Chemical databases: curation or integration by user-defined equivalence?

Chemical databases: curation or integration by user-defined equivalence? by Anne Hersey, Jon Chambers, Louisa Bellis, A. PatrĂ­cia Bento, Anna Gaulton, John P. Overington.

Abstract:

There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual database applications mean that exact chemical structure equivalence between databases is unlikely to ever be a reality. The ability to identify compound equivalence has been made significantly easier by the use of the International Chemical Identifier (InChI), a non-proprietary line-notation for describing a chemical structure. More importantly, advances in methods to identify compounds that are the same at various levels of similarity, such as those containing the same parent component or having the same connectivity, are now enabling related compounds to be linked between databases where the structure matches are not exact.

The authors identify a number of reasons why databases of chemical identifications have different structures recorded for the same chemicals. One problem is that there is no authoritative source for chemical structures so upon publication, authors publish those aspects most relevant to their interest. Or publish images and not machine readable representations of a chemical. To say nothing of the usual antics with simple names and their confusions. But there are software limitations, business rules and other sources of a multiplicity of chemical structures.

Suffice it to say that the authors make a strong case for why there are multiple structures for any given chemical now and why that is going to continue.

The author’s openly ask if it is time to ask users for their assistance in mapping this diversity of structures:

Is it now time to accept that however diligent database providers are, there will always be differences in structure representations and indeed some errors in the structures that cannot be fixed with a realistic level of resource? Should we therefore turn our attention to encouraging the use and development of tools that enable the mapping together of related compounds rather than concentrate our efforts on ever more curation?

You know my answer to that question.

What’s yours?

I first saw this in a tweet by John P. Overington.

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