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Layout-Aware Semi-automatic Information Extraction for Pharmaceutical Documents

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Data Integration in the Life Sciences (DILS 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10649))

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Abstract

Pharmaceutical companies and regulatory authorities are also affected by the current digitalization process and transform their paper-based, document-oriented communication to a structured, digital information exchange. The documents exchanged so far contain a huge amount of information that needs to be transformed into a structured format to enable a more efficient communication in the future. In such a setting, it is important that the information extracted from documents is very accurate as the information is used in a legal, regulatory process and also for the identification of unknown adverse effects of medicinal products that might be a threat to patients’ health. In this paper, we present our layout-aware semi-automatic information extraction system LASIE that combines techniques from rule-based information extraction, flexible data management, and semantic information management in a user-centered design. We applied the system in a case study with an industrial partner and achieved very satisfying results.

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Notes

  1. 1.

    The example has been taken from http://agence-tst.ansm.sante.fr/html/pdf/3/expor.pdf which is actually an export license of the French authority (ANSM). The manufacturing licenses which we considered in our use case had a similar structure; due to reasons of confidentiality, we cannot show the documents which we processed.

  2. 2.

    http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000645.jsp.

  3. 3.

    Optical character recognition.

  4. 4.

    MedDRA® trademark is owned by IFPMA on behalf of ICH. There are other medical terminology systems (or ontologies) available, but we have to use MedDRA® as it is the terminology required by the authorities.

  5. 5.

    https://www.meddra.org/how-to-use/basics/hierarchy.

  6. 6.

    https://poi.apache.org/.

  7. 7.

    https://pdfbox.apache.org/.

  8. 8.

    The final layout of such documents depend on many factors, including especially the settings of the selected printer. Thus, the layout of a certain page is not stored in the file, but only created when the document is rendered on a screen or printer.

  9. 9.

    https://www.drools.org/.

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Acknowledgements

This work has been partially funded by the German Federal Ministry of Education and Research (BMBF) (project HUMIT, http://humit.de/, grant no. 01IS14007A).

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Authors and Affiliations

  1. Fraunhofer Institute for Applied Information Technology FIT Schloss Birlinghoven, 53754, Sankt Augustin, Germany

    Simon Harmata, Katharina Hofer-Schmitz, Phuong-Ha Nguyen, Christoph Quix & Bujar Bakiu

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  1. Simon Harmata
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  2. Katharina Hofer-Schmitz
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  3. Phuong-Ha Nguyen
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  4. Christoph Quix
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  5. Bujar Bakiu
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Corresponding author

Correspondence to Christoph Quix .

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Editors and Affiliations

  1. Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg

    Marcos Da Silveira

  2. Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg

    CĂ©dric Pruski

  3. Université du Luxembourg, Esch-sur-Alzette, Luxembourg

    Reinhard Schneider

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Harmata, S., Hofer-Schmitz, K., Nguyen, PH., Quix, C., Bakiu, B. (2017). Layout-Aware Semi-automatic Information Extraction for Pharmaceutical Documents. In: Da Silveira, M., Pruski, C., Schneider, R. (eds) Data Integration in the Life Sciences. DILS 2017. Lecture Notes in Computer Science(), vol 10649. Springer, Cham. https://doi.org/10.1007/978-3-319-69751-2_8

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  • DOI: https://doi.org/10.1007/978-3-319-69751-2_8

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