Cover Pages: Chemical Markup Language (CML)

[May 11, 2001] From the web site description: "Chemical Markup Language brings the power of XML to the management of chemical information. In simple terms it is 'HTML with Molecules', but there is a great deal more. CML, and associated tools, allows for the conversion of current files without semantic loss, structured documents including chemical publications, and precise location of information within files. CML has been designed carefully so that it is as easy as possible for the 'average chemist' to understand it. Like a lot of chemistry it's not trivial, but it's no harder than Cahn-Ingold-Prelog chirality rules, and easier than Huckel theory. It helps if you know something about HTML (the hypertext language of the WWW) and have tried to transfer data files between sites or programs. It's not magic, and doesn't do anything that isn't really just common sense, but it hides a lot of the hassle that we have at present."

[May 11, 2001] "Chemical Markup Language. A Position Paper." By Peter Murray-Rust (Peter.Murray-rust@nottingham.ac.uk) and Henry S. Rzepa (rzepa@ic.ac.uk). 2001-04-10. "This paper describes Chemical Markup Language and its relationship to IUPAC and other organisations... CML deliberately does not cover all chemistry but concentrates on 'molecules' (discrete entities representatable by a formula and usually a connection table). It supports a hierarchy for compound molecules (clathrates, macromolecules, etc.). It also supports reactions, and macromolcular strucures/sequences (though it can interoperate with other macromolecular XML languages as they are developed). It has no specific support for physicochemical concepts, but can support labelled numeric datatypes of several sorts which can cover a wide range of requirements. It allows quantities and properties to be specifically attached to molecules, atoms or bonds. CML is designed to interoperate with several leading MLs and XML protocols and we have demonstrated the following (1) XHTML for text and images; (2) SVG for line diagrams, graphs, reaction schemes, phase diagrams, etc.; (3) PlotML for graphs MathML for equations; (4) XLink for hypermedia (including atom-spectralPeak assignments, reaction mapping); (5) RDF and Dublin Core for metadata; (6) XML Schemas for numeric and other data types. There are other generic tools required in physical science including units, multidimensional arrays with varied datatypes, terminology and bibliography. There are no widely accepted MLs for these at present; we shall continue to develop our own to be used with CML but will use others if they become widespread. An example is physiochemical data held as SELF (Prof. Henry Kehiaian, IUPAC+CODATA) and now converted to SELFML (PMR+HK) as a IUPAC/CODATA project... Many different types of organisation have adopted, or are adopting CML. We list a few examples: (1) Governmental and global agencies (e.g., drug regulatory agencies through the International Committee on Harmonisation - ICH/M2). We have had additional meetings or discussions with several other agencies. Non-profit research (government). National Cancer Institute, Developmental Therapeutics program (NCI/DTP). ca. 500K compounds are being converted to CML Non-profit research (academia). (2) The University of California at San Diego (UCSD) has adopted CML as the chemical technology for its new terascale information and computing grid portals. This will also by used by the Protein Data Bank (PDB) at the same site..."

References:

XML-CML A centre for Chemical Markup Language (CML) resources, for definitions and the tools needed to process CML
Chemical Markup Language as a SourceForge Project. For "the development and curation of a range of XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering." See the discussion list.
CML Information and Useful Documents
"CML: A Current Position White Paper."
[May 11, 2001] "Chemical Markup Language 1.0 reference with examples." A Zvon resource. Written by Jiri Jirat. The indexes were extracted from the CML 1.0 specification. Main features: (1) Clickable indexes; (2) Graphical representation of examples: PNG and SVG created from CML using XSLT, both molecules and spectra; (3) Click on an atom in the example leads to relevant part of CML source."
CML Peer Reviewed Publications and Reviews
DTD and Schemas for CML. "These are formal declarations of XML languages, DTDs are better supported but schemas are significantly easier to read. Either can be used to validate documents using parsers that understand them. Namespace should point to the relevant DTD or schema e.g., http://www.xml-cml.org. The XML schemas were "experimental" as of 2001-05-11.
CML XML DTD version 2001-04, [cache]
Examples of CML "CML is initially designed to support molecules, reactions and their components. It can be extended to provide complex documents such as
reports, synthetic recipes, instrumental or computer output. the current distribution concentrates on molecules, though some other examples
may be included..."
ChiMeraL - CML Transformation and Display. "Michael Wright's proof of concept for combined chemistry/data/spectral manipulation. It uses stylesheets to process compound documents into their CML and other components and display these appropriately. Main demonstrations only works in MSIE5.
Useful XML/CML Software
Earlier reference list [?]:
- JUMBO XML/CML Browser
- PDB2CML - A public domain PDB to CML converter
- CML DTD - By P.Murray-Rust and H.Rzepa. Documented in Journal of Chemical Information and Computer Science, 1999. [local archive copy]
- Open Molecule Foundation
- "XML and the Launch of Chemical Markup Language," by Peter Murray-Rust.
- Design Considerations for CML
- CML Reference
- Chemical Markup Language (CML) - Local database entry, historical.
- [February 03, 1998] Online/virtual ChemWeb Lectures, by Peter Murray-Rust and others. Featuring XML and CML.
- See also: An Introduction to Structured Documents", by Peter Murray-Rust, discusses XML (http://www.venus.co.uk/omf/cml/doc/tutorial/xml.html); [associated note]
Related topics:


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