Journal article
Annokey: An annotation tool based on key term search of the NCBI Entrez Gene database
DJ Park, T Nguyen-Dumont, S Kang, K Verspoor, BJ Pope
Source Code for Biology and Medicine | BMC | Published : 2014
Abstract
Background: The NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual search for a small number of genes but impractical for the kinds of outputs seen in typical genomics projects.Results: We have developed an efficient open source tool implemented in Python called Annokey, which annotates gene lists with the results of a keyword search of the NCBI Entrez Gene database and linked Pubmed article information. The user steers the search by specifying a ranked list of keywords (including multi-word phrases and regular expressions) that are correlated ..
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Grants
Awarded by European Molecular Biology Laboratory
Funding Acknowledgements
This work was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0182 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government. This work was also supported by National Health and Medical Research Council (NHMRC) of Australia Project Grants 1028280 and 1025145. SK's work at VLSCI was made possible through the 2012 AMSI Bioinformatics Internships supported by EMBL Australia and Bio Platforms Australia. KV participated in this work initially while working at NICTA. NICTA is supported by Australian Federal and Victorian State Governments and the Australian Research Council through the ICT Centre of Excellence program. TN-D is the recipient of a post-doctoral fellowship from Susan G. Komen