Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content - Supplemental Information (XML)

Peter Murray-Rust² Henry. S. Rzepa¹ Michael Wright¹

(1) Department of Chemistry, Imperial College of Science, Technology and Medicine, UK - (2) School of Pharmaceutical Sciences, University of Nottingham, UK - August 15, 2000

Additional Figures

Figure 1: 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
		You must have Java turned on!

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Figure 2: Dynamic selection of stylesheets - this is a much simpler version of the ChiMeraL demonstration

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Figure 3: Ethanol using the .mol format

ethanol from CML 9 8 1.0303 0.8847 0.9763 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8847 1.9889 1.5717 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1883 1.4807 1.7425 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.2330 0.8324 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9949 0.0000 1.6255 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4097 0.5558 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9050 2.8742 0.9059 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4753 2.3225 2.5456 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7056 2.1820 2.1139 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 4 1 0 0 0 0 1 5 1 0 0 0 0 1 6 1 0 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 2 8 1 0 0 0 0 3 9 1 0 0 0 0 M END

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 $$$$).

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Figure 4: JME editor with Java Script integration - toolbars used for editing, left click/drag to translate, right click/drag to rotate

You have to enable Java and JavaScript on your machine !

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

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Figure 5: 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

You have to enable Java and JavaScript on your machine !

17 histamine from CML C -1.7560 0.0000 0.3080 C -0.3600 0.0760 0.2880 N 0.1400 -1.1520 0.5080 C -0.9160 -1.9680 0.6520 N -2.0640 -1.2800 0.5320 C 0.4520 1.3600 0.0640 C 1.9560 1.0720 0.1080 N 2.7360 2.3040 -0.1040 H -2.4520 0.8120 0.1640 H -0.8520 -3.0320 0.8400 H 0.1880 2.0880 0.8320 H 0.1840 1.7800 -0.9040 H 2.2240 0.3480 -0.6600 H 2.2240 0.6560 1.0840 H 2.4960 3.0320 0.6680 H 2.4920 2.7240 -1.0840 H -3.0120 -1.7840 0.6240

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Figure 6: 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

You must have Java turned on!

You must have Java turned on!

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Figure 7: Tetrahydrofuran mass spectrum using the JCAMP-DX format

##TITLE= Furan, tetrahydro- ##JCAMP-DX= 4.24 ##DATA TYPE= MASS SPECTRUM ##XUNITS= M/Z ##YUNITS= RELATIVE ABUNDANCE ##FIRSTX= 24 ##LASTX= 73 ##FIRSTY= 4 ##MINY= 3 ##MAXY= 3 ##NPOINTS= 32 ##PEAK TABLE= (XY..XY)24, 4 25, 30 26, 171 27, 1545 29, 792 30, 21 31, 258 33, 5 34, 26 35, 10 37, 105 38, 165 39, 1182 40, 906 41, 4060 42, 9999 43, 1586 44, 325 45, 100 46, 3 49, 7 50, 11 51, 19 53, 27 54, 10 55, 6 68, 7 69, 20 70, 107 71, 2557 72, 2868 73, 147 ##END=

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Figure 8: JSpec spectra viewer showing caffeine mass and UV/Vis spectra - click drag to select an area then click buttons

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Figure 9: SVG molecule and infra red spectrum - right click for menu

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Figure 10: Cross Metathesis (example of a catalytic cycle)

Cycle 4 Reaction: Mechanism of Cross Metathesisid: cycle_rxn_1Description: Catalytic cycleYield:Notes: from Dr. Braddock's lecture notes You must have Java turned on! You must have Java turned on! You must have Java turned on! You must have Java turned on! You must have Java turned on! You must have Java turned on! You must have Java turned on! You must have Java turned on!

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Warning: you need to be online and the server-returned page will overwrite this one

Figure 11: 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: MDL .mol molecule JCAMP .dx spectrum REACSS .rxn reaction Title: Author: Date: File:

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These resources are available from the ChiMeraL website - http://www.ch.ic.ac.uk/chimeral/

Demonstrations

• Markup and display of molecules, spectra and reactions
• Multiple stylesheet selection and the use of data islands
• Testing XML/XSL functionality with various browsers
• Scaling test - ECTOC database (9 Mb XML file)
• Writing a complex XML document and display through IE and .pdf (via FOP)

Schema

• CML schema 0.2 - based on published DTD
• CML schema 0.2 (IE version) - includes unique @id and data links
• ChiMeraL schema 0.1 - extends CML to include <spectrum>
• Document schema 0.1 - developed to write this report

XSL Stylesheets

• generic.xsl - displays all CML
• datasheet.xsl - property information as an HTML table
• jme.xsl - Java Molecular Editor applet - editor
• jme_format.xsl - JME data string
• marvinview.xsl - Marvin applet, 3D viewer mode
• marvinedit.xsl - Marvin applet, editor mode
• sda.xsl - Structure Drawing Applet - editor
• mol.xsl - MDL .mol file format
• jmol.xsl - Open Source applet - 3D viewer
• xyz.xsl - .xyz file format
• jspec.xsl - Java Spectrum Viewer - viewer
• jcamp.xsl - JCAMP .dx format
• reaction.xsl - stepwise, linear and cycle.4 reactions using Marvin
• document.xsl - displaying complex XML document in IE5
• document.css - CSS stylesheet for above
• doc2fo.xsl - convert complex XML document to formatting object (for use with FOP)

perl converters

• MDL .mol to CML
• MDL .mol to JME format
• .sd to CML (multiple mol archive)
• .xyz to CML
• JCAMP .dx and .cs to CML
• REACSS .rxn to CML
• .rd to CML
• .mol, .rxn and .dx 2 CML are all available as an online cgi script

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.

