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Drug Discov Today. 2018 Jun;23(6):1183-1186. doi: 10.1016/j.drudis.2018.03.005. Epub 2018 Mar 17.

Redundancy in two major compound databases.

Author information

1
Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, D-53113 Bonn, Germany.
2
Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, D-53113 Bonn, Germany. Electronic address: bajorath@bit.uni-bonn.de.

Abstract

Public repositories of compounds and activity data are of prime importance for pharmaceutical research in academic and industrial settings. Major databases have evolved over the years. Their growth is accompanied by an increasing tendency toward data sharing. This is a positive development but not without potential problems. Using ChEMBL and PubChem as examples, we show that crosstalk between databases also leads to substantial data redundancy that might not be obvious. Redundancy is an important issue because it biases data analysis and knowledge extraction and leads to inflated views of available compounds, assays and activity data. Going forward it will be important to further refine data exchange and deposition criteria and make redundancy as transparent as possible.

PMID:
29559364
DOI:
10.1016/j.drudis.2018.03.005
[Indexed for MEDLINE]

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