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Ivanisenko TV, Saik OV, Demenkov PS, Ivanisenko NV, Savostianov AN, Ivanisenko VA. ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. BMC Bioinformatics 2020; 21:228. [PMID: 32921303 PMCID: PMC7488989 DOI: 10.1186/s12859-020-03557-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products. Previously, we developed the Associative Network Discovery System (ANDSystem), which also implements such a cycle. However, the drawback of these systems is dependence on the employed ontologies describing the subject area, which limits their functionality in searching information based on user-specified queries. RESULTS The ANDDigest system is a new web-based module of the ANDSystem tool, permitting searching within PubMed by using dictionaries from the ANDSystem tool and sets of user-defined keywords. ANDDigest allows performing the search based on complex queries simultaneously, taking into account many types of objects from the ANDSystem's ontology. The system has a user-friendly interface, providing sorting, visualization, and filtering of the found information, including mapping of mentioned objects in text, linking to external databases, sorting of data by publication date, citations number, journal H-indices, etc. The system provides data on trends for identified entities based on dynamics of interest according to the frequency of their mentions in PubMed by years. CONCLUSIONS The main feature of ANDDigest is its functionality, serving as a specialized search for information about multiple associative relationships of objects from the ANDSystem's ontology vocabularies, taking into account user-specified keywords. The tool can be applied to the interpretation of experimental genetics data, the search for associations between molecular genetics objects, and the preparation of scientific and analytical reviews. It is presently available at https://anddigest.sysbio.ru/ .
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Affiliation(s)
- Timofey V Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
- Laboratory of Computer Genomics, Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia.
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Olga V Saik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Pavel S Demenkov
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia
| | - Nikita V Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | | | - Vladimir A Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia
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Ivanisenko VA, Demenkov PS, Ivanisenko TV, Mishchenko EL, Saik OV. A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression. BMC Bioinformatics 2019; 20:34. [PMID: 30717676 PMCID: PMC6362586 DOI: 10.1186/s12859-018-2567-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, there are a number of computer systems that allow the user to reconstruct molecular-genetic networks using the data automatically extracted from the texts of scientific publications. Examples of such systems are STRING, Pathway Commons, MetaCore and Ingenuity. The MetaCore and Ingenuity systems permit taking into account tissue-specific gene expression during the reconstruction of gene networks. Previously, we developed the ANDSystem tool, which also provides an automated extraction of knowledge from scientific texts and allows the reconstruction of gene networks. The main difference between our system and other tools is in the different types of interactions between objects, which makes the ANDSystem complementary to existing well-known systems. However, previous versions of the ANDSystem did not contain any information on tissue-specific expression. RESULTS A new version of the ANDSystem has been developed. It offers the reconstruction of associative gene networks while taking into account the tissue-specific gene expression. The ANDSystem knowledge base features information on tissue-specific expression for 272 tissues. The system allows the reconstruction of combined gene networks, as well as performing the filtering of genes from such networks using the information on their tissue-specific expression. As an example of the application of such filtering, the gene network of the extrinsic apoptotic signaling pathway was analyzed. It was shown that considering different tissues can lead to changes in gene network structure, including changes in such indicators as betweenness centrality of vertices, clustering coefficient, network centralization, network density, etc. CONCLUSIONS: The consideration of tissue specificity can play an important role in the analysis of gene networks, in particular solving the problem of finding the most significant central genes. Thus, the new version of ANDSystem can be employed for a wide range of tasks related to biomedical studies of individual tissues. It is available at http://www-bionet.sscc.ru/and/cell /.
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Affiliation(s)
- Vladimir A. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Pavel S. Demenkov
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Timofey V. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Elena L. Mishchenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Olga V. Saik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
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A Web-Based Tool for Automatic Data Collection, Curation, and Visualization of Complex Healthcare Survey Studies including Social Network Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:2579848. [PMID: 28529537 PMCID: PMC5424185 DOI: 10.1155/2017/2579848] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/12/2017] [Indexed: 11/17/2022]
Abstract
There is a great concern nowadays regarding alcohol consumption and drug abuse, especially in young people. Analyzing the social environment where these adolescents are immersed, as well as a series of measures determining the alcohol abuse risk or personal situation and perception using a number of questionnaires like AUDIT, FAS, KIDSCREEN, and others, it is possible to gain insight into the current situation of a given individual regarding his/her consumption behavior. But this analysis, in order to be achieved, requires the use of tools that can ease the process of questionnaire creation, data gathering, curation and representation, and later analysis and visualization to the user. This research presents the design and construction of a web-based platform able to facilitate each of the mentioned processes by integrating the different phases into an intuitive system with a graphical user interface that hides the complexity underlying each of the questionnaires and techniques used and presenting the results in a flexible and visual way, avoiding any manual handling of data during the process. Advantages of this approach are shown and compared to the previous situation where some of the tasks were accomplished by time consuming and error prone manipulations of data.
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