492000 MichaelWright Department of Chemistry, Imperial College of Science, Technology and Medicine, UK ChiMeraL XML CML chemical markup language applet SVG FOP chemistry This document is intended to demonstrate the capabilities of docML using the stylesheet docml.xsl. You'll need Internet Explorer 5,x along with SVG and Chime plugins. Read this document source to see the structure of docML and the code for each section. For more information please see the ChiMeraL website.

A document writen in docML may consist of the following components;

Information in the metadata block is used to form the document header (above the first rule). Multiple authors, links to institutions and date conversions are handled automatically. Additonal meta information could be used in the hidden META tags of an HTML document (for example).

'Normal' XHTML elements are used for text formating; p, br/, i, b, ul, ol and li should be recognised by most stylesheets. Other elements will only be recognised by the document2.xsl (which assumes anything it doesn't understand is XHTML). Inline code uses docml:code display="inline" and is displayed using a fixed width font.

Numbering on chapter/subsection/appendix/labels is according to the following rules:

  • docml:chapter title="Example" - no number given - 'Example'
  • docml:chapter title="Example" index="4" - use number given (force) - '4 - Example'
  • docml:chapter title="Example" index="" - calculate number - '3 - Example'

Subsections and labels use x.y.z numbering in a similar fashion, appendices use letters. I suggest you don't mix calculated and forced numbers or confusion will occur! Hence:

docml:chapter title="docML Tutorial" index="" ptext/p docml:subsection title="Metadata" index="" /docml:subsection /docml:chapter

gives the structure seen above.

Web images (gif, jpg, png) and external links can be embedded using standard XHTML (img and a) or using docml:link with a suitable type and display attributes. Attributes idref and href are used for id referenced objects and URLs respectively. For example:

  • type="external":
  • ChiMeaL
  • type="external" display="image":
  • type="external" display="molFile":
  • type="external" display="svg":

Note the use of altWeb and altPrint on the SVG, this give alternate graphics the stylesheets can use for FOP or RSC conversion. Links can also point to references, figure labels (see ) or CML objects.

  • type="molecule"
    • display="datasheet":
    • display="jmeRaw":
    • display="molRaw":
    • display="xyzRaw":
    • display="jme":
    • display="jmeSimple":
    • display="jmol":
    • display="marvin":
    • display="sda":
    • display="svg":??
  • type="spectrum"
    • display="jcampRaw":
    • display="jspec":
    • display="svg":??
  • type="reaction"
    • display="marvin": broken
    • display="jme": broken
    • display="svg":??

Any of these objects can be 'wrapped' in a box and given a docml:label For example:

Example of boxed applets

Boxes are used instead of XHTML tables since ROWSPAN and COLSPAN concepts don't transfer to FO and other print formatting languages. At the moment, limitations are up to 3 columns and 2 rows, @type sets the box coloured/white).

A bibliography consists of optional text and a series of references; any of the following elements can be within the docml:ref:

  • ref (@href)
    • index
    • title
    • abstract
    • list
      • author
      • keyword
      • keyphrase
    • author
    • publication
    • volume
    • page
    • date
    • year
    • ISnumber
    • institution
    • comment

Common elements are: index, list/author, publication, volume, page and year (all others are optional). It should be noted that URL of a references is stored in the docml:ref @href attribute and that an index is required. Unlike the rest of docML, index is an element not an attribute (due to missing datatypes in IE), it's value affects the number shown in citations and the ordering of the reference list. If no docml:publication exists, stylesheets will assume a web reference and format the information appropriately. Additional text can be included within docml:ref as required.

Data blocks (annotated code, SVG and CML) can be included at the end of a document and then referenced from within the body of the text as required. This increases the human readability of the docML code. Use @docml:display="hidden" to hide blocks from the stylesheet and reference them via their @id, for example:

