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| Item Type: | Article |
|---|---|
| Title: | LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships |
| Creators Name: | Barbosa-Silva, A. and Soldatos, T.G. and Magalhaes, I.L. and Pavlopoulos, G.A. and Fontaine, J.F. and Andrade-Navarro, M.A. and 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 |
| ISSN: | 1471-2105 |
| Publisher: | BioMed Central |
| Volume: | 11 |
| Number: | 1 |
| 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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