QpShqLlw9YsNZwHwW+17PeBFuM4= tOjjuUOWg26YAY9SfHv48wzdQOpMY8gSVFWotAkogaVvqZfcZjXdzbzOTpllhRMBcvbc8ehw 4UsCfjC/YzuS+oGnc3OufeADU7ASj0e2lw4XlLKYBtdBfGg71GQqGdXrn2Xcmjbnnsn1mg3c ro3nIB+8A4i4j5/XotsW7Fmyvqk= y/gFMIdUnK4/WTFlAPjtQbOBGEFrwhpB9R10KrxAiAsteuQ70hG++ReLedY6hE3Tru yRLACVqe1vZPNM2G3ySyGkm2ZTjDEryk/QjqikHXko41WtJmhtrIxnnnjlLcM24Yre WO3wt3lI19Te5WINZiaojvzAAdEcXjIy+IeU6Gs= AQAB CN=XML-CML, OU=http://www.xml-cml.org/, O=n/a, L=London, ST=n/a, C=UK MIICTjCCAbcCBDo0y2cwDQYJKoZIhvcNAQEEBQAwbjELMAkGA1UEBhMCVUsxDDAKBgNVBAgTA24v YTEPMA0GA1UEBxMGTG9uZG9uMQwwCgYDVQQKEwNuL2ExIDAeBgNVBAsTF2h0dHA6Ly93d3cueG1s LWNtbC5vcmcvMRAwDgYDVQQDEwdYTUwtQ01MMB4XDTAwMTIxMTEyNDExMVoXDTAxMDMxMTEyNDEx MVowbjELMAkGA1UEBhMCVUsxDDAKBgNVBAgTA24vYTEPMA0GA1UEBxMGTG9uZG9uMQwwCgYDVQQK EwNuL2ExIDAeBgNVBAsTF2h0dHA6Ly93d3cueG1sLWNtbC5vcmcvMRAwDgYDVQQDEwdYTUwtQ01M MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQDL+AUwh1Scrj9ZMWUA+O1Bs4EYQWvCGkH1HXQq vECICy165DvSEb75F4t51jqETdOu7JEsAJWp7W9k80zYbfJLIaSbZlOMMSvKT9COqKQdeSjjVa0m aG2sjGeeeOUtwzbhit5Y7fC3eUjX1N7lYg1mJqiO/MAB0RxeMjL4h5ToawIDAQABMA0GCSqGSIb3 DQEBBAUAA4GBABYyetfClkvB4CL214PSnoti+sdQK2cgPAb0UQeNkd9MQ4vUcr5JKyAUgbL9skOB JuyenInmqQU7HUhyIgmDEnMi7DYx2Psc82RaRZlyaeRF7BqQB9mMtAWL/5H935GE48Pf6g9b9Z3q 9qh9rwwM2spqL6MCHjEEBJZYjPJ2MERv Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content - Supplemental Information (XML) Chemical Markup Language; CML; XML signature; XSign; chemistry; eXtensible Markup Language; XML 2000-08-25 2000-08-28 2000-10-24 Peter Murray-Rust Henry S. Rzepa Michael Wright School of Pharmaceutical Sciences, University of Nottingham, UK Department of Chemistry, Imperial College of Science, Technology and Medicine, UK New Journal of Chemistry en text/xml Copyright: Peter Murray-Rust, Henry S. Rzepa and Michael Wright Additional Figures Comparing different ways of displaying chemical structures Taxol intermediate as a .gif image (bitmap) - a 'dead' format, human comprehensible but chemical information can't be automatically extracted Riboflavin using a plugin - Uses the EMBED tag and an external data file (Chime or an equivalent is required) Cochineal using Chemaxion's Marvin applet - the structure is being stored as CML within this document, hence no data file is needed

Dynamic selection of stylesheets - this is a much simpler version of the ChiMeraL demonstration

[obsolete figure - please see the ChiMeraL website]

CML (Ethanol) transformed to the MDL molFile format (v2000 and v3000)

Brief Description of v2000 format (for v3000 see www.mdli.com)

rows 1-3:: Comment lines; sometimes these contain a title, a filename and the source of the file but there is no common convention. These lines are normally discarded on converting to CML (note line 3 is blank).
row 4:: The first digit is the total number of atoms in the molecule, the second is the total number of bonds (hydrogen atoms and bonds to them, are sometimes neglected).
rows 5-13:: Each row refers to an atom and gives (in order) Cartesian coordinates x, y and z (in Angstrom) and the element type (as its periodic table letter). The remaining columns are used for electrons, charges etc. and are not yet included in CML, since mol files rarely use them.
rows 14-21:: Each row refers to a bond. The first two digits refer to the atoms the bond is between (hence 2 3 means a bond between the second and third atoms in the list above) and the third digit refers to the empirical bond order (2 = double bond etc.) Again, the remaining columns are rarely used.
row 22:: M END indicates the end of the molecule. Files that contain multiple .mol molecules (e.g. reaction .rxn or .sd files) also include a delimiter between molecules ($MOL or $$$$).

