<stmml xmlns="http://www.xml-cml.org/schema/stmml">



<actionList 

 xmlns="http://www.xml-cml.org/schema/stmml"

  title="boiling two eggs for breakfast">

  <!-- start cooking at 9am -->

  <action title="turn on heat" start="T09:00:00" convention="xsd"/>

  <!-- human readable description of time to start action -->

  <action title="put egg into pan" startCondition="water is boiling" count="2"/>

  <!-- the duration is expressed in ISO8601 format -->

  <action title="boil eggs for 4 minutes" duration="04:00"/>

  <!-- action immediately follows last action -->

  <action title="remove egg from pan" count="1"/>

  <action title="boil second egg for a bit longer" duration="about half a minute"/>

  <!-- action immediately follows last action -->

  <action title="remove egg from pan" count="1"/>

</actionList>

<actionList title="preparation of silanols">

  <p>This is a conversion of a chemical synthesis to STMML. We

  have deliberately not marked up the chemistry in this example!</p>

  <action title="step2">

    <p>Take 1 mmol of the diol and dissolve in dioxan in 

      <object title="flask">

        <scalar title="volume" units="units:ml">25</scalar>

      </object>

    </p>

  </action>

  <action title="step2">

    <p>Place flask in water bath with magnetic stirrer</p>

  </action>

  <!-- wait until certain condition -->

  <actionList endCondition="bath temperature stabilised"/>

  <action title="step3">

    <p>Add 0.5 ml 1 M H2SO4</p>

  </action>



  <!-- carry out reaction -->

  <actionList endCondition="reaction complete; no diol spot remains on TLC">

    <actionList title="check tlc">

      <!-- wait for half an hour -->

      <action duration="half an hour"/>

      <action title="tlc">

        <p>extract solution and check diol spot on TLC</p>

      </action>

    </actionList>

  </actionList>

  

  <!-- work up reaction -->

  <action title="step5">

    <p>Add 10 ml water to flask</p>

  </action>

  <action title="step6">

    <p>Neutralize acid with 10% NaHCO3</p>

  </action>

  <action title="step7" count="3">

    <p>Extract with 10ml ether</p>

  </action>

  <action title="step8">

    <p>Combine ether layers</p>

  </action>

  <action title="step9" count="2">

    <p>Wash ether with 10 ml water</p>

  </action>

  <action title="step10">

    <p>Wash ether with 10 ml saturated NaCl</p>

  </action>

  <action title="step11">

    <p>Dry over anhydrous Na2SO4 and remove solvent on rotary evaporator</p>

  </action>

</actionList>

<!-- demonstrating parallel and sequential actions -->

<actionList order="parallel" endCondition="all food cooked">

  <!-- meat and potatoes are cooked in parallel -->

  <actionList title="meat">

    <action title="cook" endCondition="cooked">

      <p>Roast meat</p>

    </action>

    <action><p>Keep warm in oven</p></action>

  </actionList>

  <actionList title="vegetables">

    <actionList title="cookVeg" endCondition="cooked">

      <action title="boil water" endCondition="water boiling">

        <p>Heat water</p>

      </action>

      <action title="cook" endCondition="potatoes cooked">

        <p>Cook potatoes</p>

      </action>

    </actionList>

    <action><p>Keep warm in oven</p></action>

  </actionList>

</actionList>

<!-- contains all elements in STMML in correct contexts, but not all attributes -->

<!-- useful for testing SAX-like parsers -->

<stmml xmlns="http://www.xml-cml.org/schema/stmml">



  <array dataType="xsd:string">A B C</array>

  <scalar></scalar>

  <matrix rows="3" columns="4" dataType="xsd:float">1 0 0 0  0 1 0 0.5  0 0 -1 0.5</matrix>

  <table rows="3" columns="2">

<!--

    <array dataType="xsd:float" title="foo">1 2 3</array>

    <array dataType="xsd:string" title="bar">A B C</array>

-->

    <array dataType="xsd:float">1 2 3</array>

    <array dataType="xsd:string">A B C</array>

  </table>

  <list></list>



  <link></link>



<!-- ==================== GENERAL COMPONENTS =========== -->



  <actionList>

    <action type="the type" title="the title"></action>

  </actionList>

  <object></object>

  <observation></observation>



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



  <dictionary>

    <unitList>

      <unitType id="ut" name="energy">

        <dimension name="length" power="1"></dimension>

      </unitType>

<!-- WHY NOT????????????????

