SMILES (Simplified Molecular Input Line Entry System) is a specification for describing the connection table of a molecule using text. It was invented by Dr. David Weininger at the EPA. Weininger and brother Art Weininger later founded Daylight Information Systems, and their implementation is the canonical standard.

Due to the popularity of the SMILES language, many other chemistry toolkits (both commercial and open source) read and write SMILES. Unfortunately, a complete description of the original SMILES standard does not exist, and so different toolkits implement slightly different variants. In addition, some toolkits have tried to address what they see as deficiencies in the original specification and implement ‘non-standard’ extensions.

Craig James, CTO eMolecules, is leading a campaign to develop an Open Standard for SMILES. The discussion is taking place under the umbrella of the Blue Obelisk Group, and involves contributors from both industry and open source. This is your chance to have your say in the development of the new standard. It’s all happening right now at the blueoblelisk-smiles mailing list.