The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track.

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ID: 61914
2019
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Abstract
Knowledge of the molecular interactions of biological and chemical entities and their involvement in biological processes or clinical phenotypes is important for data interpretation. Unfortunately, this knowledge is mostly embedded in the literature in such a way that it is unavailable for automated data analysis procedures. Biological expression language (BEL) is a syntax representation allowing for the structured representation of a broad range of biological relationships. It is used in various situations to extract such knowledge and transform it into BEL networks. To support the tedious and time-intensive extraction work of curators with automated methods, we developed the BEL track within the framework of BioCreative Challenges. Within the BEL track, we provide training data and an evaluation environment to encourage the text mining community to tackle the automatic extraction of complex BEL relationships. In 2017 BioCreative VI, the 2015 BEL track was repeated with new test data. Although only minor improvements in text snippet retrieval for given statements were achieved during this second BEL task iteration, a significant increase of BEL statement extraction performance from provided sentences could be seen. The best performing system reached a 32% F-score for the extraction of complete BEL statements and with the given named entities this increased to 49%. This time, besides rule-based systems, new methods involving hierarchical sequence labeling and neural networks were applied for BEL statement extraction.
Reference Key
madan2019thedatabase Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Madan, Sumit;Szostak, Justyna;Komandur Elayavilli, Ravikumar;Tsai, Richard Tzong-Han;Ali, Mehdi;Qian, Longhua;Rastegar-Mojarad, Majid;Hoeng, Julia;Fluck, Juliane;
Journal Database : the journal of biological databases and curation
Year 2019
DOI
baz084
URL
Keywords
experimental methods spanish syntax weird word order

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