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2013 ; 16
(3
): 189-98
Nephropedia Template TP
gab.com Text
Twit Text FOAVip
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English Wikipedia
An overview of computational life science databases & exchange formats of
relevance to chemical biology research
#MMPMID22934944
Smalter Hall A
; Shan Y
; Lushington G
; Visvanathan M
Comb Chem High Throughput Screen
2013[Mar]; 16
(3
): 189-98
PMID22934944
show ga
Databases and exchange formats describing biological entities such as chemicals
and proteins, along with their relationships, are a critical component of
research in life sciences disciplines, including chemical biology wherein small
information about small molecule properties converges with cellular and molecular
biology. Databases for storing biological entities are growing not only in size,
but also in type, with many similarities between them and often subtle
differences. The data formats available to describe and exchange these entities
are numerous as well. In general, each format is optimized for a particular
purpose or database, and hence some understanding of these formats is required
when choosing one for research purposes. This paper reviews a selection of
different databases and data formats with the goal of summarizing their purposes,
features, and limitations. Databases are reviewed under the categories of 1)
protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4)
drug discovery. Representation formats will be discussed according to those
describing chemical structures, and those describing genomic/proteomic entities.