Article (Scientific journals)
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships.
Barbosa Da Silva, Adriano; Soldatos, Theodoros G.; Magalhaes, Ivan L. F. et al.
2010In BMC Bioinformatics, 11, p. 70
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Keywords :
Computational Biology/methods; Data Mining/methods; Information Storage and Retrieval/methods; MEDLINE; Publications; Software; United States
Abstract :
[en] BACKGROUND: Biological knowledge is represented in scientific literature that often describes the function of genes/proteins (bioentities) in terms of their interactions (biointeractions). Such bioentities are often related to biological concepts of interest that are specific of a determined research field. Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context. RESULTS: We created a text mining system (LAITOR: Literature Assistant for Identification of Terms co-Occurrences and Relationships) that analyses co-occurrences of bioentities, biointeractions, and other biological terms in MEDLINE abstracts. The method accounts for the position of the co-occurring terms within sentences or abstracts. The system detected abstracts mentioning protein-protein interactions in a standard test (BioCreative II IAS test data) with a precision of 0.82-0.89 and a recall of 0.48-0.70. We illustrate the application of LAITOR to the detection of plant response genes in a dataset of 1000 abstracts relevant to the topic. CONCLUSIONS: Text mining tools combining the extraction of interacting bioentities and biological concepts with network displays can be helpful in developing reasonable hypotheses in different scientific backgrounds.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Biochemistry, biophysics & molecular biology
Identifiers :
UNILU:UL-ARTICLE-2012-051
Author, co-author :
Barbosa Da Silva, Adriano ;  European Molecular Biology Laboratory - EMBL
Soldatos, Theodoros G.
Magalhaes, Ivan L. F.
Pavlopoulos, Georgios A.
Fontaine, Jean-Fred
Andrade-Navarro, Miguel A.
Schneider, Reinhard ;  European Molecular Biology Laboratory - EMBL
Ortega, J. Miguel
Language :
English
Title :
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships.
Publication date :
2010
Journal title :
BMC Bioinformatics
ISSN :
1471-2105
Publisher :
BioMed Central, United Kingdom
Volume :
11
Pages :
70
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 25 June 2014

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