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LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

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Item Type:Article
Title:LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships
Creators Name:Barbosa-Silva, A., Soldatos, T.G., Magalhaes, I.L., Pavlopoulos, G.A., Fontaine, J.F., Andrade-Navarro, M.A., Schneider, R. and Ortega, J.M.
Abstract: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.
Keywords:Computational Biology, Data Mining, Information Storage and Retrieval, MEDLINE, Publications, Software, United States
Source:BMC Bioinformatics
Publisher:BioMed Central
Page Range:70
Date:1 February 2010
Official Publication:https://doi.org/10.1186/1471-2105-11-70
PubMed:View item in PubMed

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