JME editor with Java Script integration - toolbars used for editing, left click/drag to translate, right click/drag to rotate

JavaScript is able to access functions within the applet. Click a button to see a demonstration of this

Jmol 3D viewer and .xyz format - click/drag to rotate, shift-c/d to zoom, ctrl-c/d to translate, TAB changes drawing style, L adds atom labels

Marvin (left) and SDA applets - Marvin: left click/drag to rotate, shift-lc/d to zoom, ctrl-lc/d to translate, right click for menu - SDA: tool bars contain editing tools, applet can be 'floated' to a separate window by clicking the top left button

Tetrahydrofuran mass spectrum using the JCAMP-DX format

JSpec spectra viewer showing caffeine mass and UV/Vis spectra - click drag to select an area then click buttons

SVG molecule and infra red spectrum - right click for menu

Cross Metathesis (example of a catalytic cycle)

THIS IS NOW OUT OF DATE - please see www.xml-cml.org for the latest examples.

Server side conversion of .mol, .rxn and .dx files to CML - http://www.ch.ic.ac.uk/chimeral/resources/file2cml.html

Converts MDL .mol, REACSS .rxn and JCAMP .dx files to CML
Either select an example file or;
1) Open file in a text editor
2) Copy and paste file contents into the textarea
3) Fill in the other fields (they are used in 'id') and select file and display types
4) Press GO

