Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing

Standard

Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing. / Mukhin, A. M.; Genaev, M. A.; Rasskazov, D. A. et al.

In: Mathematical Biology and Bioinformatics, Vol. 15, No. 2, 2020, p. 455-470.

Research output: Contribution to journal › Article › peer-review

Harvard

Mukhin, AM, Genaev, MA, Rasskazov, DA, Lashin, SA & Afonnikov, DA 2020, 'Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing', Mathematical Biology and Bioinformatics, vol. 15, no. 2, pp. 455-470. https://doi.org/10.17537/2020.15.455

APA

Mukhin, A. M., Genaev, M. A., Rasskazov, D. A., Lashin, S. A., & Afonnikov, D. A. (2020). Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing. Mathematical Biology and Bioinformatics, 15(2), 455-470. https://doi.org/10.17537/2020.15.455

Vancouver

Mukhin AM, Genaev MA, Rasskazov DA, Lashin SA , Afonnikov DA. Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing. Mathematical Biology and Bioinformatics. 2020;15(2):455-470. doi: 10.17537/2020.15.455

Author

Mukhin, A. M. ; Genaev, M. A. ; Rasskazov, D. A. et al. / Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing. In: Mathematical Biology and Bioinformatics. 2020 ; Vol. 15, No. 2. pp. 455-470.

BibTeX

@article{ba20f0e7f33248dda3f8f20a03905d6a,

title = "Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing",

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/",

keywords = "crops, database, indexing, NoSQL, plants, queries, RDBMS, SQL, transcriptomes",

author = "Mukhin, {A. M.} and Genaev, {M. A.} and Rasskazov, {D. A.} and Lashin, {S. A.} and Afonnikov, {D. A.}",

year = "2020",

doi = "10.17537/2020.15.455",

language = "English",

volume = "15",

pages = "455--470",

journal = "Mathematical Biology and Bioinformatics",

issn = "1994-6538",

publisher = "Institute of Mathematical Problems of Biology",

number = "2",

}

RIS

TY - JOUR

T1 - Rdbms And Nosql Based Hybrid Technology for Transcriptome Data Structuring and Processing

AU - Mukhin, A. M.

AU - Genaev, M. A.

AU - Rasskazov, D. A.

AU - Lashin, S. A.

AU - Afonnikov, D. A.

PY - 2020

Y1 - 2020

N2 - 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/

AB - 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/

KW - crops

KW - database

KW - indexing

KW - NoSQL

KW - plants

KW - queries

KW - RDBMS

KW - SQL

KW - transcriptomes

UR - http://www.scopus.com/inward/record.url?scp=85099614614&partnerID=8YFLogxK

U2 - 10.17537/2020.15.455

DO - 10.17537/2020.15.455

M3 - Article

AN - SCOPUS:85099614614

VL - 15

SP - 455

EP - 470

JO - Mathematical Biology and Bioinformatics

JF - Mathematical Biology and Bioinformatics

SN - 1994-6538

IS - 2

ER -

ID: 27527709