The published CML 1.0 DTD2 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 particularl 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 chimeral:spectrum and reaction (still experimental) is as follows: (comments on syntax are in green)

<?xml version="1.0"?>

<?xml-stylesheet type="text/xsl" href="document.xsl" ?>



<!-- Declares this document as XML and indicate the URL of its stylesheet -->



<document title="Lipids" id="cmldoc_karne_lipids"

	xmlns="http://www.w3.org/1999/xhtml"

	xmlns:chimeral="x-schema:http://www.ch.ic.ac.uk/chimeral/spectrum_schema_ie_01.xml"> 

	

<!-- <document> isn't part of CML but represents the top element of any XML compliant 

document, this might contain CML, XHTML, MaML etc. - note the XHTML and chimeral namespaces -->



<cml title="Cholesterol" id="cml_karne_cholesterol" 

	xmlns="x-schema:http://www.ch.ic.ac.uk/chimeral/cml_schema_ie_02.xml">

	 

<!-- The CML namespace points to a copy of the schema, <cml> this may contain any number of 

CML 'objects' e.g. <molecule>, <reaction> or <chimeral:spectrum> -->



	<molecule title="cholesterol" id="mol_cholesterol">

		<formula>C27 H46 O</formula>

		

<!-- Information specific to this molecule is included here as <string>, <float> or <integer>

 - additional elements can be added as required but note the use of @title to label them. 

Alternate names are marked up as a <list> of <string>s -->



		<string title="CAS">57-88-5</string>

		<string title="ACX">I1001660</string>

		<string title="RTECS">FZ8400000</string>

		<float title="molecule weight">386.6598</float>

		<float title="melting point" units="degC">148.5</float>

		<float title="boiling point" units="degC">360</float>

		<float title="specific gravity">1.067</float>

		<list title="alternate names">

			<string title="name">Cholesterin</string>

			<string title="name">(3beta)-Cholest-5-en-3-ol</string>

			<string title="name">Cholest-5-en-3-ol (3beta)-</string>

			<string title="name">cholest-5-ene-3beta-ol</string>

			<string title="name">3beta-hydroxycholest-5-ene</string>

		</list>

		

<!-- The following is used for small molecular structures 

- this format is much preferred but rather verbose. <integer builtin="atomId"> 

would normally be that used in the MDL .mol format but in contrast, 'id' must be unique 

over (at least) this document. Additional strings are 'formalCharge' and 'hydrogenCount'. 

2D structures will use builtin="x2 | y2" but are otherwise the same -->



		<list title="atoms"> 

			<!-- repeat -->

			<atom id="cholesterol_a_1">

				<integer builtin="atomId">1</integer>

				<float builtin="x3" units="A">-1.9901</float>

				<float builtin="y3" units="A">2.1889</float>

				<float builtin="z3" units="A">-1.8776</float>

				<string builtin="elementType">H</string>

			</atom>

			<!-- /repeat (74 atoms) --> 

		</list>

		

<!-- Large molecular structures - this format is terse but much harder to format/refer 

to in XSL. I have chosen not to use it -->



		<atomArray id="methanol"> 

			<stringArray title="label">a1 a2 a3 a4 a5 a6</stringArray> 

			<stringArray builtin="elementType">C O H H H H</stringArray>

			<floatArray builtin="x3">-0.748 ..</floatArray> 

			<floatArray builtin="y3">-0.015 ..</floatArray> 

			<floatArray builtin="z3">0.024 ..</floatArray> 

			<integerArray builtin="formalCharge"></integerArray> 

		</atomArray>

		

<!-- A <list> of <bond>s is used for small molecules 

- large ones will probably ignore bonds and calculate then directly -->



		<list title="bonds"> 

			<!-- repeat --> 

			<bond id="cholesterol_b_1">

				<integer title="bondId">1</integer>

				<integer builtin="atomRef">2</integer>

				<integer builtin="atomRef">1</integer>

				<integer builtin="order" convention="MDL">1</integer>

			</bond>

			<!-- /repeat (77 bonds) -->

		</list>

	</molecule>

	

<!-- Elements in spectra tend to match the LDHs in the JCAMP format. The namespace chimeral: is 

very important as spectrum isn't found in CML 1.0 -->



	<chimeral:spectrum title="Cholesterol" id="spect_cholesterol_ms_1"

	 	convention="JCAMP-DX=4.24">

		<string title="datatype">MASS SPECTRUM</string>

		<string title="EPA">67286</string>

		<string title="origin">T.IIDA NIHON UNIVERSITY, KORIYAMA,

		 FUKUSHIMA-KEN, JAPAN</string>

		<string title="owner">NIST Mass Spectrometry Data Center</string>

		<string title="spectrometer">LKB 9000</string>



<!-- The following information is required for the rendering of spectra in Jspec -->



		<float title="xunits">M/Z</float>

		<float title="yunits">RELATIVE ABUNDANCE</float>

		<float title="firstx" convention="M/Z">18</float>

		<float title="lastx" convention="M/Z">387</float>

		<float title="deltax" convention="M/Z"></float>

		<float title="xfactor">1</float>

		<float title="firsty" convention="RELATIVE ABUNDANCE">700</float>

		<float title="miny" convention="RELATIVE ABUNDANCE">100</float>

		<float title="maxy" convention="RELATIVE ABUNDANCE">9999</float>

		<float title="yfactor">1</float>

		<float title="npoints">169</float>

		

<

!-- One of the following syntaxes is then used, depending on the type of spectrum -->