File Type:		Title:
Author:		Date:
File: </td> </tr> <tr> <td align="center" colspan="4"> <input type="SUBMIT" value="************ GO **********"/> </td> </tr> </table> <!-- examples --> <input name="mol" type="hidden" value="caffeine.mol 24 25 0 0 0 0 0 0 0 0 0 -2.8709 -1.0499 0.1718 C 0 0 0 0 0 -2.9099 0.2747 0.1062 N 0 0 0 0 0 -1.8026 0.9662 -0.1184 C 0 0 0 0 0 -0.6411 0.2954 -0.2316 C 0 0 0 0 0 -0.6549 -1.0889 -0.1279 C 0 0 0 0 0 -1.7352 -1.7187 0.0624 N 0 0 0 0 0 0.6052 0.7432 -0.4434 N 0 0 0 0 0 1.2863 -0.4175 -0.4514 C 0 0 0 0 0 0.5994 -1.5633 -0.2698 N 0 0 0 0 0 1.0875 2.0867 -0.6139 C 0 0 0 0 0 -1.8349 2.1699 -0.2205 O 0 0 0 0 0 -4.2178 0.9810 0.2003 C 0 0 0 0 0 -3.8944 -1.6746 0.3323 O 0 0 0 0 0 -1.6764 -3.1997 0.1458 C 0 0 0 0 0 2.3776 -0.4481 -0.6036 H 0 0 0 0 0 2.1902 2.0944 -0.7699 H 0 0 0 0 0 0.6074 2.5547 -1.5032 H 0 0 0 0 0 0.8606 2.6915 0.2934 H 0 0 0 0 0 -4.0942 2.0097 0.6091 H 0 0 0 0 0 -4.6699 1.0338 -0.8167 H 0 0 0 0 0 -4.9101 0.4518 0.8943 H 0 0 0 0 0 -2.3049 -3.6334 -0.6659 H 0 0 0 0 0 -0.6444 -3.6030 0.0359 H 0 0 0 0 0 -2.0682 -3.5218 1.1381 H 0 0 0 0 0 1 2 1 0 0 0 1 6 1 0 0 0 1 13 2 0 0 0 2 3 1 0 0 0 2 12 1 0 0 0 3 4 1 0 0 0 3 11 2 0 0 0 4 5 2 0 0 0 4 7 1 0 0 0 5 6 1 0 0 0 5 9 1 0 0 0 6 14 1 0 0 0 7 8 1 0 0 0 7 10 1 0 0 0 8 9 2 0 0 0 8 15 1 0 0 0 10 16 1 0 0 0 10 17 1 0 0 0 10 18 1 0 0 0 12 19 1 0 0 0 12 20 1 0 0 0 12 21 1 0 0 0 14 22 1 0 0 0 14 23 1 0 0 0 14 24 1 0 0 0 M END"/> <input name="rxn" type="hidden" value="$RXN ISIS 041120001449 2 2 $MOL -ISIS- 04110014492D 8 8 0 0 0 0 0 0 0 0999 V2000 -4.1716 -0.8711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8861 -0.4585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5986 -0.8710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5978 -1.6958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8785 -2.1065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1690 -1.6918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4583 -0.4542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7458 -0.8667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4 5 1 0 0 0 0 1 2 2 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 3 4 2 0 0 0 0 1 7 1 0 0 0 0 2 3 1 0 0 0 0 7 8 2 0 0 0 0 M END $MOL -ISIS- 04110014492D 12 12 0 0 0 0 0 0 0 0999 V2000 -0.7348 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7359 -1.8023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0211 -2.2152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6953 -1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6925 -0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0229 -0.5622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4042 -0.5542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1167 -0.9667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8292 -0.5500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5417 -0.9625 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4000 0.2708 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0292 -3.0375 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 3 4 2 0 0 0 0 5 7 1 0 0 0 0 2 3 1 0 0 0 0 7 8 1 0 0 0 0 4 5 1 0 0 0 0 8 9 1 0 0 0 0 1 2 2 0 0 0 0 9 10 1 0 0 0 0 5 6 2 0 0 0 0 7 11 2 0 0 0 0 6 1 1 0 0 0 0 3 12 1 0 0 0 0 M END $MOL -ISIS- 04110014492D 9 10 0 0 0 0 0 0 0 0999 V2000 8.4076 -1.0878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6930 -0.6752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9806 -1.0876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9814 -1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7007 -2.3232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4102 -1.9084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1208 -0.6708 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 9.8333 -1.0833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8333 -0.2542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 3 4 2 0 0 0 0 1 7 1 0 0 0 0 2 3 1 0 0 0 0 7 8 1 0 0 0 0 4 5 1 0 0 0 0 7 9 1 0 0 0 0 9 8 1 0 0 0 0 M END $MOL -ISIS- 04110014492D 11 11 0 0 0 0 0 0 0 0999 V2000 12.3069 -1.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.3016 -1.8982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.0107 -2.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.7256 -1.9049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.7270 -1.0785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.0172 -0.6678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.0042 -3.1375 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 14.4375 -0.