      <unit id="uu1" multiplierToSi="10.0" constantToSi="0.0"></unit>

-->

    </unitList>

    <annotation>

      <documentation></documentation>

      <appinfo></appinfo>

    </annotation>

    <entry term="xyzzy">

      <definition></definition>

      <alternative></alternative>

      <description></description>

      <enumeration></enumeration>

      <relatedEntry></relatedEntry>

    </entry>

  </dictionary>

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



  <metadataList>

    <metadata></metadata>

  </metadataList>



<!-- =================  SCIENTIFIC UNITS ================== -->





</stmml>





 <entry term="ammonia" id="a1">

   <alternative type="synonym">Spirits of hartshorn</alternative>

   <alternative type="my:formula">NH3</alternative>

 </entry>

   <entry term="1,2-dichloroethane" id="dce">

     <alternative type="synonym">ethylene dichloride</alternative>

     <alternative type="abbreviation">DCE</alternative>

     <alternative type="quasi-synonym">dichloroethane</alternative>

   </entry>

<entry term="matrix" xmlns="http://www.xml-cml.org/schema/stmml">

  <annotation>

    <documentation><!--This refers to mathematical matrices-->></documentation>

    <appinfo><!-- ...some code to describe and support matrices ... --></appinfo>

  </annotation>

</entry>

<s:appinfo 

  xmlns:s="http://www.xml-cml.org/schema/cml2/core"

  xmlns="http://www.w3.org/1999/XSL/Transform">

  <template match="foo">

    <call-template name="processFoo"/>

  </template>

</s:appinfo>

<array size="5" title="value" 

  dataType="xsd:decimal">  1.23 2.34 3.45 4.56 5.67</array>

<array size="5" title="initials" dataType="xsd:string" 

  delimiter="/">/A B//C/D-E/F/</array>

<array title="mass" size="4"

  units="unit:g"

  errorBasis="observedStandardDeviation"

  minValues="10 11 10 9"

  maxValues="12 14 12 11"

  errorValues="1 2 1 1"

  dataType="xsd:float">11 12.5 10.9 10.2

</array><bond convention="fooChem" order="-5"

   xmlns:fooChem="http://www.fooChem/conventions"/>



<list>

  <array dataType="xsd:decimal"

      >1.2,3.4   3.2,4.5   6.7,23.1 </array>

  <array delimiter="/" dataType="xsd:decimal"

      >/1.2 3.4/3.2 4.5/6.7 23.1/</array>

</list><list>

  <array dataType="xsd:decimal">1.2,3.4,1.2   

    3.2,4.5,7.3   6.7,23.1,5.6 </array>

  <array delimiter="/" dataType="xsd:decimal"

  >/1.2 3.4 3.3/3.2 4.5 4.5/6.7 23.1 5.6/</array>

</list>

<cml:atomArray 

  xmlns:cml="http://www.xml-cml.org/schema/cml2/core"

  x2="1.2 2.3 4.5 6.7"/>

  <list>

<object title="frog" count="10"/>

<action title="step3" count="3">

  <p>Add 10 ml reagent</p>

</action>

</list><list xmlns="http://www.xml-cml.org/schema/cml2/core">

  <scalar dataType="xsd:boolean" title="she loves me">true</scalar>

  <scalar dataType="xsd:float" title="x">23.2</scalar>

  <scalar dataType="xsd:duration" title="egg timer">PM4</scalar>

  <scalar dataType="xsd:dateTime" title="current data and time">2001-02-01:00:30</scalar>

