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Comparison of the NCI open database with seven large chemical structural databases
J H Voigt1, B Bienfait, S Wang
1Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI at Frederick, 376 Boyles Street, Frederick, Maryland 21702, USA.
Journal of Chemical Information and Computer Sciences
|June 21, 2001
Summary
The National Cancer Institute (NCI) database contains the most unique chemical structures, with 200,000 compounds not found in other major chemical databases. Commercial databases show significant overlap, but each database retains unique value.
Area of Science:
- Chemical informatics
- Database analysis
- Drug discovery resources
Background:
- Eight major chemical databases were compared to assess their content and overlap.
- The National Cancer Institute (NCI) database, with ~250,000 structures, was central to the analysis.
- Databases included commercial catalogs, vendor compilations, and specialized collections.
Purpose of the Study:
- To compare the content and overlap of eight diverse chemical databases.
- To identify unique compounds within each database, particularly the NCI database.
- To evaluate the redundancy and diversity across chemical structure repositories.
Main Methods:
- Analysis of internal duplication rates and unique compounds per database.
- Assessment of cumulative compound occurrence across multiple databases.
- Comparison of identical and similarity-based compound overlap between databases.
Main Results:
- The NCI database contains a substantial number of unique compounds (~200,000).
- Commercial databases (ACD, ACX, Maybridge, Asinex, Sigma-Aldrich) exhibit significant overlap among themselves.
- The Cambridge Crystallographic Database (CSD) and World Drug Index (WDI) showed less overlap with other databases.
Conclusions:
- Each chemical database possesses a unique niche and value.
- No single database is a complete subset of another, highlighting the need for diverse resources.
- The NCI database serves as a critical repository for unique chemical structures in research.