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. 2011 Oct 14;3(1):44.
doi: 10.1186/1758-2946-3-44.

CML: Evolution and design

Peter Murray-Rust  1 , Henry S Rzepa
Affiliations

CML: Evolution and design

Peter Murray-Rust et al. J Cheminform. .

Abstract

A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.

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Figures

Figure 1
Figure 1
The PMRz symbiote in a familiar environment.
Figure 2
Figure 2
Analysis of bond lengths (horizontal axis = frequency) from the Cambridge Crystallographic Database ca. 1995. This has evolved into the bond length analysis tool in CrystalEye [60] which allows interactive clicking of points to bring up structures. (Note: Image is a scan of the original line printer output).
Figure 3
Figure 3
The Black Horse pub at Greenford.
Figure 4
Figure 4
Early CML markup, ca. 1995. Many of the current concepts were prototyped at this level, such as the CONVENTION and DICTNAME (now dictRef). The BUILTIN attribute is now hard-coded as CML attributes. The XVAR notation has now become cml:scalar and all the elements and attribute values have become QNames. (Note: Image is a scan of an original overhead transparency with handwritten annotation).
Figure 5
Figure 5
JUMBO screenshots (ca. 1997) showing support for spectra, properties, molecular structure in 2D and 3D and a variety of applets and widgets. Note the considerable change in syntax from the earlier picture; we have prototyped a namespace approach (e.g. XML.* and CML.*). These were later separated into CML and STMML [61]. The molecules and spectra had clickable locations so that peaks and molecules could be linked. (Note: Image is a scan of original overhead transparencies).
Figure 6
Figure 6
A multi-namespace design from 1997 - the first use of the CML alembic logo. This was before the XML Working Group created the current namespace syntax and while CML was still based on DTDs. (Note: Image is a scan of an original overhead transparency).
Figure 7
Figure 7
The auto-complete functionality in IDEs is underpinned by the content model approach.
Figure 8
Figure 8
A version of the CML DTD (in SGML) from ca. 1996. Note the early development of a namespace philosophy although there was no technology to support it at the time. (Note: Image is a scan of an original overhead transparency with handwritten annotation).
See this image and copyright information in PMC

References

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