Towards automatic pathway generation from biological full-text publications

Authors:
Ekaterina Buyko;Jörg Linde;Steffen Priebe;Udo Hahn
Affiliations:
Jena University Language & Information Engineering Lab, Friedrich-Schiller-Universität Jena, Germany;Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute;Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute;Jena University Language & Information Engineering Lab, Friedrich-Schiller-Universität Jena, Germany
Venue:
IDA'11 Proceedings of the 10th international conference on Advances in intelligent data analysis X
Year:
2011

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Abstract

We introduce an approach to the automatic generation of biological pathway diagrams from scientific literature. It is composed of the automatic extraction of single interaction relations which are typically found in the full text (rather than the abstract) of a scientific publication, and their subsequent integration into a complex pathway diagram. Our focus is here on relation extraction from full-text documents. We compare the performance of automatic full-text extraction procedures with a manually generated gold standard in order to validate the extracted data which serve as input for the pathway integration procedure.