vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ18.325vavilov-1357Research ArticleГЕНЕТИКА И СЕЛЕКЦИЯ КАРТОФЕЛЯPOTATO GENETICS AND BREEDINGБАЗА ЗНАНИЙ SOLANUM TUBEROSUM: РАЗДЕЛ ПО МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКОЙ РЕГУЛЯЦИИ МЕТАБОЛИЧЕСКИХ ПУТЕЙTHE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYSИванисенкоТ. В.IvanisenkoT. V.

Новосибирск

Novosibirsk

СайкО. В.SaikO. V.

Новосибирск

Novosibirsk

ДеменковП. С.DemenkovP. S.

Новосибирск

Novosibirsk

ХлесткинВ. К.KhlestkinV. K.ХлесткинаЕ. К.KhlestkinaE. K.КолчановН. А.KolchanovN A.

Новосибирск

Novosibirsk

ИванисенкоВ. А.IvanisenkoV. А.

Новосибирск

Novosibirsk

salix@bionet.nsc.ruФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics SB RASRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics SB RAS; Novosibirsk State UniversityRussian Federation201821032018221817Copyright © Иванисенко Т.В., Сайк О.В., Деменков П.С., Хлесткин В.К., Хлесткина Е.К., Колчанов Н.А., Иванисенко В.А., 20182018Иванисенко Т.В., Сайк О.В., Деменков П.С., Хлесткин В.К., Хлесткина Е.К., Колчанов Н.А., Иванисенко В.А.Ivanisenko T.V., Saik O.V., Demenkov P.S., Khlestkin V.K., Khlestkina E.K., Kolchanov N.A., Ivanisenko V.А.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/1357

Быстрое развитие высокопроизводительных геномных, транскриптомных, протеомных и метаболомных технологий обусловило эффект «информационного взрыва» в области биологии растений. На сегодняшний день число научных публикаций только по одной важнейшей сельскохозяйственной культуре Solanum tuberosum L. (картофель) превышает 1.5 млн. Эффективный доступ к знаниям, распределенным по такому множеству неформализованных естественно-языковых текстовых источников, требует применения специальных компьютерных интеллектуальных методов анализа текстов (text mining). Однако в литературе нет данных о широком использовании интеллектуальных методов автоматического извлечения знаний из научных публикаций по сельскохозяйственным культурам, таким как картофель. Ранее нами была разработана пилотная версия базы знаний SOLANUM TUBEROSUM, представляющая собой компьютерную платформу для комплексной интеллектуальной обработки больших данных, включая: 1) автоматический анализ текстов научных публикаций и фактографических баз данных, направленный на экстракцию информации по генетике, маркерам, селекции, семеноводству, диагностике возбудителей заболеваний, средствам защиты и технологиям хранения картофеля; 2) формализованное представление извлеченной информации в базе знаний; 3) пользовательский доступ к этим данным; 4) анализ и визуализацию результатов запросов. В онтологии базы знаний SOLANUM TUBEROSUM представлены словари молекулярно-генетических объектов (белков, генов, метаболитов, микроРНК, биомаркеров и др.), сортов картофеля и их фенотипических признаков, болезней и вредителей картофеля, биотических и абиотических факторов окружающей среды, агробиотехнологий возделывания, а также технологий переработки и хранения картофеля. В статье дано описание текущей версии базы знаний SOLANUM TUBEROSUM, полученной в результате расширенного анализа научных публикаций по молекулярно-генетической регуляции метаболических путей у картофеля, а также модельных растительных организмов (кукурузы, риса, арабидопсиса). Всего было проанализировано около 9 000 полнотекстовых статей и более 130 000 рефератов PubMed. С помощью автоматического анализа текстов научных публикаций выявлено более 59 000 фактов о молекулярно-генетических взаимодействиях и генетической регуляции, а анализ фактографических баз данных позволил выявить более 380 000 таких взаимодействий у рассмотренных организмов. При этом оказалось, что к Solanum tuberosum L. относится около 3 % экстрагированных фактов о молекулярно-генетических взаимодействиях и генетической регуляции. Таким образом, включение сведений о хорошо изученных модельных видах при извлечении информации о молекулярно-генетической регуляции метаболических процессов является важным и позволит предсказывать гены-ортологи у картофеля и проводить их дальнейшую идентификацию и выделение на основе гомологии. Сконструирована ассоциативная сеть генетической регуляции биосинтеза крахмала у картофеля, включающая 33 метаболита, 36 белков, 6 метаболических путей и 132 взаимодействия между ними, 86 из которых описывают каталитические реакции, а остальные – регуляторные события. Сконструированная сеть является основой для поиска генов-мишеней для направленного мутагенеза и маркер-ориентированной селекции сортов картофеля с заданными свойствами крахмала. Тестовая версия базы знаний SOLANUM TUBEROSUM доступна по адресу http://www-bionet.sysbio.cytogen.ru/and/plant/.

Rapid development of high-performance genomic, transcriptomic, proteomic and metabolic technologies led to an information explosion in the field of plant biology and agrobiology. To date, the number of scientific publications on only one of the most important agricultural crops of Solanum tuberosum L. (potato) has exceeded 1.5 million. Effective access to knowledge distributed over such a multitude of non-formalized natural language textual sources requires the use of special computer-assisted intelligent methods of data mining (text-mining). However, in the literature, there is no data on the application of intellectual methods of automatic knowledge extraction from publications on agricultural crops, such as potato. Previously we have developed a pilot version of the SOLANUM TUBEROSUM knowledge base. SOLANUM TUBEROSUM is a computer platform for complex intellectual processing of large data bodies, including (1) automatic analysis of scientific publications and databases for extraction of information on genetics, markers, breeding, diagnostics, protection and storage technologies for potato, (2) formalized representation of extracted information in the knowledge base, (3) user access to these data, (4) analysis and visualization of query results. The ontology of the SOLANUM TUBEROSUM knowledge base contains dictionaries of molecular genetic objects (proteins, genes, metabolites, microRNAs, biomarkers); phenotypic characteristics of potato varieties; potato diseases and pests; biotic/abiotic environmental factors; potato agrobiotechnologies. This article describes the current version of the SOLANUM TUBEROSUM knowledge base developed from an extensive analysis of scientific publications on the moleculargenetic regulation of metabolic pathways in potatoes, as well as model plant organisms (maize, rice, Arabidopsis  thaliana). In total, about 9,000 full-text articles and more than 130,000 abstracts of PubMed were analyzed. With the help of automatic analysis of scientific publications, more than 59,000 facts on molecular genetic interactions and genetic regulation were identified, and the analysis of factual databases revealed more than 380,000 such interactions in the examined organisms. It turned out that about 3 % of extracted facts about molecular genetic interactions and genetic regulation were related to Solanum tuberosum L. Thus, the inclusion of information on well-studied model species during the extraction of information on the molecular-genetic regulation of metabolic processes is important. It allows prediction of orthologous genes in potato and their further identification and analysis based on homology. An associative network of genetic regulation of starch biosynthesis in potatoes, including 33 metabolites, 36 proteins, 6 metabolic pathways and 132 interactions between them, 86 of which describe catalytic reactions, and the rest – regulatory events, was reconstructed. The reconstructed network is the basis for the search for target genes for directed mutagenesis and marker-oriented selection of potato varieties with specified starch properties. The trial version of the SOLANUM TUBEROSUM knowledge base is available at http://www-bionet.sysbio.cytogen.ru/and/ plant/.

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The authors declare that there are no conflicts of interest present.