Relative Scalability of NoSQL Databases for Genotype Data Manipulation

Almeida, Arthur Lorenzi; Schettino, Vinícius Junqueira; Barbosa, Thiago Jesus Rodrigues; Freitas, Pedro Fernandes; Guimarães, Pedro Gabriel Silva; Arbex, Wagner

dc.contributor	Coord. de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)	pt-BR
dc.contributor	Cons. Nac. de Des. Científico e Tecnológico (CNPq)	pt-BR
dc.contributor	Fund. de Amparo à Pesq. do Estado de Minas Gerais (FAPEMIG)	pt-BR
dc.contributor	Univ. Fed. de Juiz de Fora (UFJF)	pt-BR
dc.contributor	Emp. Bras. de Pesq. Agropecuária (Embrapa)	pt-BR
dc.contributor	Coord. de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)	en-US
dc.contributor	Cons. Nac. de Des. Científico e Tecnológico (CNPq)	en-US
dc.contributor	Fund. de Amparo à Pesq. do Estado de Minas Gerais (FAPEMIG)	en-US
dc.contributor	Univ. Fed. de Juiz de Fora (UFJF)	en-US
dc.contributor	Emp. Bras. de Pesq. Agropecuária (Embrapa)	en-US
dc.creator	Almeida, Arthur Lorenzi
dc.creator	Schettino, Vinícius Junqueira
dc.creator	Barbosa, Thiago Jesus Rodrigues
dc.creator	Freitas, Pedro Fernandes
dc.creator	Guimarães, Pedro Gabriel Silva
dc.creator	Arbex, Wagner
dc.date	2018-07-17
dc.date.accessioned	2018-11-07T21:09:54Z
dc.date.available	2018-11-07T21:09:54Z
dc.identifier	https://seer.ufrgs.br/rita/article/view/RITA-VOL-25-NR2-93
dc.identifier	10.22456/2175-2745.79334
dc.identifier.uri	http://repositorioslatinoamericanos.uchile.cl/handle/2250/2187579
dc.description	Genotype data manipulation is one of the greatest challenges in research fields such as population genetics, bioinformatics and genomics mainly because of high dimensionality and unbalancing characteristics. These peculiarities explain why relational database management systems (RDBMS), the "de facto" standard storage solution, have not been presented as the best tools for this kind of data. However, the Big Data advent has been pushing the development of modern database systems that might be able to overcome RDBMS deficiencies. In this context, we extended our previous works on the evaluation of relative performance among NoSQLs engines from different families, adapting the schema design in order to achieve better performance based on its conclusions, thus being able to store more SNP markers for each individual. Using Yahoo! Cloud Serving Benchmark (YCSB) benchmark framework, we assessed each database system over hypothetical genotype data (SNP markers). Results indicate that Tarantool is approximately 21,8% more efficient than MongoDB when storing 770,000 SNP markers, but MongoDB is less impacted by the increase of SNP markers per individual.	pt-BR
dc.description	Genotype data manipulation is one of the greatest challenges in bioinformatics and genomics mainly because of high dimensionality and unbalancing characteristics. These peculiarities explains why Relational Database Management Systems (RDBMSs), the "de facto" standard storage solution, have not been presented as the best tools for this kind of data. However, Big Data has been pushing the development of modern database systems that might be able to overcome RDBMSs deficiencies. In this context, we extended our previous works on the evaluation of relative performance among NoSQLs engines from different families, adapting the schema design in order to achieve better performance based on its conclusions, thus being able to store more SNP markers for each individual. Using Yahoo! Cloud Serving Benchmark (YCSB) benchmark framework, we assessed each database system over hypothetical SNP sequences. Results indicate that although Tarantool has the best overall throughput, MongoDB is less impacted by the increase of SNP markers per individual.	en-US
dc.format	application/pdf
dc.language	eng
dc.publisher	Instituto de Informática - Universidade Federal do Rio Grande do Sul	en-US
dc.relation	https://seer.ufrgs.br/rita/article/view/RITA-VOL-25-NR2-93/pdf
dc.rights	Direitos autorais 2018 Arthur Lorenzi Almeida, Vinícius Junqueira Schettino, Thiago Jesus Rodrigues Barbosa, Pedro Fernandes Freitas, Maurício Henrique Laier, Pedro Gabriel Silva Guimarães, Wagner Arbex	pt-BR
dc.rights	http://creativecommons.org/licenses/by-nc-nd/4.0	pt-BR
dc.source	Revista de Informática Teórica e Aplicada; v. 25, n. 2 (2018); 93-100	en-US
dc.source	Revista de Informática Teórica e Aplicada; v. 25, n. 2 (2018); 93-100	pt-BR
dc.source	21752745
dc.source	01034308
dc.subject	Computer Science; Bioinformatics	pt-BR
dc.subject	Database; NoSQL; Bionformatics; Data Science; SNP; Genotype	pt-BR
dc.title	Relative Scalability of NoSQL Databases for Genotype Data Manipulation	pt-BR
dc.title	Relative Scalability of NoSQL Databases for Genotype Data Manipulation	en-US
dc.type	Artículos de revistas
dc.type	Artículos de revistas

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