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]:

{*Y2SiO5}{cr}{IMa=Nd}

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).

References
[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 [www.axeleratio.com/csm/proj/miscelinterann.htm].
[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.

No comments:

Post a Comment