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Coreference resolution improves extraction of Biological Expression Language statements from texts
We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreference resolution, biological event extraction and a...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930833/ https://www.ncbi.nlm.nih.gov/pubmed/27374122 http://dx.doi.org/10.1093/database/baw076 |
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author | Choi, Miji Liu, Haibin Baumgartner, William Zobel, Justin Verspoor, Karin |
author_facet | Choi, Miji Liu, Haibin Baumgartner, William Zobel, Justin Verspoor, Karin |
author_sort | Choi, Miji |
collection | PubMed |
description | We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreference resolution, biological event extraction and a previously formally untested strategy for BEL statement generation. Although addressing the BEL track (Track 4) at BioCreative V (2015), we also investigate how incorporating coreference resolution might impact event extraction in the biomedical domain. In this paper, we report that our system achieved the best performance of 20.2 and 35.2 in F-score for the full BEL statement level on both stage 1, and stage 2 using provided gold standard entities, respectively. We also report that our results evaluated on the training dataset show benefit from integrating coreference resolution with event extraction. |
format | Online Article Text |
id | pubmed-4930833 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-49308332016-07-05 Coreference resolution improves extraction of Biological Expression Language statements from texts Choi, Miji Liu, Haibin Baumgartner, William Zobel, Justin Verspoor, Karin Database (Oxford) Original Article We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreference resolution, biological event extraction and a previously formally untested strategy for BEL statement generation. Although addressing the BEL track (Track 4) at BioCreative V (2015), we also investigate how incorporating coreference resolution might impact event extraction in the biomedical domain. In this paper, we report that our system achieved the best performance of 20.2 and 35.2 in F-score for the full BEL statement level on both stage 1, and stage 2 using provided gold standard entities, respectively. We also report that our results evaluated on the training dataset show benefit from integrating coreference resolution with event extraction. Oxford University Press 2016-07-02 /pmc/articles/PMC4930833/ /pubmed/27374122 http://dx.doi.org/10.1093/database/baw076 Text en © The Author(s) 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Choi, Miji Liu, Haibin Baumgartner, William Zobel, Justin Verspoor, Karin Coreference resolution improves extraction of Biological Expression Language statements from texts |
title | Coreference resolution improves extraction of Biological Expression Language statements from texts |
title_full | Coreference resolution improves extraction of Biological Expression Language statements from texts |
title_fullStr | Coreference resolution improves extraction of Biological Expression Language statements from texts |
title_full_unstemmed | Coreference resolution improves extraction of Biological Expression Language statements from texts |
title_short | Coreference resolution improves extraction of Biological Expression Language statements from texts |
title_sort | coreference resolution improves extraction of biological expression language statements from texts |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930833/ https://www.ncbi.nlm.nih.gov/pubmed/27374122 http://dx.doi.org/10.1093/database/baw076 |
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