Sunday, 3 October 2010

CML - who uses it?

I was very intrigued to hear from a colleague/fellow developer, that apparently CML (Chemical Markup Language) is not very well used in the field of cheminformatics. Is this true of just industry and private companies? Does academia (other than the Murray-Rust group and Henry S. Rzepa) relish this format, I would be interested to hear peoples' views.

From the Journal of Chemical Information and Modeling, "Chemical Markup Language" has retrieved 76 hits. Of which, 17 of these papers have included either PMR or Henry S. Rzepa (approx 22.4%).

If CML is not the chosen chemical format, what is the predominate format? SMILES, Inchi, Inchi key, sdf, mol2, etc? What will be the predominate format of the future? RDF, OWL?


  1. I've never used cml in academia or industry. Smiles and sdf/mol2 are the most common formats I see.

  2. At GSK SMILES seemed most popular. It is almost certainly the easiest format for humans to read and is well supported by the vast majority of cheminformatics toolkits.
    For holding databases SDF seems quite common.

  3. Bioclipse relies on CML as it is the only format that can hold all the data we want to keep.