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.0208 -1.2417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 14.4333 0.1667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 15.8458 -1.2417 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6 1 1 0 0 0 0 3 4 2 0 0 0 0 3 7 1 0 0 0 0 2 3 1 0 0 0 0 5 8 1 0 0 0 0 4 5 1 0 0 0 0 8 9 1 0 0 0 0 1 2 2 0 0 0 0 8 10 2 0 0 0 0 5 6 2 0 0 0 0 9 11 1 0 0 0 0 M END "/> <input name="dx" type="hidden" value="##TITLE=Caffeine ##JCAMP-DX=4.24 ##DATA TYPE=MASS SPECTRUM ##CAS REGISTRY NO=58-08-2 ##EPA MASS SPEC NO=250547 ##MOLFORM=C8H10N4O2 ##MW=194 ##ORIGIN=Virginia Division of Forensic Science ##ORIGIN CODE=VIR ##.IONIZATION ENERGY=70 ##FIRSTX=14 ##LASTX=197 ##FIRSTY=70 ##MINY=10 ##MAXY=9999 ##NPOINTS=104 ##OWNER=NIST Mass Spectrometry Data Center ##XUNITS=M/Z ##YUNITS=RELATIVE ABUNDANCE ##XFACTOR=1 ##YFACTOR=1 ##PEAK TABLE=(XY..XY) 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 ##END= "/> </form></p> </docml:box> </docml:section> <!-- ********************** --> <!-- **** appendix **** --> <!-- ********************** --> <docml:appendix id="append_resources" index="auto"> <rdf:Description> <dc:title>List of ChiMeraL Resources</dc:title> </rdf:Description> <p>These resources are available from the ChiMeraL website - <a href="http://www.ch.ic.ac.uk/chimeral/" target="new">http://www.ch.ic.ac.uk/chimeral/</a></p> <p><b>Demonstrations</b></p> <ul> <li>Markup and display of molecules, spectra and reactions</li> <li>Multiple stylesheet selection and the use of data islands</li> <li>Testing XML/XSL functionality with various browsers</li> <li>Scaling test - ECTOC database (9 Mb XML file)</li> <li>Writing a complex XML document and display through IE and .pdf (via FOP)</li> </ul> <p><b>Schema</b></p> <ul> <li>CML schema 0.2 - based on published DTD</li> <li>CML schema 0.2 (IE version) - includes unique @id and data links</li> <li>ChiMeraL schema 0.1 - extends CML to include <font class="code"><docml:lt/>spectrum<docml:gt/></font></li> <li>Document schema 0.1 - developed to write this report</li> </ul> <p><b>XSL Stylesheets</b></p> <ul> <li>generic.xsl - displays all CML</li> <li>datasheet.xsl - property information as an HTML table</li> <li>jme.xsl - Java Molecular Editor applet - editor</li> <li>jme_format.xsl - JME data string</li> <li>marvinview.xsl - Marvin applet, 3D viewer mode</li> <li>marvinedit.xsl - Marvin applet, editor mode</li> <li>sda.xsl - Structure Drawing Applet - editor</li> <li>mol.xsl - MDL .mol file format</li> <li>jmol.xsl - Open Source applet - 3D viewer</li> <li>xyz.xsl - .xyz file format</li> <li>jspec.xsl - Java Spectrum Viewer - viewer</li> <li>jcamp.xsl - JCAMP .dx format</li> <li>reaction.xsl - stepwise, linear and cycle.4 reactions using Marvin</li> <li>document.xsl - displaying complex XML document in IE5</li> <li>document.css - CSS stylesheet for above</li> <li>doc2fo.xsl - convert complex XML document to formatting object (for use with FOP)</li> </ul> <p><b>perl converters</b></p> <ul> <li>MDL .mol to CML</li> <li>MDL .mol to JME format</li> <li>.sd to CML (multiple mol archive)</li> <li>.xyz to CML</li> <li>JCAMP .dx and .cs to CML</li> <li>REACSS .rxn to CML</li> <li>.rd to CML</li> <li>.mol, .rxn and .dx 2 CML are all available as an online cgi script</li> </ul> <p>A large number of example CML files are also available, these contain properties, structures, spectra and reactions. Further archives of CML files will be made available as they are converted.</p> </docml:appendix> <!-- ********************** --> <!-- **** appendix **** --> <!-- ********************** --> <docml:appendix id="append_cmlsyntax" index="auto"> <rdf:Description> <dc:title>CML Syntax and Notes</dc:title> </rdf:Description> <p>The published <a href="http://www.xml-cml.org/cml_10.dtd" target="new">CML 1.0 DTD</a> declares valid elements and attributes but puts few restrictions on how these elements and attributes are used. As a consequence of this, it is possible to markup a CML object (e.g. a molecule) using a variety of different syntaxes. Whilst this gives great flexibility, it also makes it significantly more difficult to build CML applications. In particular some of these syntaxes can not be easily parsed using stylesheets. I have selected what I feel is the syntax best suited to XSL and small molecule markup. This, along with the syntax for <b>chimeral:spectrum</b> and <b>reaction</b> (still experimental) is as follows: <font class="comment">(comments on syntax are in green)</font> </p> <docml:link xlink:href="cml_objects/cmlnotes.xml" xlink:title="code"/> </docml:appendix> <!-- ********************** --> <!-- **** appendix **** --> <!-- ********************** --> <docml:appendix id="append_schema" index="auto"> <rdf:Description> <dc:title>CML Schema (IE 0.2) Notes</dc:title> </rdf:Description> <p>This version of the schema is based directly on the CML 1.0 DTD but includes datatype declarations for use in IE 5.x. These datatypes allow the use of @id and @href for intra-document linking. A platform independent version (plus schemas for chimeral: and docml:) are available from the <a href="http://www.ch.ic.ac.uk/chimeral/" target="new">ChiMeraL site.</a> <font class="comment">(comments on syntax are in green)</font></p> <docml:link xlink:href="cml_objects/cmlschema.xml" xlink:title="code"/> </docml:appendix> <!