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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| Published in: | Nucleic acids research Vol. 41; no. W1; pp. W518 - W522 |
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| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Oxford University Press
01.07.2013
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| Subjects: | |
| ISSN: | 0305-1048, 1362-4962, 1362-4962 |
| Online Access: | Get full text |
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| Abstract | 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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| AbstractList | 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/. 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/.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/. |
| Author | Wei, Chih-Hsuan Lu, Zhiyong Kao, Hung-Yu |
| AuthorAffiliation | 1 National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA and 2 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, 701, Taiwan, R.O.C |
| AuthorAffiliation_xml | – name: 1 National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA and 2 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, 701, Taiwan, R.O.C |
| Author_xml | – sequence: 1 givenname: Chih-Hsuan surname: Wei fullname: Wei, Chih-Hsuan – sequence: 2 givenname: Hung-Yu surname: Kao fullname: Kao, Hung-Yu – sequence: 3 givenname: Zhiyong surname: Lu fullname: Lu, Zhiyong |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23703206$$D View this record in MEDLINE/PubMed |
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| Title | PubTator: a web-based text mining tool for assisting biocuration |
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