Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Choi, Miji, Liu, Haibin, Baumgartner, William, Zobel, Justin, Verspoor, Karin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
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
_version_ 1782440793023184896
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
work_keys_str_mv AT choimiji coreferenceresolutionimprovesextractionofbiologicalexpressionlanguagestatementsfromtexts
AT liuhaibin coreferenceresolutionimprovesextractionofbiologicalexpressionlanguagestatementsfromtexts
AT baumgartnerwilliam coreferenceresolutionimprovesextractionofbiologicalexpressionlanguagestatementsfromtexts
AT zobeljustin coreferenceresolutionimprovesextractionofbiologicalexpressionlanguagestatementsfromtexts
AT verspoorkarin coreferenceresolutionimprovesextractionofbiologicalexpressionlanguagestatementsfromtexts