TY - JOUR
T1 - Accelerating literature curation with text-mining tools
T2 - a case study of using PubTator to curate genes in PubMed abstracts.
AU - Wei, Chih Hsuan
AU - Harris, Bethany R.
AU - Li, Donghui
AU - Berardini, Tanya Z.
AU - Huala, Eva
AU - Kao, Hung Yu
AU - Lu, Zhiyong
PY - 2012
Y1 - 2012
N2 - Today's biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/
AB - Today's biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/
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U2 - 10.1093/database/bas041
DO - 10.1093/database/bas041
M3 - Article
C2 - 23160414
AN - SCOPUS:84876499465
SN - 1758-0463
VL - 2012
SP - bas041
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
ER -