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

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W518-22. doi: 10.1093/nar/gkt441. Epub 2013 May 22.


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

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Data Mining / methods*
  • Databases, Factual*
  • Internet
  • PubMed
  • Software*