<

!--  A: simplest and prefered spectra format. Try and avoid (X++(Y..Y)) -->



		<list title="xypairs" convention="(XY..XY)"> 

			<!-- repeat -->

			<coordinate2 id="cholesterol_ms_c_1">18, 700</coordinate2>

			<!-- /repeat (169 data pairs) --> 

		</list>

		

<!-- B: alternate format for peak tables rather then data -->



		<list title="peak table" convention="(XY..XY)">

			<!-- repeat -->

			<coordinate2 id="mol_s_1">X, Y</coordinate2>

			<!-- /repeat --> 

		</list>

		

<!-- C: convention often used for NMR peak tables is (XYM) -->



		<list title="peak table" convention="(XYM)"> 

			<!-- repeat -->

			<coordinate3 id="mol_s_1">X, Y, M</coordinate3>

			<!-- /repeat --> 

		</list>

	</chimeral:spectrum>

	

<!-- Reactions are made up of a series of lists, each list containing a number of links @href 

to molecule @id -->



	<reaction title="Reactions" id="simple_rxn_1" 

		convention="stepwise | linear | cycle.4 | ..">

		

<!-- Linear markup is much preferred since it's the simplest, others provided for formatting 

purposes. The following three elements can be used either at the reaction level or at 

each reaction step -->



		<string title="description">Diels-Alder cycloaddition</string>

		<float title="yield" units="%">88</float>

		<string title="notes">example</string>



<!-- Stepwise (x1 > y1, x2 > y2); use as many reactants, reagents and products 

as needed for each step, reactions steps will be displayed separately. Additional links to 

catalysts, intermediates, transition states etc. can be used as required -->



			<!-- repeat --> 

			<list title="reactionStep" id="simple_s_1">

				<link title="reactant" href="mol_x"/>

				<link title= "reagent" href= "mol_r">

					<integer title="index">1</integer>

					<string title="solvent">Acetonitrile</string>

					<string title="temperature" units="degC">100</string>

					<string title="duration" units="hours">3</string>

					<string title= "notes">reflux</string>

				</link>

				<link title="reagent">

					<integer title="index">2</integer>

					<string title="notes">workup</string>	

				</link>

				<link title="product" href="mol_y"/>

			</list>

			<!-- /repeat -->

			

<!-- Linear (x > y > z); reactant refers to the first reactants, product 

refers to the final product; intermediates use linearReactant and linearProduct	 -->



			<list title= "linearstep" id="step_1">

				<link title="reactant" href="mol_1"/>

				<link title="reagent" href="mol_r1">

					<!-- .. -->

				</link>

				<link title="linearProduct" href="mol_2"/>

			</list>

			<list title= "linearstep" id="step_2">

				<link title="linearReactant" href="mol_2"/>

				<link title="reagent" href="mol_r2">

					<!-- .. -->

				</link>

				<link title="linearProduct" href="mol_3"/>

			</list>

			<list title= "linearstep" id="step_3">

				<link title="linearReactant" href="mol_3"/>

				<link title="reagent" href="mol_r3">

					<!-- .. -->

				</link>

				<link title="Product" href="mol_4"/>

			</list>

			

<!-- Catalytic cycle - much more complex (.. > x > y > z > ..) reactant and product 

refer to substances 'in' and 'out' of the cycle in each step, use cycleReactant and 

cycleProduct for 'within' the cycle. Markup should be cyclic 

(final cycleProduct == first cycleReactant) -->



			<list title="reactionStep" id="step_1">

   				<link title="cycleReactant" href="mol_1" id="cycle_lk_1"/>

   				<link title="reactant" href="mol_3" id="cycle_lk_2"/>

 				<link title="cycleProduct" href="mol_7" id="cycle_lk_3"/>

 			</list>

 			<list title="reactionStep" id="step_2">

   				<link title="cycleReactant" href="mol_7" id="cycle_lk_4"/>

   				<link title="cycleProduct" href="mol_6" id="cycle_lk_5"/>

   				<link title="product" href="mol_8" id="cycle_lk_6"/>

 			</list>

 			<list title="reactionStep" id="step_3">

   				<link title="cycleReactant" href="mol_6" id="cycle_lk_7"/>

   				<link title="reactant" href="mol_5" id="cycle_lk_8"/>

   				<link title="cycleProduct" href="mol_4" id="cycle_lk_9"/>

 			</list>

 			<list title="reactionStep" id="step_4">

   				<link title="cycleReactant" href="mol_4" id="cycle_lk_10"/>

   				<link title="cycleProduct" href="mol_1" id="cycle_lk_11"/>

   				<link title="product" href="mol_2" id="cycle_lk_12"/>

 			</list>

			

<!-- list title="atomMap" could be placed within each step -->



 	</reaction>

</document>

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 ChiMeraL site.1 (comments on syntax are in green)

<?xml version="1.0"?>

<Schema name="cml_dev_karne" 

	xmlns="urn:schemas-microsoft-com:xml-data" 

	xmlns:dt="urn:schemas-microsoft-com:datatypes">

<description>

CML development - Version 0.2 - 7/4/00



This document is the first draft of an XML Schema compatible with CML

V1.0 published in JCICS... In converting the schema we have suggested

some closed and some open content models. As CML develops it seems likely

that there will be advantage in opening some of the models (e.g. angle),

perhaps for annotations and ancillary information. Readers should note

that the XML Schema activity is still at draft stage and that this schema

may be revised in the future for compatibility. 



This schema is intended for use with IE5 - a platform independent version

is available. XML documents can be validated against this schema by adding

xmlns="x-schema:URL" within the cml element. 



Please see cml_schema_ie_02.html for further comments and explanations.



