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

Abstract

BackgroundSufficient 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.ResultsThe 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.ConclusionThe 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.

Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks

“…The reconstruction of associative gene networks of asthma and hypertension was carried out using the ANDSystem tool [29,30]. The ANDSystem was developed to automatically analyse scientific publications in order to extract knowledge on the molecular genetic interactions and associations of proteins, genes, metabolites, drugs, and microRNAs with diseases, biological processes, drug side effects, and the phenotypes of various organisms.…”

“…To further assess the structural role of the apoptosis genes in the graphs of the complete and genetic regulatory networks of asthma/hypertension, we evaluated the fundamental cycles using the "Find fundamental rings" function of ANDSystem [29,30]. Fundamental cycles are those that form the basis of a cyclic space of a graph, that is, any cycle of a graph can be represented by the sum of fundamental cycles.…”

“…There are a number of resources in the world that allow reconstruction of such associative gene networks, for example, MetaCore [27], Ingenuity [28] and ANDSystem [29,30]. In particular, using the developed by us ANDSystem tool, the following studies were performed: analysis of proteomic data on Helicobacter pylori infection [31]; analysis of the urine proteomic profile in control and under the influence of space flight factors [32]; analysis of tissue-specific gene knockout effect and the search for potential drug targets [33]; analysis of hepatitis C virus life cycle gene networks [34]; analysis of comorbid relations of bronchial asthma and tuberculosis [35], preeclampsia, diabetes and obesity [36], glaucoma [37]; search for novel candidate genes of susceptibility to tuberculosis [38].…”

“…The associative network reconstructed in this work by ANDSystem [29,30] details the interactions between genes/proteins that are linked to both asthma and hypertension, specifically including 205 genes and 9638 relations. It is worth noting that 69 genes from the network are related to apoptosis and 44 participate in central nervous system (CNS) functioning, suggestive of the important role of these processes for the formation of combined asthma and hypertension.…”

Role of apoptosis genes in aggression revealed using combined analysis of ANDSystem gene networks, expression and genomic data in grey rats with aggressive behavior

“…Реконструкцию ассоциативных генных сетей, описыва-ющих молекулярно-генетические взаимодействия между генами и белками, осуществляли с помощью системы ANDSystem (Demenkov et al, 2012;Ivanisenko et al, 2015). Система ANDSystem предназначена для автоматического анализа текстов научных публикаций с целью извлечения информации о взаимодействиях между молекулярно-генетическими объектами (гены, белки, метаболиты, микро-РНК), а также их ассоциативных и регуляторных связях с заболеваниями, биологическими процессами и фенотипическими признаками различных организмов.…”