Electronic Laboratory Notebooks (ELNs) are widely used in the pharmaceutical industry for recording the details of chemical synthesis experiments. The primary use of this information is often for the capture of intellectual property for future patent filings, however this data can also be used in a number of additional applications, including synthetic accessibility calculations, reaction planning, and reaction yield prediction/optimization. Not only does a pharmaceutical ELN capture those classes of reactions suitable for small scale medicinal chemistry, but it is also uniquely a source of information on failed and poor yield reactions; an important class of data rarely found in the scientific literature or commercial reaction databases.This poster describes several of the technical chemoinformatics challenges in exploiting the wealth of synthetic chemistry information in ELNs. Starting with the hand-drawn sketches stored in relational databases, we describe the steps required to transform and normalize this data into a clean and annotated reaction database in an 'open' file format such as MDL's RD and RXN formats, or reaction SMILES. This process includes the tricky steps of reaction atom mapping, role assignment of reactants, reagents, catalysts and solvents, and the recognition of a reaction as an example of a known named reaction (Suzuki coupling, Diels-Alder cyclization, nitro reduction, chiral separation etc.) Novel (and improved) algorithms for each of these tasks will be described, and where appropriate compared to and benchmarked against previous methods and implementations.

Extraction, analysis, atom-mapping, classification, and naming of reactions from pharmaceutical ELNs

246th National Meeting (2013)

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