Chemical File Format - Chemical Markup Language (CML)

CML (Chemical Markup Language) is a new approach to managing molecular information using recently developed Internet tools such as XML and Java. It is based strictly on SGML, the most robust and widely used system for precise information management in many areas. It has been developed over several years and has been tested in many areas and on a variety of machines. Below is a sample chemical record in CML format:

<?xml version="1.0"?>
<document>
<cml title="carotine" id="cml_carotine_karne"
 xmlns="x-schema:cml_schema_ie_02.xml">
  <molecule title="carotine" id="mol_carotine_karne">
    <atomArray>
      <atom id="carotine_karne_a_1">
        <float builtin="x2" units="A">17.3280</float>
        <float builtin="y2" units="A">2.0032</float>
        <string builtin="elementType">C</string>
      </atom>
      ... many atoms deleted, for space ...
    </atomArray>
    <bondArray>
      <bond id="carotine_karne_b_1">
        <string builtin="atomRef">carotine_karne_a_1</string>
        <string builtin="atomRef">carotine_karne_a_2</string>
        <string builtin="order" convention="MDL">2</string>
      </bond>
      ... many bonds deleted, for space ...
    </bondArray>
  </molecule>
</cml>
</document>

Resources on Chemical Markup Language (CML)

1. Cover Pages: Chemical Markup Language (CML) A nice short report on Chemical Markup Language (CML)....
2. Chemical Markup Language (CML) The Original Site for Chemical Markup Language...
3. Introduction to JChemPaint opensource XML-aware browser (part of the Mozilla project) for CML made to render using XBL (XML Binding language) and SVG (Scalable vector graphics)...
4. Chemical Markup Language A Position Paper on Chemical Markup Language (CML)...
5. Chemical Markup Language (CML) The Original Site for Chemical Markup Language...
6. Chemical Markup Language 1.0 reference with examples With Clickable indexes; Graphical representation of examples (PNG and SVG created from CML; Using XSLT) - both molecules and spectra; Click on an atom in the example leads to relevant part of CML source...
7. Chemical Rendering using SVG and CML These are examples of how chemical objects expressed in XML languages such as CML (Chemical Markup Language) or SVG (Scalable Vector Graphics) can be rendered. The examples include transformations/bindings between CML and SVG....
8. ChiMeraL - CML transformation and display Demonstrates how a XML marked up molecule (CML) can be displayed in a variety of different ways - in particular, passing structural and spectral information onto applets (JME, JMol, Marvin, SDA and JSpec). All displays are created on the fly, via the use...
9. Jmol Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems....
10. JUMBO 3.0-J and JS JUMBO 3.0-J XML-CML molecular browser and toolkit: The complete JUMBO runtime on any Java 1.2/Java3D-enabled platform. A standalone CML editor based on JME (available for Windows and MacOS X). Source code for the jumbo.* libraries....
11. JUMBO 3.0-JS This is a Javascript version of a molecular browser for XML/CML files. It runs on "any XML-aware browser" which at present is MSIE5 or 6. It dynamically converts cml2svg and for this reason also requires an SVG plugin such as Adobe's....
12. Resources for Mozilla's native Scalable Vector Graphics implemen opensource XML-aware browser (part of the Mozilla project) for CML made to render using XBL (XML Binding language) and SVG (Scalable vector graphics)...
13. SourceForge.net: Chemical Markup Language 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....
14. SourceForge.net: cml-discuss cml-discuss mailing list archive...
15. SVG Zone - Developer Track - Chemical Markup Language (CML) demo In a series of related demonstration programs, chemical data for 2D and 3D molecules (including adrenalin, caffeine, cortisone, ethanol, and melatonin) are visualized using SVG. The molecular data is originally stored in another XML-related markup languag...
16. The Blue Obelisk Movement The Internet has brought together a group of chemists/programmers/informaticians who find themselves working together using collaborative tools and sharing commonality of vision. They are driven by wanting to do things better, but are frustrated with the...
17. XML-CML Development - DTD and Schema 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....
18. XML-CML Development - Examples of CML CML 2.0 examples: A ZIP file containing the XSD and supporting files is available as a 740,326 byte download. The XSD file itself is a 212,978 byte download. The example files are present in this directory and are available for download here. A single con...