Free online resources:Layout 1 14/1/10 19:53 Page 34
Cheminformatics
Figure 1
A graphical interpretation of
the history of
60
chem/bioinformatics software,
model and database
development, and increasing
50
drug development costs versus
registered compounds in the
CAS Registry and the
ChemSpider database
40
30
ed compounds (millions)
20
Register
10
0
1960 1965 1970 1975 1980 1985 1990 1995 2000 2005 2010
Year
References
launched by the NIH in 2004 to support the ‘New The Chemical Entities of Biological Interest, or
1 Williams, AJ (2008). A
Pathways to Discovery’ component of the ChEBI database (http://www.ebi.ac.uk/chebi/) is a
perspective of publicly
Roadmap for Medical Research
4
. PubChem highly curated database of molecular entities
accessible/open-access
archives and organises information about the bio- focused on small chemical compounds. The entities
chemistry databases. Drug
Discov Today 13 (11-12), 495-
logical activities of chemical compounds into a are either natural products or synthetic products
501.
comprehensive database and is the informatics used to intervene in the processes of living organ-
2 Williams, AJ (2008). Internet-
backbone for the Molecular Libraries and Imaging isms. ChEBI includes an ontological classification
based tools for communication
Initiative, which is part of the NIH Roadmap. (Figure 2), whereby the relationships between
and collaboration in chemistry.
Pubchem is also intended to empower the scientif- molecular entities or classes of entities and their
Drug Discov Today 13 (11-12),
502-506.
ic community to use small molecule chemical com- ‘parents’ and/or ‘children’ are specified. While the
3 Southan, C et al (2009).
pounds in their research as molecular probes to database presently offers access to close to 19,000
Quantitative assessment of the
investigate important biological processes or gene entities this is expected to expand to more than
expanding complementarity
functions. The PubChem compound repository 440,000 by the end of October
between public and
presently contains more than 25 million unique (http://www.ebi.ac.uk/chebi/newsForward.do#Ch
commercial databases of
bioactive compounds. J
structures with biological property information EMBL%20data%20integration). The database is
Cheminformatics 1, 10.
provided for many of the compounds. For now, available for download by anonymous FTP
4 Office of Portfolio Analysis
PubChem remains focused on its initial intent to (ftp://ftp.ebi.ac.uk/pub/databases/chebi/).
and Strategic Initiatives,
support the Molecular Libraries Initiative and
N.I.o.H (2008). The NIH
serves as an extremely valuable and authoritative The Human Metabolome Database
Roadmap Initiative.
5Wishart, DS et al (2007).
resource for cheminformatics and chemical (http://www.hmdb.ca)
5,6
(HMDB) is a compre-
HMDB: the Human Metabolome
genomics. However, there are a number of con- hensive curated collection of human metabolite
Database. Nucleic Acids Res 35
straints around the system, especially in its place and human metabolism data. It contains records
(Database issue), D521-526.
as a repository of data and information without a for more than 6,800 endogenous metabolites. In
6 Wishart, DS et al (2009).
special effort toward curating these data. addition to its comprehensive literature-derived
HMDB: a knowledgebase for
the human metabolome.
Naturally, in the absence of data curation any data, the HMDB also contains an extensive col-
Nucleic Acids Res 37
errors in the data are transferred across many lection of experimental metabolite concentration
(Database issue), D603-610.
online databases that depend on PubChem and data compiled from hundreds of mass spectra
ultimately, the errors influence the quality of com- (MS) and Nuclear Magnetic resonance (NMR)
Continued on page 36 putational models based on this data. metabolomic analyses performed on urine, blood
34 Drug Discovery World Winter 2009/10
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