Chemical Markup Language, CML

Other structure-encoding schemas are developed by software vendors and academia such as Daylight Smiles, CambridgeSoft ChemDraw Exchange (CDX), and Chemical Markup Language (CML), and they all have advantages and disadvantages. The MDL CT File Format is the only one that is supported by almost all chemical informatics software vendors. 

The most commonly used identifiers today include line notation identifiers (e.g., Simplified Molecular Input Line Entry System [SMILES] and International Chemical Identifier [InChls]), tabular identifiers (e.g., Molfile and Structure Definition [SD] file types), and portable mark-up language identifiers (e.g., Chemical Markup Language [CML] and FlexMol). Each identifier has its strengths and weaknesses as detailed in Chapter 5. Chapters 5 and 6 provide enough information to guide researchers in choosing the most appropriate formats for their individual use. 

There have been numerous attempts to develop standard connection table formats for data exchange, almost all of which have sunk rapidly and without trace. An XML-based connection table format, Chemical Markup Language (CML) was proposed in the late 1990s and has now reached version 2.4 which incorporates a number of extensions for representation of features such as spectra, reactions and polymers. Though there is now an extensive CML literature, its adoption by commercial software vendors has thus far been very limited. Greater penetration has been achieved by the lUPAC Chemical Identifier, which is essentially a highly-compacted connection table, discussed in the next section. 

The chemical markup language (CML) is based on the extensible markup language (XML) in order to code chemical structures [21-24], Besides chemical structures and reactions, CML is capable of drawing spectra, etc. 

Phadungsukanan W, Kraft M, Townsend JA, Murray-Rust P (2012) The semantics of chemical markup language(CML) for computaEonal chemistry. J Cheminform 4( 1) 15... 

A set of components (CMLReact) for managing chemical and biochemical reactions have been added to Chemical Markup Language (CML) which can be combined to support most of the strategies for the formal representation of reactions... 

The chemical markup language (CML), under development by the Open Molecule Foundation for description of chemical structures for Internet transmission. 

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