-- ********************** --> <!-- **** appendix **** --> <!-- ********************** --> <docml:appendix id="append_dtd" index="auto"> <rdf:Description> <dc:title>CML 1.0 DTD</dc:title> </rdf:Description> <p>This is a copy of the DTD for CML 1.0 published in JCICS by Peter Murray-Rust and Henry S. Rzepa (see <a href="http://www.xml-cml.org" target="new">see www.xml-cml.org</a>)</p> <docml:link xlink:href="cml_objects/cmldtd.xml" xlink:title="code"/> </docml:appendix> <!-- ********************** --> <!-- **** appendix **** --> <!-- ************************ --> <docml:appendix id="append_glossary" index="auto"> <rdf:Description> <dc:title>Glossary</dc:title> </rdf:Description> <dl> <dt><b>Applet (Java)</b></dt> <dd docml:id="glos_applet">A small program designed to run embedded within a web page (either HTML or XML). The applet is downloaded from the same site as the web page and does not require installation (unlike a plugin). For security reasons, applets has restricted access to the local hard drive.</dd> <dt><b>ASCII</b></dt> <dd>Refers to the standard set of text characters used for all computers. An ASCII file can be opened in a normal text editor (in contrast to a binary file which can not). XML/HTML and most of the legacy formats use ASCII.</dd> <dt><b>Attribute</b></dt> <dd docml:id="glos_attribute">Used to give more specific information within an HTML/XML tag (hence <docml:lt/>FONT SIZE="+1"<docml:gt/> has attribute 'SIZE'), @href is shorthand for 'attribute called href'</dd> <dt><b>CML (Chemical Markup Language)</b></dt> <dd docml:id="glos_cml">XML language optimised for marking up chemistry.</dd> <dt><b>CSS (Cascading stylesheet)</b></dt> <dd docml:id="glos_css">Stylesheet primarily designed for HTML, allows tag properties to be changed (over-riding the parser defaults).</dd> <dt><b>DTD</b></dt> <dd docml:id="glos_dtd">Older standard for describing XML languages, uses a unique syntax.</dd> <dt><b>DOM (Document Object Model)</b></dt> <dd docml:id="glos_dom">'Tree' model of a document, allows the parser scripting access to all 'objects' within the tree. Under development by the W3C</dd> <dt><b>Element</b></dt> <dd docml:id="glos_element">XML equivalent to HTML tags. Refers to the tag pair, any attributes and their contents</dd> <dt><b>HTML(hypertext markup language)</b></dt> <dd docml:id="glos_html">Text formatting and display language - standard electronic format on the web</dd> <dt><b>JavaScript</b></dt> <dd docml:id="glos_javascript">A scripting language (which has little to do with Java, although they can communicate) used to add interactivity to web pages. Javascript functions need to be triggered in some way (normally using a <docml:lt/>FORM<docml:gt/> button).</dd> <dt><b>Markup</b></dt> <dd docml:id="glos_markup">Procedure of labelling and organising information using <docml:lt/>tag<docml:gt/> <docml:lt/>/tag<docml:gt/> pairs and attributes. Basis for most formatting languages.</dd> <dt><b>Namespaces</b></dt> <dd docml:id="glos_namespaces">System for assigning elements to different XML languages. Very important if a document is to be validated.</dd> <dt><b>Parser</b></dt> <dd docml:id="glos_parser">Program able to read XML, comprehend its structure and build a DOM and/or use a stylesheet to display it. This project uses Internet Explorer 5.x</dd> <dt><b>Plugin</b></dt> <dd docml:id="glos_plugin">Small, platform dependent program that 'plugs into' a web browser and allows it to display additional file formats (e.g. .mol, .svg, .vrml). Needs to be installed by the user.</dd> <dt><b>Perl</b></dt> <dd docml:id="glos_perl">Powerful text search and replace language (amongst other things) and used to build all the legacy2CML converters in this project. Also used for server-side cgi scripts.</dd> <dt><b>Schema</b></dt> <dd docml:id="glos_schema">Newer standard for describing XML languages, uses XML rules and syntax.</dd> <dt><b>SVG (Scalable Vector Graphics)</b></dt> <dd docml:id="glos_svg">XML language optimised for describing vector ('line' as compared to bitmap/gif/jpg) images.</dd> <dt><b>Tag</b></dt> <dd docml:id="glos_tag">Basic unit of markup, delimited by square brackets: <docml:lt/>tag<docml:gt/></dd> <dt><b>Well formed</b></dt> <dd docml:id="glos_wellformed">A well formed document is one that complies to XML rules and syntax.</dd> <dt><b>Valid</b></dt> <dd docml:id="glos_valid">A valid document is well formed and conforms to a language description given in a DTD or schema.</dd> <dt><b>XHTML(extensible hypertext markup language)</b></dt> <dd docml:id="glos_xhtml">HTML tags corrected to follow XML rules</dd> <dt><b>XML(extensible markup language)</b></dt> <dd docml:id="glos_xml">A series of rules for writing other 'XML compliant' languages</dd> <dt><b>XSL(extensible stylesheet language)</b></dt> <dd docml:id="glos_xsl">Stylesheet language, includes powerful scripting and querying features.</dd> </dl> </docml:appendix> </docml:document>