title: BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.
abstract: Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text.
authors.affiliation: Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland fabio.rinaldi@uzh.ch juliane.fluck@scai.fraunhofer.de.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rinaldi
authors.affiliation: Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland.
authors.forename: Tilia Renate
authors.initials: TR
authors.lastname: Ellendorff
authors.affiliation: Fraunhofer Institute for Algorithms and Scientiﬁc Computing, Schloss Birlinghoven, Sankt Augustin, Germany.
authors.forename: Sumit
authors.initials: S
authors.lastname: Madan
authors.affiliation: Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland.
authors.forename: Simon
authors.initials: S
authors.lastname: Clematide
authors.affiliation: Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland.
authors.forename: Adrian
authors.initials: A
authors.lastname: van der Lek
authors.affiliation: Fraunhofer Institute for Algorithms and Scientiﬁc Computing, Schloss Birlinghoven, Sankt Augustin, Germany.
authors.forename: Theo
authors.initials: T
authors.lastname: Mevissen
authors.affiliation: Fraunhofer Institute for Algorithms and Scientiﬁc Computing, Schloss Birlinghoven, Sankt Augustin, Germany fabio.rinaldi@uzh.ch juliane.fluck@scai.fraunhofer.de.
authors.forename: Juliane
authors.initials: J
authors.lastname: Fluck
mesh_terms: D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D011381:Programming Languages