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PIPE: a protein–protein interaction passage extraction module for BioCreative challenge
Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioC...
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/PMC4983456/ https://www.ncbi.nlm.nih.gov/pubmed/27524807 http://dx.doi.org/10.1093/database/baw101 |
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author | Chang, Yung-Chun Chu, Chun-Han Su, Yu-Chen Chen, Chien Chin Hsu, Wen-Lian |
author_facet | Chang, Yung-Chun Chu, Chun-Han Su, Yu-Chen Chen, Chien Chin Hsu, Wen-Lian |
author_sort | Chang, Yung-Chun |
collection | PubMed |
description | Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL: |
format | Online Article Text |
id | pubmed-4983456 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-49834562016-08-17 PIPE: a protein–protein interaction passage extraction module for BioCreative challenge Chang, Yung-Chun Chu, Chun-Han Su, Yu-Chen Chen, Chien Chin Hsu, Wen-Lian Database (Oxford) Original Article Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL: Oxford University Press 2016-08-14 /pmc/articles/PMC4983456/ /pubmed/27524807 http://dx.doi.org/10.1093/database/baw101 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 Chang, Yung-Chun Chu, Chun-Han Su, Yu-Chen Chen, Chien Chin Hsu, Wen-Lian PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title | PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title_full | PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title_fullStr | PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title_full_unstemmed | PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title_short | PIPE: a protein–protein interaction passage extraction module for BioCreative challenge |
title_sort | pipe: a protein–protein interaction passage extraction module for biocreative challenge |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983456/ https://www.ncbi.nlm.nih.gov/pubmed/27524807 http://dx.doi.org/10.1093/database/baw101 |
work_keys_str_mv | AT changyungchun pipeaproteinproteininteractionpassageextractionmoduleforbiocreativechallenge AT chuchunhan pipeaproteinproteininteractionpassageextractionmoduleforbiocreativechallenge AT suyuchen pipeaproteinproteininteractionpassageextractionmoduleforbiocreativechallenge AT chenchienchin pipeaproteinproteininteractionpassageextractionmoduleforbiocreativechallenge AT hsuwenlian pipeaproteinproteininteractionpassageextractionmoduleforbiocreativechallenge |