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Caipirini: using gene sets to rank literature

Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Carolina Wanderley-Nogueira, Nina Mota Soares-Cavalcanti, Reinhard Schneider
2012 BioData Mining  
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:// that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes  ...  These gene sets were then used as input to Caipirini to rank the results of a PubMed query that specifies~4,000 abstracts known to be related to S-phase.  ... 
doi:10.1186/1756-0381-5-1 pmid:22297131 pmcid:PMC3307494 fatcat:23kojsxtwnbxlmdv6izswjdhsm

CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation

Nan Qiao, Yi Huang, Hammad Naveed, Christopher D. Green, Jing-Dong J. Han, Vladimir B. Bajic
2013 PLoS ONE  
A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways.  ...  Co-citation analysis is widely used in ranking articles and predicting protein-protein interactions (PPIs).  ...  To find the co-citation literature related to a gene, Caipirini [18] and Martini [15] use the ''gene2pubmed'' dataset (a manually curated gene to PubMed literature relationship dataset provided by  ... 
doi:10.1371/journal.pone.0074074 pmid:24086311 pmcid:PMC3781068 fatcat:qphuyfiwqfau7iypsuwcaqne74

Accessing Biomedical Literature in the Current Information Landscape [chapter]

Ritu Khare, Robert Leaman, Zhiyong Lu
2014 Msphere  
The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results.  ...  The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar,  ...  Caipirini, for example, allows the user to specify a set of genes that are of interest and a set of genes that are not of interest [44] .  ... 
doi:10.1007/978-1-4939-0709-0_2 pmid:24788259 pmcid:PMC4593617 fatcat:xilfx32asrd3lhrmfirfgq7o4u

BioTextQuest + : a knowledge integration platform for literature mining and concept discovery

Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos
2014 Computer applications in the biosciences : CABIOS  
BioTextQuest + enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within  ...  The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users.  ...  ACKNOWLEDGEMENTS The authors wish to thank the four anonymous reviewers for invaluable comments. I.I. and V.P.S. would like to thank I. Manolakis for fruitful discussions.  ... 
doi:10.1093/bioinformatics/btu524 pmid:25100685 fatcat:gyf7y7qvxfbb5maq4ofsrrh25a