Example of a link to a code block For a formal description of CML version 1.0, see 1 P.Murray-Rust H. S.Rzepa J. Chem. Inf. Comp. Sci. 1999 39 928 2 World Wide Web Consortium (W3C). Specifications for XML, XHTML, XSL, SVG, Schemas and other standards can be found at this site. cml title="tetrahydrofuran" id="cml_THF" molecule title="Furan, tetrahydro-" id="mol_thf_1" formulaC4 H8 O/formula string title="CAS"109-99-9/string float title="molecular weight"72.1066/float string title="ACX"I1001473/string string title="DOT"UN 2056/string string title="RTECS"LU5950000/string float title="melting point" units="degC"-108.3/float float title="boiling point" units="degC"65.0/float float title="specific gravity"0.886/float float title="water solubility" convention="g/100 mL at 23 degC"30.0/float string title="comments" Colorless liquid with an ether-like odor detectable at 2 to 50 ppm. HYGROSCOPIC/string list title="alternate names" string title="name"THF/string string title="name"1,4-Epoxybutane/string string title="name"Butylene oxide/string string title="name"Cyclotetramethylene/string string title="name"tetramethylene oxide/string !-- etc -- /list /molecule /cml C8 H10 N4 O2 58-08-2 I1001269 UN 1544 EV6475000 194.19 238 1.23 1-5 White powder or white glistening needles usually melted together. LIGHT SENSITIVE 1,3,7-Trimethylxanthine 3,7-dihydro-1,3,7-trimethyl-1H-Purine-2,6-dione 1,3,7-Trimethyl-2,6-dioxopurine 7-Methyltheophylline Alert-Pep Cafeina Cafipel Guaranine Koffein Mateina Methyltheobromine No-Doz Refresh'n Stim Theine 1-methyltheobromine methyltheobromide eldiatric c organex 1,3,7-trimethyl-2,6-dioxo-1,2,3,6-tetrahydropurine caffenium -2.8709 -1.0499 0.1718 C -2.9099 0.2747 0.1062 N -1.8026 0.9662 -0.1184 C -0.6411 0.2954 -0.2316 C -0.6549 -1.0889 -0.1279 C -1.7352 -1.7187 0.0624 N 0.6052 0.7432 -0.4434 N 1.2863 -0.4175 -0.4514 C 0.5994 -1.5633 -0.2698 N 1.0875 2.0867 -0.6139 C -1.8349 2.1699 -0.2205 O -4.2178 0.9810 0.2003 C -3.8944 -1.6746 0.3323 O -1.6764 -3.1997 0.1458 C 2.3776 -0.4481 -0.6036 H 2.1902 2.0944 -0.7699 H 0.6074 2.5547 -1.5032 H 0.8606 2.6915 0.2934 H -4.0942 2.0097 0.6091 H -4.6699 1.0338 -0.8167 H -4.9101 0.4518 0.8943 H -2.3049 -3.6334 -0.6659 H -0.6444 -3.6030 0.0359 H -2.0682 -3.5218 1.1381 H caffeine_karne_a_1 caffeine_karne_a_2 1 caffeine_karne_a_1 caffeine_karne_a_6 1 caffeine_karne_a_1 caffeine_karne_a_13 2 caffeine_karne_a_2 caffeine_karne_a_3 1 caffeine_karne_a_2 caffeine_karne_a_12 1 caffeine_karne_a_3 caffeine_karne_a_4 1 caffeine_karne_a_3 caffeine_karne_a_11 2 caffeine_karne_a_4 caffeine_karne_a_5 2 caffeine_karne_a_4 caffeine_karne_a_7 1 caffeine_karne_a_5 caffeine_karne_a_6 1 caffeine_karne_a_5 caffeine_karne_a_9 1 caffeine_karne_a_6 caffeine_karne_a_14 1 caffeine_karne_a_7 caffeine_karne_a_8 1 caffeine_karne_a_7 caffeine_karne_a_10 1 caffeine_karne_a_8 caffeine_karne_a_9 2 caffeine_karne_a_8 caffeine_karne_a_15 1 caffeine_karne_a_10 caffeine_karne_a_16 1 caffeine_karne_a_10 caffeine_karne_a_17 1 caffeine_karne_a_10 caffeine_karne_a_18 1 caffeine_karne_a_12 caffeine_karne_a_19 1 caffeine_karne_a_12 caffeine_karne_a_20 1 caffeine_karne_a_12 caffeine_karne_a_21 1 caffeine_karne_a_14 caffeine_karne_a_22 1 caffeine_karne_a_14 caffeine_karne_a_23 1 caffeine_karne_a_14 caffeine_karne_a_24 1 C -0.2969 0.8979 C -0.2969 -0.6121 C -1.6273 1.6566 C 0.9896 1.8655 C -1.6419 -1.3780 C -2.9577 0.8869 C 2.2650 1.0555 O 0.0073 3.0676 C -2.9650 -0.6047 O -1.6566 -2.9320 N 3.7017 1.9791 O -4.3027 -1.3634 C 5.0687 1.0372 H 2.1440 2.8844 a1 a2 1 a1 a3 2 a1 a4 1 a2 a5 2 a3 a6 1 a4 a7 1 a4 a8 1 W a5 a9 1 a5 a10 1 a7 a11 1 a9 a12 1 a11 a13 1 a6 a9 2 a4 a14 1 H MASS SPECTRUM 250547 Virginia Division of Forensic Science NIST Mass Spectrometry Data Center M/Z RELATIVE ABUNDANCE 14 197 1 70 10 9999 1 104 14, 70 15, 840 16, 50 17, 40 18, 60 20, 10 25, 10 26, 50 27, 150 28, 900 29, 150 30, 40 31, 10 32, 150 34, 10 38, 120 39, 190 40, 680 41, 580 42, 1241 43, 60 44, 10 45, 10 50, 10 51, 130 52, 350 53, 470 54, 570 55, 3383 56, 730 57, 110 58, 140 59, 10 62, 10 63, 10 64, 30 65, 120 66, 640 67, 4153 68, 450 69, 170 70, 430 71, 10 72, 10 76, 10 77, 70 78, 70 79, 120 80, 230 81, 740 82, 2742 83, 330 85, 10 91, 10 92, 20 93, 60 94, 390 95, 130 96, 60 97, 210 104, 10 105, 10 106, 20 107, 70 109, 5935 110, 750 111, 120 112, 10 120, 10 121, 20 122, 90 123, 50 124, 60 125, 10 126, 10 132, 10 133, 10 134, 10 135, 70 136, 500 137, 460 138, 200 139, 10 140, 10 147, 10 148, 10 149, 50 150, 120 151, 40 152, 40 153, 10 161, 10 163, 20 164, 60 165, 570 166, 90 167, 10 179, 10 190, 10 193, 1461 194, 9999 195, 1050 196, 90 197, 10