  <scalar dataType="xsd:time" title="wake up">06:00</scalar>

  <scalar dataType="xsd:date" title="where is it">1752-09-10</scalar>

  <scalar dataType="xsd:anyURI" title="CML site">http://www.xml-cml.org/</scalar>

  <scalar dataType="xsd:QName" title="CML atom">cml:atom</scalar>

  <scalar dataType="xsd:normalizedString" title="song">the mouse ran up the clock</scalar>

  <scalar dataType="xsd:language" title="UK English">en-GB</scalar>

  <scalar dataType="xsd:Name" title="atom">atom</scalar>

  <scalar dataType="xsd:ID" title="XML ID">_123</scalar>

  <scalar dataType="xsd:integer" title="the answer">42</scalar>

  <scalar dataType="xsd:nonPositiveInteger" title="zero">0</scalar>

</list><entry id="a7" term="Allosteric enzyme">

  <definition>An <a href="#e3">enzyme</a>

that contains a region to which small, regulatory molecules

("effectors") may bind in addition to and separate from the

substrate binding site and thereby affect the catalytic

activity.

  </definition>

  <description>On binding the effector, the catalytic activity of the

<strong>enzyme</strong> towards the substrate may be enhanced, in

which case the effector is an activator, or reduced, in which case

it is a de-activator or inhibitor.

  </description>

</entry>

<array size="4"  dataType="xsd:string" delimiter="|">|A|B12||D and   E|</array>

<entry id="e3" term="Enzyme">

  <definition>An <strong>enzyme</strong> is a macromolecule, usually a

protein, that functions as a (bio) catalyst by increasing the

reaction rate.

  </definition>

  <description>In general, an <strong>enzyme</strong> catalyzes only one

reaction type (reaction selectivity) and operates on only one type

of substrate (substrate selectivity). Substrate molecules are

transformed at the same site (regioselectivity) and only one or

preferentially one of chiral a substrate or of a racemate is

transformed (enantioselectivity[special form of

stereoselectivity]).

  </description>

  <description class="example">Alcohol Dehydrogenase (EC.1.1.1.1)</description>

</entry>

<stm:dictionary xmlns:stm="http://www.xml-cml.org/schema/stmml">

  <stm:entry id="a001" term="Amplitude for charge density mixing"

    dataType="stm:decimal"

    units="arbitrary">

    <stm:annotation>

      <stm:documentation>

        <div class="summary">Amplitude for charge density mixing</div>

        <div class="description">Not yet filled in...</div>

      </stm:documentation>

    </stm:annotation>

    <stm:alternative type="abbreviation">CDMixAmp</stm:alternative>

  </stm:entry>

</stm:dictionary>

<list>

  <dictionary

     dictRef="core" href="../dictionary/coreDict.xml"/>

</list>

<scalar dataType="xsd:float" title="surfaceArea" 

  dictRef="cmlPhys:surfArea" 

  xmlns:cmlPhys="http://www.xml-cml.org/dict/physical"

  units="units:cm2">50</scalar>

<stm:list xmlns:stm="http://www.xml-cml.org/schema/stmml">

  <stm:observation>

    <p>We observed <object count="3" dictRef="foo:p1"/> 

      constructing dwellings of different material</p>

  </stm:observation>

  <stm:entry id="p1" term="pig">

    <stm:definition>A domesticated animal.</stm:definition>

    <stm:description>Predators include wolves</stm:description>

    <stm:description class="scientificName">Sus scrofa</stm:description>

  </stm:entry>

</stm:list>

<unitType id="energy" name="energy">

  <dimension name="length" power="1"/>

  <dimension name="mass" power="1"/>

  <dimension name="time" power="-1"/>

</unitType>



<unitType id="energy" name="energy">

  <dimension name="length" power="2"/>

  <dimension name="mass" power="1"/>

  <dimension name="time" power="-2"/>

</unitType>

<stm:documentation id="source"