Peter Murray Rust, Henry Rzepa, Michael Wright



Comments to Michael Wright - karne@innocent.com

</description>



<!-- ********** Attribute Types ********** -->

<!-- *** common *** -->



<!-- It is expected that these attributes will be found on almost all elements. 

@title is used for display and general labelling and @id indicates a document 

unique identity string for that element. This identity can then be used to 

reference that element (and hence the object it represents) by the use of 

@href. Care must be taken that @id is unique. The use (for example) of 

<atom id="1"> will cause trouble in a document with more 

than one molecule and should be avoided. Note that @title on data elements 

(string/integer/float) can be used to markup data for which there is no 

explicit CML element (e.g. <string title="CAS">58-08-2</string>) 

and @convention should be declared if this is not obvious. @builtin implies 

an element with a meaning predefined in the DTD -->



<AttributeType name="title" required="no"/>

<AttributeType name="id" required="no" dt:type="id"/>			

<AttributeType name="convention" required="no"/>

<AttributeType name="builtin" required="no" dt:type="enumeration"

	dt:values="x2 y2 xy2 x3 y3 z3 xyz3 xFract yFract zFract xyzFract elementType

		atomId isotope occupancy hydrogenCount atomParity residueType residueId 

		formalCharge atomRef atomRefs length order stereo acell bcell ccell alpha 

		beta gamma z spacegroup" />





<!-- *** linkers *** -->



<!-- Designed to allow the linking of an element to another via @id. For example 

<link href="mol_543"> indicates a link to any element with @id="mol_543".

@unitsRef and @dictRef are intended for future use -->



<AttributeType name="href" required="no" dt:type="idrefs"/>

<AttributeType name="dictRef" required="no" dt:type="idrefs"/>

<AttributeType name="unitsRef" required="no" dt:type="idrefs"/>

<AttributeType name="atomRef" required="no" dt:type="idref"/>

<AttributeType name="atomRefs" required="no" dt:type="idrefs"/>



<!-- *** quantifiers/constraints *** -->



<!-- Various constraints on the values of data elements, only 'units' is in common use -->



<AttributeType name="count" required="no"/>

<AttributeType name="size" required="no"/>

<AttributeType name="rows" required="no"/>

<AttributeType name="columns" required="no"/>

<AttributeType name="min" required="no"/>

<AttributeType name="max" required="no"/>

<AttributeType name="units" required="no"/>



<!-- ********** Element Types ************ -->

<!-- *** data  *** -->



<!-- These elements are intended to contain only text string and attributes - they may 

not contain other elements - and are hence 'closed' (no additional markup can be 

added beyond the schema). If additional data holders are required, they should be of 

the form <string title="CAS">58-08-2</string> 

where the title value is used to identify the elements contents. For full list of 

attributes, please see the schema -->



<ElementType name="string" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="float" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="integer" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<!-- The arrays should be used only when large amounts of data need 

to be stored. In all cases explicit markup of each unit of data is preferred since this 

is much easier to manipulate with a stylesheet. In some cases this may not be possible 

(e.g. large molecules with 200+ atoms) and arrays can be used. These would probably need 

to be parsed by dedicated chemical tools. floatMatrix is intended for computational 

chemistry -->



<ElementType name="stringArray" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="size"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="floatArray" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="size"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="integerArray" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="size"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="floatMatrix" content="textOnly" model="closed">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="rows"/>

	<attribute type="columns"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<!-- Coordinates consist of 2 or 3 comma separated numbers. They should 

be used for logically linked number groups - e.g. a data point in a spectrum -->



<ElementType name="coordinate2" content="textOnly" model="closed">

	<!-- use for data pairs (e.g spectra xy) -->

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="coordinate3" content="textOnly" model="closed">

	<!-- use for data triplets (e.g spectra x, y, m) -->			

	<attribute type="id"/>

	<attribute type="builtin"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="units"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<!-- Angle and torsion haven't yet been developed, hence they have been left open -->



<ElementType name="angle" content="textOnly" model="open">		

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="atomRefs"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units" default="deg"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="torsion" content="textOnly" model="open">		

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="atomRefs"/>

	<attribute type="min"/>

	<attribute type="max"/>

	<attribute type="units" default="deg"/>

	<attribute type="unitsRef"/>

	<attribute type="dictRef"/>

</ElementType>



<!-- *** mixed *** -->



<!-- Link is used as a 'holder' element - e.g. for 'href' or 'unitsRef' 

and indicates a logical link to another CML object -->



<ElementType name="link" content="mixed" model="open">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="href"/>

</ElementType>	



<ElementType name="formula" content="mixed" model="open">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="count"/>

	<attribute type="dictRef"/>

</ElementType>

	

<!-- *** structural *** -->	



<!-- These elements define the tree structure of the CML document and are not expected to 

contain text strings - only other elements. Since they are 'open', additional sub elements 

- whether CML or not - can be added with correct namespacing. Attributes and elements 

for these elements have been declared in the schema but these are only suggestions - 

the DTD allows anything. Many, like electron and the crystalagraphic markup have yet 

to be developed -->



<ElementType name="atom" content="eltOnly" model="open" order="many">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention" default="mol"/>

	<attribute type="count"/>

	<attribute type="dictRef"/>

	<element type="float" minOccurs="0" maxOccurs="*"/>

	<element type="string" minOccurs="0" maxOccurs="*"/>

	<element type="integer" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="bond" content="eltOnly" model="open" order="many">

	<attribute type="id"/>

	<attribute type="convention" default="mol"/>

	<attribute type="atomRef"/>

	<attribute type="atomRefs"/>

	<!-- avoid using these and use a subelement with builtin="atomRef" -->

	<element type="integer" minOccurs="0" maxOccurs="*"/>

	<element type="float" minOccurs="0" maxOccurs="*"/>

	<element type="string" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

	<element type="angle" minOccurs="0" maxOccurs="*"/>

	<element type="torsion" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="list" content="eltOnly" model="open" order="many">

