Evaluation of relational and NoSQL database architectures to manage genomic annotations

Journal of Biomedical Informatics

Volumn 64, Issue , 2016, Pages 288-295

  Schulz, Wade L ^a   Nelson, Brent G ^b   Felker, Donn K ^c   Durant, Thomas J S ^a   Torres, Richard ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c Agilevent   (United States)

Author keywords

Genomics; MongoDB; MySQL; NoSQL; PostgreSQL; Relational database

Indexed keywords

CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; GENOME ANALYSIS; INFORMATION PROCESSING; MEDICAL INFORMATICS; NOTE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PUBLICATION; SINGLE NUCLEOTIDE POLYMORPHISM; DATABASE MANAGEMENT SYSTEM; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION RETRIEVAL;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFORMATION STORAGE AND RETRIEVAL;

EID: 85002263449     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2016.10.015     Document Type: Note

References (24)

1. [1] Xuan, J., Yu, Y., Qing, T., Guo, L., Shi, L., Next-generation sequencing in the clinic: promises and challenges. Cancer Lett. 340 (2013), 284–295.
2. [2] Lin, E., Chien, J., Ong, F.S., Fan, J.B., Challenges and opportunities for next-generation sequencing in companion diagnostics. Expert Rev. Mol. Diagn. 15 (2015), 193–209.
3. [3] Medicine, Nlo, (eds.) National Library of Medicine Congressional Justification FY2015, 2014, National Library of Medicine, Bethesda, MD.
4. [4] Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A., McKusick, V.A., Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33 (2005), D514–D517.
5. [5] Shepherd, R., Forbes, S.A., Beare, D., Bamford, S., Cole, C.G., Ward, S., et al. Data mining using the catalogue of somatic mutations in cancer BioMart. Database (Oxford), 2011 (2011:bar018).
6. [6] Issa, N.T., Byers, S.W., Dakshanamurthy, S., Big data: the next frontier for innovation in therapeutics and healthcare. Expert Rev. Clin. Pharmacol. 7 (2014), 293–298.
7. [7] Frelinger, J.A., Big data, big opportunities, and big challenges. J. Investig. Dermatol. Symp. Proc. 17 (2015), 33–35.
8. [8] Codd, E.F., A relational model of data for large shared data banks. Commun. ACM 13 (1970), 377–387.
9. [9] Astrahan, M.M., Blasgen, M.W., Chamberlin, D.D., Eswaran, K.P., Gray, J.N., Griffiths, P.P., et al. System R: relational approach to database management. ACM Trans. Database Syst. 1 (1976), 97–137.
10. [10] Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., et al. The human genome browser at UCSC. Genome Res. 12 (2002), 996–1006.
11. [11] Cattell, R., Scalable SQL and NoSQL data stores. SIGMOD Rec. 39 (2011), 12–27.
12. [12] Leavitt, N., Will NoSQL databases live up to their promise?. Computer 43 (2010), 12–14.
13. [13] Kuznetsov, V., Evans, D., Metson, S., The CMS data aggregation system. Procedia Comput. Sci. 1 (2010), 1529–1537.
14. [14] Wang, S., Pandis, I., Wu, C., He, S., Johnson, D., Emam, I., et al. High dimensional biological data retrieval optimization with NoSQL technology. BMC Genomics, 15(Suppl. 8), 2014, S3.
15. [15] Aniceto, R., Xavier, R., Guimaraes, V., Hondo, F., Holanda, M., Walter, M.E., et al. Evaluating the Cassandra NoSQL database approach for genomic data persistency. Int. J. Genomics, 2015, 2015, 502795.
16. [16] R. Hecht, S. Jablonski, NoSQL Evaluation: A Use Case Oriented Survey, 2011.
17. [17] Clifton, C., Garcie-Molina, H., The design of a document database. Proceedings of the ACM Conference on Document Processing Systems, 1988, ACM, Santa Fe, New Mexico, USA, 125–134.
18. [18] Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., et al. The variant call format and VCFtools. Bioinformatics 27 (2011), 2156–2158.
19. [19] Parker, Z., Poe, S., Vrbsky, S.V., Comparing NoSQL MongoDB to an SQL DB. Proceedings of the 51st ACM Southeast Conference, 2013, ACM, Savannah, Georgia, 1–6.
20. [20] MongoDB, I., MongoDB manual: indexing. Strategies, 2015 https://docs.mongodb.org/manual/tutorial/ensure-indexes-fit-ram/.
21. [21] Mishra, P., Eich, M.H., Join processing in relational databases. ACM Comput. Surv. 24 (1992), 63–113.
22. [22] Mackert, L.F., Lohman, G.M., R∗ optimizer validation and performance evaluation for local queries. SIGMOD Rec. 15 (1986), 84–95.
23. [23] Robu, I., Robu, V., Thirion, B., An introduction to the semantic web for health sciences librarians. J. Med. Libr. Assoc. 94 (2006), 198–205.
24. [24] World Wide Web Consortium, Resource Description Framework (RDF). < https://www.w3.org/RDF/>.