xmlns:stm="http://www.xml-cml.org/schema/stmml">

Transcribed from IUPAC website

</stm:documentation>

<entry id="a003" term="alpha"

  dataType="float"

  minInclusive="0.0"

  maxInclusive="180.0"

  recommendedUnits="degrees">

  <definition>The alpha cell angle</definition>

</entry>

<entry id="a003" 

  term="matrix1"

  dataType="float"

  rows="3"

  columns="4"

  unitType="unit:length"

  minInclusive="0.0"

  maxInclusive="100.0"

  recommendedUnits="unit:m"

  totalDigits="8"

  fractionDigits="3">

    <definition>A matrix of lengths</definition>

    <description>A data instance will have a matrix which points

  to this entry (e.g. dictRef="foo:matrix1"). The matrix must

  be 3*4, composed of floats in 8.3 format, of type length,

  values between 0 and 100 and with recommended units metres.

    </description>

</entry>

<entry term="crystal system" id="cryst1" dataType="string">

  <definition>A crystal system</definition>

  <enumeration value="triclinic">

    <annotation>

      <documentation>

        <div class="summary">No constraints on lengths and angles</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="monoclinic">

    <annotation>

      <documentation>

        <div class="summary">Two cell angles are right angles; no other constraints</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="orthorhombic">

    <annotation>

      <documentation>

        <div class="summary">All three angles are right angles; no other constraints</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="tetragonal">

    <annotation>

      <documentation>

        <div class="summary">Fourfold axis of symmetry; All three angles are right angles; two equal cell lengths; no other constraints</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="trigonal">

    <annotation>

      <documentation>

        <div class="summary">Threefold axis of symmetry; Two angles are right angles; one is 120 degrees; two equal lengths; no other constraints</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="hexagonal">

    <annotation>

      <documentation>

        <div class="summary">Sixfold axis of symmetry; Two angles are right angles; one is 120 degrees; two equal lengths; no other constraints</div>

      </documentation>

    </annotation>

  </enumeration>

  <enumeration value="cubic">

    <annotation>

      <documentation>

        <div class="summary">All three angles are right angles; all cell lengths are equal</div>

      </documentation>

    </annotation>

  </enumeration>

</entry>

<atomArray xmlns="http://www.xml-cml.org/schema/cml2/core"

  x2="1.2 2.3 3.4 5.6"/><array size="5" title="value" 

  dataType="xsd:decimal">  1.23 2.34 3.45 4.56 5.67</array>

<atomArray xmlns="http://www.xml-cml.org/schema/cml2/core"

  atomID="a1 o2 b33 n21"/><atomArray xmlns="http://www.xml-cml.org/schema/cml2/core"

  hydrogenCount="3 1 0 2"/><list>

  <object id="a">

    <object id="a1"/>

    <object id="a2"/>

    <object id="a3"/>

    <object id="a4"/>

  </object>

  <object id="b">

    <object id="b1"/>

    <object id="b2"/>

    <object id="b3"/>

  </object>

<!-- one2one link -->

  <link type="arc" role="mapping" from="a1" to="b1"/>

<!-- grouping -->

  <link type="extended" id="groupa">

    <link type="locator" ref="a1"/>

    <link type="locator" ref="a2"/>

    <link type="locator" ref="a3"/>

  </link>

<!-- grouping -->

  <link type="extended" id="groupb">

    <link type="locator" ref="b1"/>

    <link type="locator" ref="b2"/>

  </link>

<!-- many2many as a 1:1 between groups-->

  <link type="arc" role="mymapping" from="groupa" to="groupb"/>

</list><list>

  <array title="animals" dataType="xsd:string">frog bear toad</array>

  <scalar title="weight" dataType="xsd:float">3.456</scalar>

</list><matrix id="m1" title="mattrix-1" dictRef="foo:bar"

  rows="3" columns="3" dataType="xsd:decimal" 

  delimiter="|" matrixType="squareSymmetric" units="unit:m"

  >|1.1|1.2|1.3|1.2|2.2|2.3|1.3|2.3|3.3!</matrix>

<scalar dataType="xsd:float" max="20" min="12">15</scalar><list>

  <metadataList>

    <metadata name="dc:coverage" content="Europe"/>

    <metadata name="dc:description" content="Ornithological chemistry"/>

    <metadata name="dc:identifier"  content="ISBN:1234-5678"/>

    <metadata name="dc:format" content="printed"/>

    <metadata name="dc:relation" content="abc:def123"/>

    <metadata name="dc:rights" content="licence:GPL"/>

    <metadata name="dc:subject" content="Informatics"/>

    <metadata name="dc:title" content="birds"/>

    <metadata name="dc:type" content="bird books on chemistry"/>

    <metadata name="dc:contributor" content="Tux Penguin"/>

    <metadata name="dc:creator" content="author"/>

    <metadata name="dc:publisher" content="Penguinone publishing"/>

    <metadata name="dc:source" content="penguinPub"/>

    <metadata name="dc:language" content="en-GB"/>

    <metadata name="dc:date" content="1752-09-10"/>

  </metadataList>

  <metadataList>

    <metadata name="cmlm:safety" content="mostly harmless"/>

    <metadata name="cmlm:insilico" content="electronically produced"/>

    <metadata name="cmlm:structure" content="penguinone"/>

    <metadata name="cmlm:reaction" content="synthesis of penguinone"/>

    <metadata name="cmlm:identifier" content="smiles:O=C1C=C(C)C(C)(C)C(C)=C1"/>

  </metadataList>

</list>

<list>

<!-- dictRef is of namespaceRefType -->

  <scalar dictRef="chem:mpt">123</scalar>  

<!-- error -->

  <scalar dictRef="mpt23">123</scalar>  

</list><scalar dataType="nonNegativeAngleType">123</scalar>  

<object title="frog" type="amphibian" count="5">

  <scalar dataType="xsd:float" title="length" units="unit:cm">5</scalar>

  <obj1/>

</object><observation type="ornithology">

  <object title="sparrow" count="3"/>

  <observ/>

</observation><stm:entry id="a14" term="Autoreceptor" 

  xmlns:stm="http://www.xml-cml.org/schema/cml2/core">

  <stm:definition>An <strong>autoreceptor</strong>, present at a nerve ending, is

    a <a href="#r1">receptor</a>

    that regulates, via positive or negative feedback processes, the

    synthesis and/or release of its own physiological ligand. 

  </stm:definition>

  <stm:relatedEntry type="seeAlso" href="#h4">Heteroreceptor).</stm:relatedEntry>

  <stm:relatedEntry type="my:antonym" href="#h4">antiheteroreceptor).</stm:relatedEntry>

</stm:entry>

<scalar 

    dataType="xsd:decimal" 

    errorValue="1.0" 

    errorBasis="observedStandardDeviation" 

    title="body weight"

    dictRef="zoo:bodywt"

    units="units:g">34.3</scalar>

<list>

  <definition source="foo.html#a3">An animal with four legs</definition>  

  <definition source="http://www.foo.com/index.html">

    An animal with six legs</definition>

</list><stmml>

  <actionList>

    <action></action>

  </actionList>

  <object></object>

  <observation></observation>



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



  <dictionary>

    <annotation>

      <documentation></documentation>

      <appinfo></appinfo>

    </annotation>

    <entry term="foo">

      <definition></definition>

      <alternative></alternative>

      <description></description>

      <enumeration></enumeration>

      <relatedEntry></relatedEntry>

    </entry>

  </dictionary>



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



  <metadataList>

    <metadata></metadata>

  </metadataList>



<!-- =================  SCIENTIFIC UNITS ================== -->



  <unitList>

    <unitType id="ut1" name="u">

      <dimension name="mass" power="1"></dimension>

    </unitType>

    <unit id="u1"></unit>

  </unitList>



</stmml>





<atomArray xmlns="http://www.xml-cml.org/schema/cml2/core"

  title="atom1 n23 ligand"/><table rows="3" columns="2" title="people">

  <array title="age" dataType="xsd:integer">3 5 7</array>

  <array title="name" dataType="xsd:string">Sue Fred Sandy</array>

</table><action title="turn on heat" start="T09:00:00" convention="xsd"/>

<unit id="units:fahr" name="fahrenheit" parentSI="units:K"

  multiplierToSI="0.55555555555555555" 

  constantToSI="-17.777777777777777777">

    <description>An obsolescent unit of temperature still used in popular 

      meteorology</description>

</unit>

<stm:unitList xmlns:stm="http://www.xml-cml.org/schema/stmml">



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

<!-- ========================= fundamental types =========================== -->

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



<stm:unitType id="length" name="length">

  <stm:dimension name="length" power="1"/>

</stm:unitType>



<stm:unitType id="time" name="time">

  <stm:dimension name="time" power="1"/>

</stm:unitType>



<!-- ... -->



<stm:unitType id="dimensionless" name="dimensionless">

  <stm:dimension name="dimensionless" power="1"/>

</stm:unitType>



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

<!-- ========================== derived types ============================== -->

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



<stm:unitType id="acceleration" name="acceleration">

  <stm:dimension name="length" power="1"/>

  <stm:dimension name="time" power="-2"/>

</stm:unitType>



<!-- ... -->



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

<!-- ====================== fundamental SI units =========================== -->

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



<stm:unit id="second" name="second" unitType="time">

  <stm:description>The SI unit of time</stm:description>

</stm:unit>



<stm:unit id="meter" name="meter" unitType="length"

  abbreviation="m">

  <stm:description>The SI unit of length</stm:description>

</stm:unit>



<!-- ... -->



<stm:unit id="kg" name="nameless" unitType="dimensionless"

  abbreviation="nodim">

  <stm:description>A fictitious parent for dimensionless units</stm:description>

</stm:unit>



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

<!-- ===================== derived SI units ================================ -->

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



<stm:unit id="newton" name="newton" unitType="force">

  <stm:description>The SI unit of force</stm:description>

</stm:unit>



<!-- ... -->



<!-- multiples of fundamental SI units -->



<stm:unit id="g" name="gram" unitType="mass"

  parentSI="kg"

  multiplierToSI="0.001"

  abbreviation="g">

  <stm:description>0.001 kg. </stm:description>

</stm:unit>



<stm:unit id="celsius" name="Celsius" parentSI="k"

  multiplierToSI="1" 

  constantToSI="273.18">

  <stm:description><p>A common unit of temperature</p></stm:description>

</stm:unit>



<!-- fundamental non-SI units -->



<stm:unit id="inch" name="inch" parentSI="meter"

   abbreviation="in"

  multiplierToSI="0.0254" >

  <stm:description>An imperial measure of length</stm:description>

</stm:unit>



<!-- derived non-SI units -->



<stm:unit id="l" name="litre" unitType="volume"

   parentSI="meterCubed"

   abbreviation="l"

   multiplierToSI="0.001">

  <stm:description>Nearly 1 dm**3 This is not quite exact</stm:description>

</stm:unit>



<!-- ... -->



<stm:unit id="fahr" name="fahrenheit" parentSI="k"

   abbreviation="F"

  multiplierToSI="0.55555555555555555" 

  constantToSI="-17.777777777777777777">

  <stm:description>An obsolescent unit of temperature still used in popular

  meteorology</stm:description>

</stm:unit>



</stm:unitList>

<stm:unitList 

    xmlns:stm="http://www.xml-cml.org/schema/stmml"

    dictRef="unit" href="units.xml" />

</stmml>

