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Integrating Chemical Kinetic Data on the web Experiences of the MCM-IUPAC Project

Integrating Chemical Kinetic Data on the web Experiences of the MCM-IUPAC Project. Dr Stephen Pascoe. Centre for Atmospheric Data Archival, STFC Stephen.Pascoe@stfc.ac.uk. Dr Hannah Barjat Dr Jenny Young. Air Quality. Global Modelling. HiHEM: CH3CO2. Research in Chemical Kinetics.

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Integrating Chemical Kinetic Data on the web Experiences of the MCM-IUPAC Project

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  1. Integrating Chemical Kinetic Data on the web Experiences of the MCM-IUPAC Project Dr Stephen Pascoe. Centre for Atmospheric Data Archival, STFC Stephen.Pascoe@stfc.ac.uk Dr Hannah Barjat Dr Jenny Young

  2. Air Quality

  3. Global Modelling HiHEM: CH3CO2

  4. Research in Chemical Kinetics Box Models Lab. Experiments Field Experiments Mechanism IUPAC Gas Kinetics MCM Subcommittee for Gas Kinetic Data Evaluation Leeds Master Chemical Mechanism Dynamic Models

  5. IUPAC Kinetics • 900 Gas-phase Datasheets • 60 Heterogenious Datasheets

  6. MCM • 5660 Chemical Species • 13500 Reactions

  7. Integrating the sites • Harvest • Update • Search • Link

  8. Cheminformatics • Open Standards • CML, InChI • OpenSource Tools • OpenBabel, CDK, Jmol, Bioclipse • Open Data-centric websites • PubChem • NIST Webbook • Chemspider

  9. IUPAC Kinetics Database http://www.iupac-kinetic.ch.cam.ac.uk/

  10. IUPAC Datasheets

  11. IUPAC Approach XHTML Summary Table LaTeX XML (CML + MathML)‏ XSLT XHTML Datasheet Harvest MCM Search / Link

  12. CML Usage in IUPAC • CMLReact for reactions • Identify species with InChIs • Kinetic data as cml:observation/cml:table • Maths expressions in Content MathML

  13. Maths Expressions

  14. MathML Example 1 A . eE/T 5.6 . 10-34e300/T <apply><times/> <apply><exp/> <apply><divide/> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathML/temperature">T</csymbol> <cn type="e-notation">5.6<sep/>-34</cn> <cn>300</cn> </apply> </apply> </apply> <apply> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Arrhenius">Arrhenius</csymbol> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathML/Pre-exponentialFactor" type="e-notation">5.6<sep/>-34 </cn> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Ea_R">300</cn> </apply>

  15. MathML Example 2 <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply><eq/> <apply><ci>Fcm3-molecule-s</ci> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/ratecoefficientk"> <ci>k</ci> </csymbol> </apply> <piecewise> <piece> <apply><csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/arrhenius">Arrh</csymbol> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Pre-exponentialFactor" type="e-notation"> 7.6<sep />-12 </cn> <apply><csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/plusminus">PlusMinus</csymbol> <cn definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/Ea_R">-585</cn> <cn>100</cn> </apply> </apply> <apply><lt /> <cn>200</cn> <csymbol definitionURL="http://www.iupac-kinetic.ch.cam.ac.uk/mathml/temperature"> <ci>T</ci> </csymbol> <cn>300</cn> </apply> </piece> </piecewise> </apply> </math>

  16. XML -> XHTML <?xml version="1.0" encoding="UTF-8"?> <cml xmlns="http://www.xml-cml.org/schema/cml2/core" xmlns:iKin="http://www.atm.ch.cam.ac.uk/iKin" xmlns:iKinunits="http://www.atm.ch.cam.ac.uk/iKinunits" xmlns:mcm="http://mcm.leeds.ac.uk/ns#" xmlns:inchi="http://www.iupac.org/inchi" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core file:/C:/Documents%20and%20Settings/Hannah/Desktop/cmlreactCopy.xsd"> <description title="Dates and Versions"> <list> <!-- Dates given in American format (yyyy-mm-dd standard for xsd:date) --> <scalar dictRef="iKin:PubDate">2004-03-01</scalar> <scalar dictRef="iKin:RecValueDate">2004-03-01</scalar> <scalar dictRef="iKin:TextChangeDate">2004-03-01</scalar> <scalar dictRef="iKin:LatestChange">No change since last publication</scalar> </list> </description> <reactionList id="II_A2_10"> <reaction id="II_A2_10_(1)"> <reactantList> <reactant count="1" title="HO"> <molecule title="HO"> <name convention="iKin:preferredname">hydroxyl radical</name> <formula concise="H 1 O 1"/> <identifier> <inchi:basic>InChI=1/HO/h1H</inchi:basic> </identifier> </molecule> </reactant> <reactant count="1" title="CH_2=C(CH_3)CH=CH_2"> <molecule title="CH_2=C(CH_3)CH=CH_2"> <name convention="iKin:preferredname">isoprene</name> <formula concise="C 1 H 2"/> <identifier> <inchi:basic> InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3</inchi:basic> </identifier> </molecule> </reactant> </reactantList> <productList> <product title="generic products"/> </productList> <propertyList> <property title="Heat of reaction" dictRef="iKin:hreact"> <scalar units="iKinUnits:kJ-mol">not available</scalar> </property>

  17. Leeds Master Chemical Mechanism http://mcm.leeds.ac.uk/MCM [-devel]

  18. Chemical Identifiers IUPAC: 2-Methylbutadiene; 2-Methyl-1,3-butadiene; Common: Isoprene; Isopentadiene; CAS: 78-79-5 PubChem: 6557 SMILES: C=CC(C)=C; C(C)=CC=C; C(C=C)C=C; C=C(C=C)C; CSMILES: C=CC(=C)C InChI: InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3

  19. InChI data model • Stereochemistry • Radicals • Excited States • Electronic: O(1D), O(3P)‏ NoInChI=... • Vibrational:

  20. Search: A “Google” inspired approach MCM Name “C5H8” InChI “InChI=1/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3” “InChI=1/C5H8/” Synonym “isoprene” “isopentadiene” exact SMILES “C=C(C=C)C” SMARTS pattern “C=CC=C”

  21. Summary • So far • IUPAC Datsheets machine readable • Species links between MCM and IUPAC • Intuitive species search in MCM • Todo • Update MCM from IUPAC • Dedicated Search Site • Standardised CML output of MCM

  22. Acknowledgements • University of Cambridge • Dr Hannah Barjat • Dr Glenn Carver • University of Leeds • Dr Jenny Young • Dr Andrew Rickard

  23. The End http://www.iupac-kinetic.ch.cam.ac.uk/ http://mcm.leeds.ac.uk/MCM [-devel]

  24. Reserve Slides

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