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Volume 15   Issue 2   Year 2020
RDBMS and NOSQL Based Hybrid Technology for Transcriptome Data Structuring and Processing

Mukhin A.M.1,2, Genaev M.A.1,2,3, Rasskazov D.A.1,2, Lashin S.A.1,2,3, Afonnikov D.A.1,2,3

1The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
2Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3Novosibirsk State University, Novosibirsk, Russia

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/.

 

 

Key words: database, indexing, queries, plants, SQL, RDBMS, NoSQL, transcriptomes, crops.

Table of Contents Original Article
Math. Biol. Bioinf.
2020;15(2):455-470
doi: 10.17537/2020.15.455
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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