PubTator: a web-based text mining tool for assisting biocuration

Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we descr...

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Bibliographic Details
Published in:Nucleic acids research Vol. 41; no. W1; pp. W518 - W522
Main Authors: Wei, Chih-Hsuan, Kao, Hung-Yu, Lu, Zhiyong
Format: Journal Article
Language:English
Published: England Oxford University Press 01.07.2013
Subjects:
Data Mining - methods
Databases, Factual
Internet
PubMed
Software
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary:Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkt441