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BioCreative V track 4: A shared task for the extraction of causal network information using the Biological Expression Language

: Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; Lek, Adrian van der; Mevissen, Theo; Fluck, Juliane

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Database (2016), Art. baw067, 15 S.
ISSN: 1758-0463
Zeitschriftenaufsatz, Elektronische Publikation
Fraunhofer SCAI ()

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.