	<attribute type="id"/>

	<attribute type="title"/>

	<!-- required: atoms/bonds/xypairs/peak table/atom map-->

	<attribute type="convention"/>

	<!-- should be included for spectra: (XY..XY), (XYM) -->

	<element type="string" minOccurs="0" maxOccurs="*"/>

	<element type="integer" minOccurs="0" maxOccurs="*"/>

	<element type="float" minOccurs="0" maxOccurs="*"/>

	<element type="floatArray" minOccurs="0" maxOccurs="*"/>

	<element type="stringArray" minOccurs="0" maxOccurs="*"/>

	<element type="integerArray" minOccurs="0" maxOccurs="*"/>

	<element type="floatMatrix" minOccurs="0" maxOccurs="*"/>

	<element type="angle" minOccurs="0" maxOccurs="*"/>

	<element type="torsion" minOccurs="0" maxOccurs="*"/>

	<element type="coordinate2" minOccurs="0" maxOccurs="*"/>

	<element type="coordinate3" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

	<element type="formula" minOccurs="0" maxOccurs="*"/>

	<element type="atom" minOccurs="0" maxOccurs="*"/>

	<element type="bond" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="atomArray" content="eltOnly" model="open" order="many">

	<!-- only use for large molecules -->

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

	<element type="stringArray" minOccurs="0" maxOccurs="*"/>

	<element type="floatArray" minOccurs="0" maxOccurs="*"/>

	<element type="integerArray" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="bondArray" content="eltOnly" model="open" order="many">

	<!-- only use for large molecules -->

	<attribute type="id"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

	<element type="stringArray" minOccurs="0" maxOccurs="*"/>

	<element type="floatArray" minOccurs="0" maxOccurs="*"/>

	<element type="integerArray" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="electron" content="eltOnly" model="open">

	<attribute type="id"/>

	<attribute type="count"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="crystal" content="eltOnly" model="open">

	<attribute type="id"/>

	<attribute type="title" default="crystal"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="sequence" content="eltOnly" model="open">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="feature" content="eltOnly" model="open">

	<attribute type="id"/>

	<attribute type="title"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

</ElementType>



<ElementType name="molecule" content="eltOnly" model="open" order="many">

	<attribute type="id"/>

	<attribute type="title" default="molecule"/>

	<attribute type="convention" default="mol"/>

	<attribute type="dictRef"/>

	<element type="formula" minOccurs="0" maxOccurs="*"/>

	<element type="list" minOccurs="0" maxOccurs="*"/>

	<element type="atomArray" minOccurs="0" maxOccurs="*"/>

	<element type="bondArray" minOccurs="0" maxOccurs="*"/>

	<element type="string" minOccurs="0" maxOccurs="*"/>

	<element type="float" minOccurs="0" maxOccurs="*"/>

	<element type="integer" minOccurs="0" maxOccurs="*"/>

	<element type="link" minOccurs="0" maxOccurs="*"/>

</ElementType>



<ElementType name="reaction" content="eltOnly" model="open" order="many">

	<attribute type="id"/>

	<attribute type="title" default="reaction"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

	<element type="string" minOccurs="0" maxOccurs="*"/>

	<element type="float" minOccurs="0" maxOccurs="*"/>

	<element type="integer" minOccurs="0" maxOccurs="*"/>

	<element type="list" minOccurs="0" maxOccurs="*"/>

</ElementType>



<!-- **********  root ********** -->



<!--This is the general 'holder' for all CML documents. Normally this 

would then be embedded within an XML <document> Namespaces/schema 

should be declared within this element or the document root-->



<ElementType name="cml" content="mixed" model="open" order="many">

	<attribute type="id"/>

	<attribute type="title" default="cml document"/>

	<attribute type="convention"/>

	<attribute type="dictRef"/>

	<element type="molecule" minOccurs="0" maxOccurs="*"/>

	<element type="crystal" minOccurs="0" maxOccurs="*"/>

	<element type="reaction" minOccurs="0" maxOccurs="*"/>

</ElementType>

</Schema>

This is a copy of the DTD for CML 1.0 published in JCICS by Peter Murray-Rust and Henry S. Rzepa 2

<!-- Appendix A - CML DTD-1999-05-15 -->

<!-- Authors:

