Chemical Markup Language

CML. cml Chemical Markup Language extension of XML with specialization in chemistry nmjw.xml-crrd.org 57-59... 

Murray-Rust P, Rzepa HS. Chemical Markup Language and XML Part I. Basic Principles. / Chem Inform Comput Sci 1999 39 928-42. 

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 second example (Scheme 8-2) is an elaboration of the first fragment, but formalized below as CML (chemical markup language) (3). We emphasize that this chapter is not meant to be an instructional manual for any given markup language, with CML here serving only to illustrate the general principles involved. Many other scientific applications of XML have been developed (3, 4), and syntactically, either of these examples could be replaced by other such modularized markup languages. 

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. 

Murray-Rust, R, and H.S. Rzepa. 1999. Chemical markup language and XML. 1. Basic principles, J. Chem. Inf. Comp. Sci. 39 928-942. 

Murray-Rust, P., Rzepa, H. S., and Leach, C. 1995. Chemical Markup Language. Abstracts of Papers of the American Chemical Society 210 40-Comp Part 1. Available at http //www. ch.ic.ac.uk/rzepa/cml/. 

CML. The Chemical Markup Language. Based on XML and HTML, it provides a standard self-documenting molecule file and information interchange format. Information is described by tags and values. A CML document... 

Peter Murray-Rust and Henry S. Rzepor, Chemical Markup Language, available online at http //www.xml-cml.org, accessed on August 14,2002. 

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. 

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