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Caipirini: using gene sets to rank literature
2012
BioData Mining
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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 ...
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
2013
PLoS ONE
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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]
2014
Msphere
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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
2014
Computer applications in the biosciences : CABIOS
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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