Article (Scientific journals)
Caipirini: using gene sets to rank literature
Soldatos, Theodoros G.; O’Donoghue, S. I.; Satagopam, V. P. et al.
2012In BioData Mining, 5 (1)
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Abstract :
[en] Background: Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be ‘interesting’. Some methods go further by allowing the user to provide a second input set of ‘uninteresting’ abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service ‘Caipirini’ (http:// caipirini.org) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes. Results: To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in Arabidopsis thaliana. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets. Conclusions: To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Biochemistry, biophysics & molecular biology
Identifiers :
UNILU:UL-ARTICLE-2012-377
Author, co-author :
Soldatos, Theodoros G.;  EMBL Heidelberg
O’Donoghue, S. I.
Satagopam, V. P.
Barbosa-Silva, A.
Pavlopoulos, Georgios A.
Wanderley-Nogueira, A. C.
Soares-Cavalcanti, N. M.
Schneider, Reinhard ;  EMBL Heidelberg
External co-authors :
yes
Language :
English
Title :
Caipirini: using gene sets to rank literature
Publication date :
2012
Journal title :
BioData Mining
ISSN :
1756-0381
Publisher :
BioMed Central, London, United Kingdom
Volume :
5
Issue :
1
Peer reviewed :
Peer Reviewed verified by ORBi
Additional URL :
Commentary :
in press
Available on ORBilu :
since 25 June 2014

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