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. 2015;9 Suppl 2(Suppl 2):S2.
doi: 10.1186/1752-0509-9-S2-S2. Epub 2015 Apr 15.

ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology

Vladimir A Ivanisenko, Olga V Saik, Nikita V Ivanisenko, Evgeny S Tiys, Timofey V Ivanisenko, Pavel S Demenkov, Nikolay A Kolchanov

ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology

Vladimir A Ivanisenko et al. BMC Syst Biol. 2015.

Abstract

Background: Sufficient knowledge of molecular and genetic interactions, which comprise the entire basis of the functioning of living systems, is one of the necessary requirements for successfully answering almost any research question in the field of biology and medicine. To date, more than 24 million scientific papers can be found in PubMed, with many of them containing descriptions of a wide range of biological processes. The analysis of such tremendous amounts of data requires the use of automated text-mining approaches. Although a handful of tools have recently been developed to meet this need, none of them provide error-free extraction of highly detailed information.

Results: The ANDSystem package was developed for the reconstruction and analysis of molecular genetic networks based on an automated text-mining technique. It provides a detailed description of the various types of interactions between genes, proteins, microRNA's, metabolites, cellular components, pathways and diseases, taking into account the specificity of cell lines and organisms. Although the accuracy of ANDSystem is comparable to other well known text-mining tools, such as Pathway Studio and STRING, it outperforms them in having the ability to identify an increased number of interaction types.

Conclusion: The use of ANDSystem, in combination with Pathway Studio and STRING, can improve the quality of the automated reconstruction of molecular and genetic networks. ANDSystem should provide a useful tool for researchers working in a number of different fields, including biology, biotechnology, pharmacology and medicine.

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Figures

Figure 1
Figure 1
Schematic illustrating literature and database mining implemented in ANDSystem.
Figure 2
Figure 2
An example of the ANDSystem semantic template.
Figure 3
Figure 3
An example of information retrieval using the ANDSystem template.
Figure 4
Figure 4
Distribution of the number of interactions for the 8 most represented in ANDCell organisms.
Figure 5
Figure 5
The ANDVisio interface.
Figure 6
Figure 6
Precision values for the six main types of ANDSystem interactions.
Figure 7
Figure 7
An example of interaction networks reconstructed with ANDSystem (A), Pathway Studio (B) and STRING (C). The networks were reconstructed for 14 genes/proteins participating in the ≪regulation of heart rate by cardiac conduction≫ of the Gene Ontology biological process (GO: 0086091). Proteins are presented with red balls and genes with double helixes in the ANDSystem network. For Pathway Studio and STRING networks, proteins are presented with red ovals and colored balls, respectively.
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References

    1. Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio--the analysis and navigation of molecular networks. Bioinformatics. 2003;1;19(16):2155–7. - PubMed
    1. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41(Database):D808–15. - PMC - PubMed
    1. Usié A, Karathia H, Teixidó I, Valls J, Faus X, Alves R, Solsona F. Biblio-MetReS: A bibliometric network reconstruction application and server. BMC bioinformatics. 2011;12:387. doi: 10.1186/1471-2105-12-387. - DOI - PMC - PubMed
    1. Cheung WA, Ouellette BF, Wasserman WW. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs) BMC Bioinformatics. 2012;13:249. doi: 10.1186/1471-2105-13-249. - DOI - PMC - PubMed
    1. Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet. 2001;28(1):21–8. - PubMed

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