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Abstract
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.
Keywords: Data exchange formats, databases, drug discovery, proteomics
Combinatorial Chemistry & High Throughput Screening
Title:An Overview of Computational Life Science Databases & Exchange Formats of Relevance to Chemical Biology Research
Volume: 16 Issue: 3
Author(s): Aaron Smalter Hall, Yunfeng Shan, Gerald Lushington and Mahesh Visvanathan
Affiliation:
Keywords: Data exchange formats, databases, drug discovery, proteomics
Abstract: 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.
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Smalter Hall Aaron, Shan Yunfeng, Lushington Gerald and Visvanathan Mahesh, An Overview of Computational Life Science Databases & Exchange Formats of Relevance to Chemical Biology Research, Combinatorial Chemistry & High Throughput Screening 2013; 16 (3) . https://dx.doi.org/10.2174/1386207311316030004
DOI https://dx.doi.org/10.2174/1386207311316030004 |
Print ISSN 1386-2073 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5402 |
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