SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit

Stöckel A, Paaßen B, Dickfelder R, Göpfert JP, Brazda N, Müller HW, Cimiano P, Hartung M, Klinger R (2015)
bioRxive.org.

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Abstract
Translational neuroscience in the field of spinal cord injuries (SCI) faces a strong disproportion between immense preclinical research efforts and a lack of therapeutic approaches success- ful in human patients: Currently, preclinical research on SCI yields more than 3,000 new publications per year (8,000 when including the whole central nervous system, growing at an exponential rate), whereas none of the result- ing therapeutic concepts has led to functional recovery of neural tissue in humans. Improving clinical researchers’ information access there- fore carries the potential to support more effec- tive selection of promising therapy candidates from preclinical studies. Thus, automated in- formation extraction from scientific publica- tions contributes to enabling meta studies and therapy grading by aggregating relevant infor- mation from the entire body of previous work on SCI. We present SCIE, an automated information extraction pipeline capable of detecting rele- vant information in SCI publications based on ontological entity and probabilistic relation de- tection. The input are plain text or PDF doc- uments. As output, the user choses between an online visualization or a machine-readable format. Compared to human gold standard annotations, our system achieves an average extraction performance of 76 % precision and 52 % recall (F1-measure 0.59). An instance of the webservice is available at http://scie.sc.cit-ec.uni-bielefeld.de/. SCIE is free software licensed under the AGPL and can be downloaded for local installation at http: //opensource.cit-ec.de/projects/scie/.
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Stöckel A, Paaßen B, Dickfelder R, et al. SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit. bioRxive.org; 2015.
Stöckel, A., Paaßen, B., Dickfelder, R., Göpfert, J. P., Brazda, N., Müller, H. W., Cimiano, P., et al. (2015). SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit. bioRxive.org. doi:10.1101/013458
Stöckel, A., Paaßen, B., Dickfelder, R., Göpfert, J. P., Brazda, N., Müller, H. W., Cimiano, P., Hartung, M., and Klinger, R. (2015). SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit. bioRxive.org.
Stöckel, A., et al., 2015. SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit, bioRxive.org.
A. Stöckel, et al., SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit, bioRxive.org: 2015.
Stöckel, A., Paaßen, B., Dickfelder, R., Göpfert, J.P., Brazda, N., Müller, H.W., Cimiano, P., Hartung, M., Klinger, R.: SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit. bioRxive.org (2015).
Stöckel, Andreas, Paaßen, Benjamin, Dickfelder, Raphael, Göpfert, Jan Philip, Brazda, Nicole, Müller, Hans Werner, Cimiano, Philipp, Hartung, Matthias, and Klinger, Roman. SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments – A Webservice and Open Source Toolkit. bioRxive.org, 2015.
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