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Management of Genotyping-Related Documents by Integrated Use of Semantic Tagging

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Transactions on Large-Scale Data- and Knowledge-Centered Systems IV

Part of the book series: Lecture Notes in Computer Science ((TLDKS,volume 6990))

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Abstract

A widespread need is present in molecular biology laboratories for software systems to support the internal management of data and documents. A typical case is represented by genotyping procedures, which produce a large amount of documents whose content may represent a potentially important knowledge base. The exploitation of such information requires a proper classification of the elements in the knowledge base, and this can be effectively achieved using concepts and tools from research on the Semantic Web. In particular, genotyping-related documents can be handled through a DMS (Document Management System) that is also able to deal with semantic metadata, e.g. in the form of tags. The use of semantic tagging at this operating level is currently hampered by the lack of proper tools. In this paper, based on experience from a practical case, we present an integrated approach to manage relevant genotyping documents and to deal with their semantic tagging. A preliminary study on the test procedures workflow is crucial to understand the document production processes. The employed semantic annotation makes use of terms taken from domain ontologies in the biomedical field. The annotation tool must be seamlessly integrated in the supporting DMS; the tool flexibility and usability guarantee a low overhead for the annotation process, paving the way for a widespread adoption of semantic tagging for genotyping-related documents.

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Author information

Authors and Affiliations

  1. Dept. of Information Engineering, Univ. of Pisa, largo Lazzarino, 56126, Pisa, Italy

    Alessio Bechini

  2. Dept. of Surgery, Univ. of Pisa, via Paradisa, 2, 56124, Pisa, Italy

    Riccardo Giannini

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  1. Alessio Bechini
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  2. Riccardo Giannini
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Editor information

Editors and Affiliations

  1. Institut de Recherche en Informatique de Toulouse (IRIT), Paul Sabatier University, 118, route de Narbonne, 31062, Toulouse Cedex, France

    Abdelkader Hameurlain

  2. University of Linz, FAW, Altenbergerstraße 69, 4040, Linz, Austria

    Josef Küng  & Roland Wagner  & 

  3. Department of Computer Science, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538, München, Germany

    Christian Böhm

  4. Institut für Informatik-Systeme, Alpen Adria Universität Klagenfurt, Universitätsstr. 65, 9020, Klagenfurt, Austria

    Johann Eder

  5. Department of Scientific Computing, Florida State University, 400 Dirac Science Library, 32306-4120, Tallahassee, FL, USA

    Claudia Plant

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Bechini, A., Giannini, R. (2011). Management of Genotyping-Related Documents by Integrated Use of Semantic Tagging. In: Hameurlain, A., Küng, J., Wagner, R., Böhm, C., Eder, J., Plant, C. (eds) Transactions on Large-Scale Data- and Knowledge-Centered Systems IV. Lecture Notes in Computer Science, vol 6990. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23740-9_2

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  • DOI: https://doi.org/10.1007/978-3-642-23740-9_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-23739-3

  • Online ISBN: 978-3-642-23740-9

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