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- Title
DTMiner: identification of potential disease targets through biomedical literature mining.
- Authors
Dong Xu; Meizhuo Zhang; Yanping Xie; Fan Wang; Ming Chen; Zhu, Kenny Q.; Jia Wei
- Abstract
Motivation: Biomedical researchers often search through massive catalogues of literature to look for potential relationships between genes and diseases. Given the rapid growth of biomedical literature, automatic relation extraction, a crucial technology in biomedical literature mining, has shown great potential to support research of gene-related diseases. Existing work in this field has produced datasets that are limited both in scale and accuracy. Results: In this study, we propose a reliable and efficient framework that takes large biomedical literature repositories as inputs, identifies credible relationships between diseases and genes, and presents possible genes related to a given disease and possible diseases related to a given gene. The framework incorporates name entity recognition (NER), which identifies occurrences of genes and diseases in texts, association detection whereby we extract and evaluate features from gene-disease pairs, and ranking algorithms that estimate how closely the pairs are related. The F1-score of the NER phase is 0.87, which is higher than existing studies. The association detection phase takes drastically less time than previous work while maintaining a comparable F1-score of 0.86. The end to- end result achieves a 0.259 F1-score for the top 50 genes associated with a disease, which performs better than previous work. In addition, we released a web service for public use of the dataset.
- Subjects
DISEASES; GENES; ALGORITHMS; WEB services; MEDICAL research
- Publication
Bioinformatics, 2016, Vol 32, Issue 23, p3619
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btw503