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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. Photochemical Smog. Global Modelling. Research in Chemical Kinetics. Box

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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. Photochemical Smog

  3. Global Modelling

  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 http://www.iupac-kinetic.ch.cam.ac.uk/

  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 Datasheet LaTeX CML + MathML XSLT XHTML Summary Table Harvest MCM Search

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

  17. 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

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

  19. Search: Keep it simple 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”

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

  21. CML • Molecules • Reactions • Spectra • Lattices • Arrays • Tables • Matrices • Metadata • Equations CMLCore CMLReact STMML CMLSpect CMLComp 168 elements ~200 attributes

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