GOTA: GO term annotation of biomedical literature

BMC Bioinformatics

Methodology Article

Luciano Margara¹  Pietro Di Lena¹  Giacomo Domeniconi¹  Gianluca Moro¹ 

[1] Department of Computer Science and Engineering, University of Bologna, Cesena Campus, Via Sacchi 3, 47521, Cesena, Italy;

关键词: Automated annotation;    Text mining;    Gene Ontology;   

DOI  :  10.1186/s12859-015-0777-8

 received in 2015-03-16, accepted in 2015-10-13,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundFunctional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes by using published literature. The annotation task is extremely time-consuming, therefore there is an increasing interest in automated tools that can assist human experts.ResultsHere we introduce GOTA, a GO term annotator for biomedical literature. The proposed approach makes use only of information that is readily available from public repositories and it is easily expandable to handle novel sources of information. We assess the classification capabilities of GOTA on a large benchmark set of publications. The overall performances are encouraging in comparison to the state of the art in multi-label classification over large taxonomies. Furthermore, the experimental tests provide some interesting insights into the potential improvement of automated annotation tools.ConclusionsGOTA implements a flexible and expandable model for GO annotation of biomedical literature. The current version of the GOTA tool is freely available at http://gota.apice.unibo.it.

【 授权许可】

CC BY   
© Di Lena et al. 2015