A cheminformatic toolkit for mining biomedical knowledge.
OBJECTIVE
Cheminformatics can be broadly defined to encompass any activity related to the application of information technology to the study of properties, effects and uses of chemical agents. One of the most important current challenges in cheminformatics is to allow researchers to search databases of biomedical knowledge, using chemical structures as input.


METHODS
An important step towards this goal was the establishment of PubChem, an open, centralized database of small molecules accessible through the World Wide Web. While PubChem is primarily intended to serve as a repository for high throughput screening data from federally-funded screening centers and academic research laboratories, the major impact of PubChem could also reside in its ability to serve as a chemical gateway to biomedical databases such as PubMed.


CONCLUSIONS
This article will review cheminformatic tools that can be applied to facilitate annotation of PubChem through links to the scientific literature; to integrate PubChem with transcriptomic, proteomic, and metabolomic datasets; to incorporate results of numerical simulations of physiological systems into PubChem annotation; and ultimately, to translate data of chemical genomics screening efforts into information that will benefit biomedical researchers and physician scientists across all therapeutic areas.
Rosania
Gus R
GR
Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, 428 Church Street, Ann Arbor, MI 48109, USA. grosania@umich.edu
Crippen
Gordon
G
Woolf
Peter
P
States
David
D
Shedden
Kerby
K
D000818:Animals; D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D019992:Databases as Topic; D015195:Drug Design; D023281:Genomics; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008958:Models, Molecular; D015394:Molecular Structure; D010641:Phenotype; D040901:Proteomics; D039781:PubMed; D021281:Quantitative Structure-Activity Relationship; D018511:Systems Integration