	P.Murray-Rust

	H.Rzepa

This DTD is fully described in Journal of Chemical Information

	and Computer Science, Vol xxx, 1999, pp. xxx

-->



<!-- =======================================================-->

<!-- PARAMETER ENTITIES                                     -->

<!-- =======================================================-->



<!-- ======attributes found on almost all elements ==========-->



<!ENTITY %	title		'title	CDATA		#IMPLIED'>

<!ENTITY %	id		'id		CDATA		#IMPLIED'>

<!ENTITY %	convention	'convention	CDATA		"CML"'>

<!ENTITY %	dictRef	'dictRef	CDATA		#IMPLIED'>



<!-- ======linking information ==============================-->



<!ENTITY %	simpleLink	'href		CDATA		#REQUIRED'>



<!-- ======quantifiers and constraints on some primitives ===-->



<!ENTITY %	count		'count	CDATA		"1"'>

<!ENTITY %	size		'size		CDATA		#IMPLIED'>

<!ENTITY %	rows		'rows		CDATA		#REQUIRED'>

<!ENTITY %	columns	'columns	CDATA		#REQUIRED'>



<!-- ======constraints on some numeric data primitives    ===-->



<!ENTITY %	min		'min		CDATA		#IMPLIED'>

<!ENTITY %	max		'max		CDATA		#IMPLIED'>

<!ENTITY %	units		'units	CDATA		#IMPLIED'>

<!ENTITY %	angleUnits	'units	(degrees | radians) "degrees"'>

<!ENTITY %	unitsRef	'unitsRef	CDATA		#IMPLIED'>



<!--  values which may be useful in min and max attributes  -->

<!ENTITY %	integer.zero		'0'>

<!ENTITY %	integer.max			'2147483647'>

<!ENTITY %	integer.min			'-2147483648'>

<!ENTITY %	float.zero			'0.0'>

<!ENTITY %	float.max			'8.98846567431158E307'>

<!ENTITY %	float.min			'4.9E-324'>



<!-- ======= builtin values for any element ================-->

<!ENTITY % 	builtinId		'id'>



<!-- ======= builtin values for atoms ======================-->

<!ENTITY % 	elementType	'elementType'>

<!ENTITY % 	atomId 	'atomId'>



<!ENTITY % 	x2	 	'x2'>

<!ENTITY % 	y2		'y2'>

<!ENTITY % 	x3		'x3'>

<!ENTITY % 	y3		'y3'>

<!ENTITY % 	z3		'z3'>

<!ENTITY % 	xy2		'xy2'>

<!ENTITY % 	xyz3		'xyz3'>

<!ENTITY % 	xFract	'xFract'>

<!ENTITY % 	yFract	'yFract'>

<!ENTITY % 	zFract	'zFract'>

<!ENTITY % 	xyzFract	'xyzFract'>

<!ENTITY % 	occupancy	'occupancy'>

<!ENTITY % 	isotope	'isotope'>

<!ENTITY % 	formalCharge	'formalCharge'>

<!ENTITY % 	nonHydrogenCount	'nonHydrogenCount'>

<!ENTITY % 	hydrogenCount	'hydrogenCount'>

<!ENTITY % 	atomParity	'atomParity'>



<!ENTITY % 	residueType	'residueType'>

<!ENTITY % 	residueId 	'residueId'>



<!ENTITY % 	atomStringBuiltin	'

				%elementType; | %atomId; |

				%residueType; | %residueId;

				'				

>

<!ENTITY % 	atomFloatBuiltin	'

				%x2; | %y2; |

				%x3; | %y3; |  %z3; | 

				%xFract; | %yFract; |  %zFract; | 

				%occupancy; | %isotope; | 

				%formalCharge; | %hydrogenCount; | %nonHydrogenCount; |

				%atomParity;

				'				

>

<!ENTITY % 	atomIntegerBuiltin	'

				%isotope; | 

				%formalCharge; | %hydrogenCount; | %nonHydrogenCount; |

				%atomParity;

				'				

>

<!ENTITY % 	atomCoordinate2Builtin	'

				%xy2; 

				'				

>

<!ENTITY % 	atomCoordinate3Builtin	'

				%xyz3; | %xyzFract;

				'				

>

<!-- ======= builtin values for bonds ======================-->

<!ENTITY % 	atomRef	 	'atomRef'>

<!ENTITY % 	builtinAtomRefs	'atomRefs'>

<!ENTITY % 	length	 	'length'>

<!ENTITY % 	order			'order'>

<!ENTITY % 	stereo		'stereo'>

<!ENTITY % 	atomRefs		'atomRefs	CDATA	#IMPLIED'>



<!ENTITY % 	bondStringBuiltin	'

				%atomRef; | %builtinAtomRefs; |

				%order; | 

				%stereo;

				'				

>

<!ENTITY % 	bondFloatBuiltin	'

				%length;

				'				

>

<!ENTITY % 	bondIntegerBuiltin	''				

>

<!-- ======= builtin values for crystal ====================-->



<!ENTITY % 	acell	 		'acell'>

<!ENTITY % 	bcell	 		'bcell'>

<!ENTITY % 	ccell	 		'ccell'>

<!ENTITY % 	alpha	 		'alpha'>

<!ENTITY % 	beta	 		'beta'>

<!ENTITY % 	gamma	 		'gamma'>

<!ENTITY % 	z	 		'z'>

<!ENTITY % 	spacegroup	 	'spacegroup'>



<!ENTITY % 	crystalStringBuiltin	'

				%spacegroup;

				'

>

<!ENTITY % 	crystalFloatBuiltin	'

				%acell; | %bcell; | %ccell; |	%alpha; | %beta; | %gamma; | %z;

				'				

>

<!ENTITY % 	crystalIntegerBuiltin	'				

				%z;

				'				

>

<!-- =======================================================-->

<!ENTITY %	stringBuiltin	'

				builtin (

				%builtinId; |

				%atomStringBuiltin; |

				%bondStringBuiltin; |

				%crystalStringBuiltin; 

				)	#IMPLIED	'

>				

<!ENTITY %	floatBuiltin	'

				builtin (

				%atomFloatBuiltin; |

				%bondFloatBuiltin; |

				%crystalFloatBuiltin; 

				)	#IMPLIED	'

>				

<!ENTITY %	integerBuiltin	'

				builtin (

				%atomIntegerBuiltin; |

				%crystalIntegerBuiltin; 

				)	#IMPLIED	'

>				

<!ENTITY %	coordinate2Builtin	'

				builtin (

				%atomCoordinate2Builtin;

				)	#IMPLIED	'

>				

<!ENTITY %	coordinate3Builtin	'

				builtin (

				%atomCoordinate3Builtin;

				)	#IMPLIED	'

>				



<!-- =======================================================-->

<!-- ELEMENTS for widely used data primitives               -->

<!-- =======================================================-->



<!ELEMENT	string		(#PCDATA)>

<!ATTLIST	string

			%title;

