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Cheminformatics Education
Introduction:
Despite some skepticism at the turn of the century1.2
the terms
“cheminformatics” and
“chemoinformatics” are
now in common parlance. The term “chemical
informatics” is
used less. The premier journal in the field, the Journal of Chemical
Information and Modeling, does not use any of these terms and its
cheminformatics papers are scattered across multiple sections including
“chemical Information”.
Unfortunately it is not just the name of the discipline that is
undefined: opinions also vary on the scope. Paris supplied the
following definition1 (shortened here):
“Chem(o)informatics
is a
generic term that encompasses the design, creation, organization,
storage, management, retrieval, analysis, dissemination, visualization
and use of chemical information, not only in its own right, but as a
surrogate or index for other data, information and
knowledge”.
Brown3 says the discipline is “mixing
of information
resources to
transform data into information, and information into knowledge, for
the intended purpose of making better decisions faster in the arena of
drug lead identification and optimization”.
Gasteiger4 says that cheminformatics is the
application of informatics
methods to solve chemical problems and Bajorath5
agrees that a broad
definition such as that is needed to cover all the different scientific
activities that have evolved, or have been assimilated, under the
cheminformatics umbrella. Varnek’s definition6.7
is rather
different. He considers that cheminformatics is a part of theoretical
chemistry based on its own molecular model; unlike quantum chemistry in
which molecules are represented as ensemble of electrons and nuclei, or
force fields molecular modeling dealing with classical
“atoms” and “bonds”,
cheminformatics considers
molecules as objects (graphs and vectors) in multidimensional chemical
space.
The Web site of Michigan Technological University (“Michigan
Tech”)8 states:
“Cheminformatics integrates a
comprehensive
knowledge of chemistry with an extensive understanding of information
technology. The intersection of chemistry and information technology
embraces an expanding territory; it includes computational modeling of
individual molecules, thermodynamic methods of estimating chemical
properties, methods of predicting biological activity of hypothetical
compounds, and organization and classification of chemical
information”. In addition, Bajorath5
notes that
“Despite
their conceptual diversity, many developments in this discipline
continue to be driven in pharmaceutical environments. In fact, without
its strong foundation in drug discovery, chemoinformatics as we
understand it today would probably not be the same”.
The field of cheminformatics is well established as a discipline in its
own right, and its importance is clear to all its practitioners
whatever their definition of the discipline, but it is not still
recognized as a scientific field by the ministries of education and
other governing academic organizations in most European countries.
Academic positions in cheminformatics are rarely advertised which can
lead to loss of continuity and expertise for cheminformatics research
groups. PhD fellowships and post doctoral funding are lacking and very
few programs are funded at the national and European levels.6
In a recent editorial, Bajorath5 wrote:
“In contrast to
bioinformatics, chemoinformatics is still fairly under-represented in
academic research and teaching, which might cause problems for the
further development of this field. Fortunately, it is increasingly
being recognized that the methodological arsenals of bioinformatics and
chemoinformatics are much more similar to each other than the diversity
of their applications might suggest. Consequently, boundaries between
these fields are becoming fluid and we can expect that interest in the
computational study of small molecules and ligand-target interactions
will further increase, also in the bioinformatics community.”
The National Science Foundation in the United States funds
cyberinfrastructure, computational science, interdisciplinary research
and bioinformatics; some workers have realized that claiming to be in
those disciplines is useful when making grant applications for
cheminformatics research. It is, however, generally agreed that there
is a need for more teaching programs that integrate chemistry and
computer science. A declaration9 about the need for cheminformatics
education was approved at Obernai, France in 2006.
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