Cheminformatics as we know it is possible because so many molecular structures can be represented with datastructures and rules that are at first glance quite trivial. This first impression is highly misleading, since even within supposedly well behaved domains, edge cases arising from issues such as resonance, tautomerization, symmetry and stereochemistry - to name but a few - quickly add up. To supplement these genuine challenges, there is a whole additional class of problems caused by the mismatch between chemists' understanding of molecules and the datatypes that are necessary to capture a structure for informatics purposes. This line is blurred by the convenience of representing structures in a form that is very closely related to the diagram styles that have been in use since the dawn of chemistry. There are currently four major approaches to structure representation: connection tables (e.g. MDL Molfile), sketches (e.g. ChemDraw), canonical strings (e.g. SMILES and InChI) and atomic models (numerous 3D formats). Not only do all of these approaches have valid use cases, but they are deceptively incompatible with each other, even when addressing identical needs. Almost without exception, format conversions are not commutative, and every translation involves losing some amount of data. Given that recording chemical structures in machine readable form has become such a critical part of scientific research, it is essential to define a fundamental representation that captures the key structural definition asserted by the experimental chemist, for a broad and useful range of molecules, and ideally in a way that is closely related to visual drawing mnemonics. The number of data concepts needed to satisfy these conditions is quite small, and is mostly satisfied by the most commonly used subset of the venerable MDL Molfile format. This presentation will discuss how this subset, with a few minor corrections and clarifications, can and should be used as the reference standard for molecules, and how the informatics community can benefit from having well defined standards.

Representing molecules with minimalism: A solution to the entropy of informatics

254th National Meeting (2017)

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