Wednesday, February 16, 2011

An acronym in cheminformatics: MIAM for miscellaneous interest annotation marker

MIAM stands for miscellaneous interest annotation marker. A MIAM is a pair of two characters that mark the beginning of a component annotation in a CurlySMILES notation [1,2].
The MIAM format supports encoding of chemical compounds and materials by including diverse attributes and structural details or modifications. The following notation demonstrates encoding of a neodymium-doped material, which, for example, is used as a quantum memory crystal [3]:


The component code {*Y2SiO5} includes the SFN (stoichiometric formula notation) for Y2SiO5. The first annotation, {cr}, specifies the material as a crystal via the SSAM cr. The second annotation starts with the MIAM IM for impurity, followed by the annotation dictionary entry representing the atomic symbol, Nd, of the impurity (dopant).

[1] Axel Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. Journal of Cheminformatics 2011, 3:1.
DOI: 10.1186/1758-2946-3-1.
[2] Axel Drefahl: CurlySMILES: miscellaneous interest annotations [].
[3] C. Clausen, I. Usmani, F. Bussières, N. Sangouard, M. Afzelius, H. de Riedmatten and N. Gisin: Quantum storage of photonic entanglement in a crystal. Nature 2011, 469 (7331), pp. 508-511. DOI: 10.1038/nature09662.

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