			%id;

			%stringBuiltin;

			%dictRef;

			%convention; 

>

<!ELEMENT	link			(#PCDATA)>

<!ATTLIST	link

			%title;

			%id;

			%simpleLink; 

			%convention; 

>

<!ELEMENT	float			(#PCDATA)>

<!ATTLIST	float

			%title;

			%id;

			%floatBuiltin;

			%min;

			%max;

			%units;

			%unitsRef;

			%dictRef;

			%convention; 

>

<!ELEMENT	integer		(#PCDATA)>

<!ATTLIST	integer

			%title;

			%id;

			%integerBuiltin;

 			%min;

			%max;

			%units;

			%unitsRef;

			%dictRef;

			%convention; 

>

<!ELEMENT	stringArray		(#PCDATA)>

<!ATTLIST	stringArray

			%title;

			%id;

			%stringBuiltin;

			%size;

			%min;

			%max;

			delimiter	CDATA		#IMPLIED

			%dictRef;

			%convention; 

>

<!ELEMENT	floatArray		(#PCDATA)>

<!ATTLIST	floatArray

			%title;

			%id;

			%floatBuiltin;

			%size;

			%min;

			%max;

			%units;

			%unitsRef;

			%dictRef;

			%convention; 

>

<!ELEMENT	integerArray	(#PCDATA)>

<!ATTLIST	integerArray

			%title;

			%id;

			%integerBuiltin;

			%size;

			%min;

			%max;

			%units;

			%unitsRef;

			%dictRef;

			%convention; 

>

<!ELEMENT	floatMatrix		(#PCDATA)>

<!ATTLIST	floatMatrix

			%title;

			%id;

			%rows;

			%columns;

			%min;

			%max;

			%units;

			%unitsRef;

			%dictRef;

			%convention; 

>



<!ELEMENT	coordinate2		(#PCDATA)>

<!ATTLIST	coordinate2

			%title;

			%id;

			%coordinate2Builtin;

			%unitsRef;

			%dictRef;

			%convention; 

>



<!ELEMENT	coordinate3		(#PCDATA)>

<!ATTLIST	coordinate3

			%title;

			%id;

			%coordinate3Builtin;

			%unitsRef;

			%dictRef;

			%convention; 

>

<!ELEMENT	angle			(#PCDATA)>

<!ATTLIST	angle

			%title;

			%id;

			%atomRefs;

			%angleUnits;

			%min;

			%max;

			%dictRef;

			%convention; 

>



<!ELEMENT	torsion		(#PCDATA)>

<!ATTLIST	torsion

			%title;

			%id;

			%atomRefs;

			%angleUnits;

			%min;

			%max;

			%dictRef;

			%convention; 

>



<!ELEMENT	list			ANY>

<!ATTLIST	list

			%title;

			%id;

>



<!-- =======================================================-->

<!-- ELEMENTS for chemical and crystallographic concepts    -->

<!-- =======================================================-->

<!-- NOTE

	for elements which have element-specific values for the

	builtin attribute, those values are already listed as 

	entities

--> 

<!-- =======================================================-->



<!ELEMENT	molecule		ANY>

<!ATTLIST	molecule

			%title;

			%id;

			%count;

			%dictRef;

			%dictRef;

			%convention; 

>



<!-- ========================================================-->

<!ELEMENT	formula		ANY>

<!ATTLIST	formula

			%title;

			%id;

			%count; 

			%dictRef;

			%convention; 

>



<!-- ========================================================-->

<!ELEMENT	atom			ANY>

<!ATTLIST	atom 

			%title;

			%id;

			%count; 

			%dictRef;

			%convention; 

>



<!-- .......................................................-->

<!ELEMENT	atomArray		ANY>

<!ATTLIST	atomArray

			%title;

			%id;

			%dictRef;

			%convention; 

>



<!-- ========================================================-->

<!ELEMENT	bond			ANY>

<!ATTLIST	bond

			%id;

			%atomRefs;

			%dictRef;

			%convention; 

>



<!-- ========================================================-->

<!ELEMENT	bondArray		ANY>

<!ATTLIST	bondArray

			%id;

			%dictRef;

			%convention; 

>

<!-- ========================================================-->

<!ELEMENT	electron		ANY>

<!ATTLIST	electron

			%id;

			%count;

			%dictRef; 

			%convention; 

>

<!-- ========================================================-->

<!ELEMENT	reaction		ANY>

<!ATTLIST	reaction

			%id;

			%dictRef; 

			%convention; 

>

<!-- ======================================================= -->

<!ELEMENT	crystal		ANY>

<!ATTLIST	crystal

			%title;

			%id;

			%dictRef; 

			%convention; 

>

<!-- ======================================================= -->

<!ELEMENT	sequence		ANY>

<!ATTLIST	sequence

			%title;

			%id;

			%dictRef;

			%convention; 

>



<!-- ======================================================= -->

<!ELEMENT	feature		ANY>

<!ATTLIST	feature

			%title;

			%id;

			%dictRef;

			%convention; 

