Relax with CouchDB - Into the non-relational DBMS era of ...

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Relax with CouchDB
-

Into the non
-
relational DBMS era of bioinformatics

Author(s):

Manyam, G
(Manyam, Ganiraju);
Payton, MA
(Payton, Michelle A.)
2
;
Roth, JA
(Roth, Jack A.)
3
;
Abruzzo, LV
(Abruzzo, Lynne V.)
2
;
Coombes, KR
(Coombes, Kevin R.)
1


Source:
GENOMICS


Volume:

100


Issue:

1


Pages:

1
-
7


DOI:

10.1016/j.ygeno.2012.05.006


Published:

JUL 2012

Times Cited:

0 (from Web of Science)

Cited References:

45

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Abstract:

With the proliferation of high
-
throughput technologies, genome
-
level data analysis has become
common in
molecular biology. Bioinformaticians are developing extensive resources to annotate and mine
biological features from high
-
throughput data. The underlying database
management

systems for most
bioinformatics
software

are based on a relational model. Modern
non
-
relational databases offer an alternative that
has flexibility, scalability, and a non
-
rigid design schema. Moreover, with an accelerated development pace, non
-
relational databases like CouchDB can be ideal tools to construct bioinformatics utilities.
We describe CouchDB
by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics
resources and provides automated gene
-
centric annotations, (b) drugBase, a database of drug
-
target interactions
with a web interfac
e powered by geneSmash, and (c) HapMap
-
CN, which provides a web interface to query copy
number variations from three SNP
-
chip HapMap datasets. In addition to the web sites, all three systems can be
accessed programmatically via web services. (C) 2012 Elsev
ier Inc. All rights reserved.

Accession Number:

WOS:000306150300001

Document Type:

Article

Language:

English

Author Keywords:

NoSQL database; Copy number variation; Drug
-
target interaction; Data integration

KeyWords Plus:

PROTEIN DATA
-
BANK; CIRCULAR BINARY SEGMENTATION; INTERNATIONAL HAPMAP
PROJECT
; THERAPEUTIC TARGET DATABASE; BIOLOGICAL DATA; WEB SITE; GENE; ANNOTATION;
DELETIONS; DRUGBANK

Reprint Address:

Coombes, KR (reprint author), Univ Texas MD Anderson Canc Ctr,
Dept Bioinformat &
Computat Biol, Unit 1410, 1400 Pressler St, Houston, TX 77030 USA.

Addresses:


1. Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Unit 1410, Houston, TX 77030 USA

2. Univ Texas MD Anderson Canc Ctr, Dept Hematopatho
l, Houston, TX 77030 USA

3. Univ Texas MD Anderson Canc Ctr, Dept Thorac & Cardiovasc Surg, Houston, TX 77030 USA

E
-
mail Address:

kcoombes@mdanderson.org


Funding:

Funding Agency

Grant Number

National
Cancer Institute of the National Institutes of Health


R01 CA123252


P30 CA016672


P50 CA070907



[Show funding text]





Publisher:

ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101
-
4495
USA

Web of Science Categories:

Biotechnology & Applied Microbiology; Genetics & Heredity

Research Areas:

Biotechnology & Applied Microbiology; Genetics &

Heredity

IDS Number:

970RP

ISSN:

0888
-
7543