540-24775-3

  • eBook Packages: Springer Book Archive

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