A multistage gene normalization system integrating multiple effective methods.

Gene/protein recognition and normalization is an important preliminary step for many biological text mining tasks. In this paper, we present a multistage gene normalization system which consists of four major subtasks: pre-processing, dictionary matching, ambiguity resolution and filtering. For the...

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Autores principales:	Lishuang Li, Shanshan Liu, Lihua Li, Wenting Fan, Degen Huang, Huiwei Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7f91ad66d832460faae95589572a508b
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id	oai:doaj.org-article:7f91ad66d832460faae95589572a508b
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spelling	oai:doaj.org-article:7f91ad66d832460faae95589572a508b2021-11-18T08:42:16ZA multistage gene normalization system integrating multiple effective methods.1932-620310.1371/journal.pone.0081956https://doaj.org/article/7f91ad66d832460faae95589572a508b2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24349160/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Gene/protein recognition and normalization is an important preliminary step for many biological text mining tasks. In this paper, we present a multistage gene normalization system which consists of four major subtasks: pre-processing, dictionary matching, ambiguity resolution and filtering. For the first subtask, we apply the gene mention tagger developed in our earlier work, which achieves an F-score of 88.42% on the BioCreative II GM testing set. In the stage of dictionary matching, the exact matching and approximate matching between gene names and the EntrezGene lexicon have been combined. For the ambiguity resolution subtask, we propose a semantic similarity disambiguation method based on Munkres' Assignment Algorithm. At the last step, a filter based on Wikipedia has been built to remove the false positives. Experimental results show that the presented system can achieve an F-score of 90.1%, outperforming most of the state-of-the-art systems.Lishuang LiShanshan LiuLihua LiWenting FanDegen HuangHuiwei ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e81956 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lishuang Li Shanshan Liu Lihua Li Wenting Fan Degen Huang Huiwei Zhou A multistage gene normalization system integrating multiple effective methods.
description	Gene/protein recognition and normalization is an important preliminary step for many biological text mining tasks. In this paper, we present a multistage gene normalization system which consists of four major subtasks: pre-processing, dictionary matching, ambiguity resolution and filtering. For the first subtask, we apply the gene mention tagger developed in our earlier work, which achieves an F-score of 88.42% on the BioCreative II GM testing set. In the stage of dictionary matching, the exact matching and approximate matching between gene names and the EntrezGene lexicon have been combined. For the ambiguity resolution subtask, we propose a semantic similarity disambiguation method based on Munkres' Assignment Algorithm. At the last step, a filter based on Wikipedia has been built to remove the false positives. Experimental results show that the presented system can achieve an F-score of 90.1%, outperforming most of the state-of-the-art systems.
format	article
author	Lishuang Li Shanshan Liu Lihua Li Wenting Fan Degen Huang Huiwei Zhou
author_facet	Lishuang Li Shanshan Liu Lihua Li Wenting Fan Degen Huang Huiwei Zhou
author_sort	Lishuang Li
title	A multistage gene normalization system integrating multiple effective methods.
title_short	A multistage gene normalization system integrating multiple effective methods.
title_full	A multistage gene normalization system integrating multiple effective methods.
title_fullStr	A multistage gene normalization system integrating multiple effective methods.
title_full_unstemmed	A multistage gene normalization system integrating multiple effective methods.
title_sort	multistage gene normalization system integrating multiple effective methods.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7f91ad66d832460faae95589572a508b
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_version_	1718421454614167552

A multistage gene normalization system integrating multiple effective methods.

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