>

1. Demonstrations, examples and further information can be found in the ChiMeraL website, (http://www.ch.ic.ac.uk/chimeral/)
2. For a formal description of CML version 1.0, see P. Murray-Rust and H. S. Rzepa, J. Chem. Inf. Comp. Sci., 1999, 39, 928 (http://www.xml-cml.org/)
3. H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Chem. Soc. Revs., 1997, 1
4. W3C - XHTML and HTML development, (http://www.w3.org/MarkUp/)
5. W3C - Scalable Vector Graphics (SVG) overview, (http://www.w3.org/Graphics/SVG/Overview.htm8)
6. Adobe SVG browser plugin, (http://www.adobe.com/svg/viewer/install/)
7. Apache.com - FOP project (XML convertion to Adobe Acrobat), (http://xml.apache.org/fop/)
8. W3C - XML Schema development, (http://www.w3.org/XML/Schema.html)
9. Microsoft - XML Schema Developer's Guide, (http://msdn.microsoft.com/library/default.asp?URL=/library/psdk/xmlsdk/xmlp7k6d.htm)
10. H. S. Rzepa, B. J. Whitaker and M. J. Winter, J. Chem. Soc., Chem. Commun., 1994, 1907 (http://www.ch.ic.ac.uk/rzepa/RSC/CC/4_02963A.html)
11. O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust, R. Sayle, H. S. Rzepa and B. J. Whitaker, J. Chem. Soc., Perkin Trans 2, 1995, 7 (http://www.ch.ic.ac.uk/rzepa/RSC/P2/4_05970K.html)
12. P. Murray-Rust, C. Leach and H. S. Rzepa, Abs. Papers. Am . Chem. Soc., 1995, 210, 40-COMP
13. MDL information systems, (http://www.mdli.com/cgi/dynamic/welcome.html)
14. Rasmol and Chime - Molecular Visualization Freeware, (http://www.umass.edu/microbio/rasmol/)
15. Brookhaven Protein Data Bank, (http://www.rcsb.org/pdb/)
16. Universal approach to Web-based Chemistry using XML and CML by Peter Murray-Rust, Henry S. Rzepa, Michael Wright and Stephen Zara (awaiting pulication), (http://www.ch.ic.ac.uk/chimeral/publications/Chemcom.html)
17. W3C - XML recommendation, (http://www.w3.org/TR/REC-xml)
18. W3C - Annotated XML specification, (http://www.xml.com/axml/axml.html)
19. W3C - Mathematical Markup Language development, (http://www.w3.org/Math/)
20. XML-CML homesite, (http://www.xml-cml.org/)
21. W3C - XML Namespaces recommendation, (http://www.w3.org/TR/REC-xml-names/)
22. Adobe Acrobat, (http://www.adobe.com/products/acrobat/main.html)
23. W3C - Cascading Stylesheets, (http://www.w3.org/Style/CSS/)
24. W3C - Extensible Stylesheet Language (XSL) development, (http://www.w3.org/Style/XSL/)
25. Microsoft - XML/XSL development, (http://msdn.microsoft.com/xml/default.asp)
26. IBM alphaworks - XML/Java development site, (http://www.alphaworks.ibm.com/)
27. Sun - Java Technology Homepage, (http://java.sun.com/)
28. W3C - Document Object Model (DOM) Level 1 Specification, (http://www.w3.org/TR/REC-DOM-Level-1/)
29. WWW-based Chemical Information System, (http://www.elsevier.com/homepage/saa/eccc3/paper6/)
30. ChemFinder.com, (http://chemfinder.camsoft.com/)
31. Jmol - Open source Java 3D viewer, (http://www.openscience.org/jmol/)
32. The Open Science Project, (http://www.openscience.org/links/Chemistry/)
33. Marvin display and editing applet - Chemaxon, (http://www.chemaxon.com/marvin/)
34. ACD Labs - Structure Drawing Applet, (http://www.acdlabs.com/products/java/sda/)
35. NIST Webbook, (http://webbook.nist.gov/)
36. SPC - Spectroscopy Software Solutions, (http://www.galactic.com/)
37. A. N. Davies and P. Lampen, App. Spec., 1993, 47, 1093-1099 (http://www.isas-dortmund.de/projects/jcamp/protocol.html)
38. P. Lampen, H. Hillig, A. N. Davis and M. Linscheid, App. Spec., 1994, 48, 1545-1552 (http://www.isas-dortmund.de/projects/jcamp/protocol.html)
39. J. Gasteiger, B. M. P. Hendriks, P. Hoever, C. Jochum and H. Somberg, App. Spec., 1991, 45, 4-11 (http://www.isas-dortmund.de/projects/jcamp/protocol.html)
40. jspec: A Java Spectral Visualiser for JCAMP-DX and SPC Format Files, (http://www.ch.ic.ac.uk/java/applets/jspec/spectra/)
41. Corel Draw 9 SVG plugin, (http://venus.corel.com/nasapps/DrawSVGDownload/index.html)
42. Mayura Draw - editor able to export SVG, (http://www.mayura.com/)
43. Csiro SVG Toolkit, (http://sis.cmis.csiro.au/svg/index.html)
44. W3C - XLink specifications, (http://www.w3.org/TR/WD-xlink)
45. W3C - XPointer specifications, (http://www.w3.org/TR/WD-xptr)
46. Perl.com Homesite, (http://www.perl.com/pub)
47. Gaussian 98, (http://www.gaussian.com/product.htm)
48. Open source Java 2D editor, (http://www.ice.mpg.de/~stein/projects/JChemPaint/)
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50. R. S. McDonald and P. A. Wilks Jr., App. Spec., 1988, 42, 151-162 (http://www.isas-dortmund.de/projects/jcamp/protocol.html)
51. Netscape XML, (http://developer.netscape.com/tech/xml/index.html)
52. Adobe Illustrator, (http://www.adobe.com/svg/main.html)
53. A. Homer, XML IE5 - Programmer's Reference, Wrox Press, 1999,
54. H. Dietel, P. Deitel, T. Lin and T. Neito, XML How to Program, Prentice Hall, 2000,
55. H. Dietel, P. Deitel, T. Lin and T. Neito, The Complete XML Training Course, Student Edition, Prentice Hall, 2000,