A language is only useful if others can understand it. The chemical structure diagram is the
universal language of chemistry, and well-understood conventions exist for most representation
needs. Stereochemical representation, however, is one area where conventions are incomplete,
particularly when it comes to the representation of structures with incomplete stereochemical
information. A number of conventions are used. One of the most common is to differentiate
the structures based on an assigned name. However, there are no established standards of
nomenclature for all the possibilities that are discussed in these examples.
BIOVIA’ chemical representation needs to be understandable by two constituencies. One is
the chemist who enters queries and retrieves the expected hits. The other constituency is the
database search engine, which has to be able to translate queries unambiguously and retrieve the
expected hits. Accuracy is vital, but in many cases the chemist wants only to retrieve a subset of
all the possible hits. In this case, the chemist needs to use query features to narrow the search
criteria and thereby reduce the number of hits.
The need for a system of chemical representation to encode structural information accurately
to provide the desired precision when used as a query, and to be understandable by both
chemists and a computer system, is a tremendous challenge. MDL’s enhanced stereochemical
representation meets this challenge