Abstract:
The transcriptome sequencing experiment (RNA-seq) has become almost a routine procedure for studying both model organisms and crops. As a result of bioinformatics processing of such experimental output, huge heterogeneous data are obtained, representing nucleotide sequences of transcripts, amino acid sequences, and their structural and functional annotation. It is important to present the data obtained to a wide range of researchers in the form of databases. This article proposes a hybrid approach to creating molecular genetic databases that contain information about transcript sequences and their structural and functional annotation. The essence of the approach consists in the simultaneous storing both structured and weakly structured data in the database. The technology was used to implement a database of transcriptomes of agricultural plants. This paper discusses the features of implementing this approach and examples of generating both simple and complex queries to such a database in the SQL language. The OORT database is freely available at https://oort.cytogen.ru/.
Received 26.10.2020, 14.12.2020, Published 28.12.2020
Document Type:
Article
Language: Russian
Citation:
A. M. Mukhin, M. A. Genaev, D. A. Rasskazov, S. A. Lashin, D. A. Afonnikov, “RDBMS and NoSQL based hybrid technology for transcriptome data structuring and processing”, Mat. Biolog. Bioinform., 15:2 (2020), 455–470
\Bibitem{MukGenRas20}
\by A.~M.~Mukhin, M.~A.~Genaev, D.~A.~Rasskazov, S.~A.~Lashin, D.~A.~Afonnikov
\paper RDBMS and NoSQL based hybrid technology for transcriptome data structuring and processing
\jour Mat. Biolog. Bioinform.
\yr 2020
\vol 15
\issue 2
\pages 455--470
\mathnet{http://mi.mathnet.ru/mbb442}
\crossref{https://doi.org/10.17537/2020.15.455}
Linking options:
https://www.mathnet.ru/eng/mbb442
https://www.mathnet.ru/eng/mbb/v15/i2/p455
This publication is cited in the following 3 articles:
Artem Yu. Pronozin, Dmitry A. Afonnikov, “ICAnnoLncRNA: A Snakemake Pipeline for a Long Non-Coding-RNA Search and Annotation in Transcriptomic Sequences”, Genes, 14:7 (2023), 1331
O. Kuzmenko, T. Dotsenko, V. Koibichuk, “Development of databases structure of internal economic agents financial monitoring”, Financ. Credit Act., 3:38 (2021), 204–213
O. Kuzmenko, T. Dotsenko, V. Koibichuk, “DEVELOPMENT OF DATABASES STRUCTURE OF INTERNAL ECONOMIC AGENTS FINANCIAL MONITORING”, FKDPTP, 3:38 (2021), 204