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					Chemistry Add-in for Word

              OR 10
          Joe Townsend
     University of Cambridge
        jat45@cam.ac.uk
            Publication




The World
                  The World
      Web Pages
                     (2003)



                       Sad


The
Lab   Journals


                    The Scientist
               Article Structure
Front Matter

                              Set up
Abstract


Introduction
                              Compound Name
Discussion

Results

Experimental
                              Synthesis



                              Analysis

References
   (6R,12aR)-6-(1,3-benzodioxol-5-yl)-2-methyl-
2,3,6,7,12,12a-hexahydropyrazino[1',2':1,6]pyrido
             [3,4-b]indole-1,4-dione
N-{[(1,1-dimethylethyl)oxy]carbonyl}-L-tryptophyl-
    L-methionyl-L-α-aspartyl-3,4,5-tribromo-L-
               phenylalaninamide
 (2R,3R,4S)-2-[(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
         [(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
         [(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
         [(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
         [(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
         [(2S,3R,4R,5S,6R)-3-acetamido-2-[(2S,3R,4S,5R,6R)-6-
          [(3R,4R,5S,6R)-3-acetamido-2-hydroxy-5-sulfooxy-6-
 (sulfooxymethyl)oxan-4-yl]oxy-2-carboxylato-4,5-disulfooxyoxan-3-
  yl]oxy-5-sulfooxy-6-(sulfooxymethyl)oxan-4-yl]oxy-2-carboxylato-
  4,5-disulfooxyoxan-3-yl]oxy-5-sulfooxy-6-(sulfooxymethyl)oxan-4-
    yl]oxy-2-carboxylato-4,5-disulfooxyoxan-3-yl]oxy-5-sulfooxy-6-
 (sulfooxymethyl)oxan-4-yl]oxy-2-carboxylato-4,5-disulfooxyoxan-3-
  yl]oxy-5-sulfooxy-6-(sulfooxymethyl)oxan-4-yl]oxy-2-carboxylato-
  4,5-disulfooxyoxan-3-yl]oxy-5-sulfooxy-6-(sulfooxymethyl)oxan-4-
    yl]oxy-2-carboxylato-4,5-disulfooxyoxan-3-yl]oxy-5-sulfooxy-6-
(sulfooxymethyl)oxan-4-yl]oxy-3,4-disulfooxy-3,4-dihydro-2H-pyran-
                             6-carboxylate
                                       Hamburgers
                                                   Paper 1

                                         Communication 2

                             Supplementary Information 2
Converting PDF to XML is a bit like converting hamburgers
into cows. You may be best off printing it and then
scanning the result through a decent OCR package. 3


[1] Org. Biomol. Chem., 2010, 8, 3149 - 3156, DOI: 10.1039/c003511d

[2] Org. Biomol. Chem., 2010, 8, 3130 - 3132, DOI: 10.1039/c004556j
[3] Michael Kay. (2009, August) xml-dev - RE: [xml-dev] How we can convert pdf data into xml?
             http://lists.xml.org/archives/xml-dev/200607/msg00509.html
  STOP!
DEMO TIME
Under the Hood
                          Validation
Is it CML?
• Does it use Chemical Mark-up Language correctly



     Is it CMLLite?
     • Tighter constraints and co-constraints



           Is it normalised?
           • Further constraints and normalization
            Chemistry Zone




                               CML
Chemistry       Function
  Zone             &
                  OPC
                             Properties
Package Structure
DOMAIN   MANIPUL-                     APP.
                           UI
MODEL     LATION                    SPECIFIC

          Chemical                  Properties
                          Zone
         Intelligence

            List of
          Depictions
NUMBO                   Show List      CML


             CID
                          Zone’     Properties’
      Linked Zones

       Properties 1
154


              CML

                          Properties 3

           Properties 2
              Copied Zones
       Properties                Properties
154                  COPY                     154
         CML                      CML




                      CML’          Fn

      155
                    Properties
Record Keeping
       What can we do with a Cow?
5-Cyclobutyl-2,3-dihydro-[1H]-2-benzazepine 82:

Potassium carbonate (0.63 g, 4.56 mmol) and thiophenol (0.19 g,
1.69 mmol) were added to the 2-nitrobenzene sulfonamide 50
(0.50 g, 1.302 mmol) in N,N-dimethylformamide (33 cm3) at room
temperature and the mixture was stirred for 16 h. Deionised water
(50 cm3) was added and the aqueous phase was extracted with
ethyl acetate (5 x 50 cm3). The organic extracts were dried (MgSO4)
and concentrated under reduced pressure to give the title
compound 82 (0.259 g, 1.302 mmol, ca. 100%) as an oil used
without further purification.
Tokenization and Chunking
Phrase identification
RDF of reaction components
 3D Boxes: Solid
 Double Circles: Oil
 Octagon: Gum
 Triple Octagon: Foam
 Diamond: Crystals or
       Needles
 Ellipses: Unknown or
       Unspecified
                      The World
      Web Pages




The    Repositories
Lab


         Journals
                         The Scientist
                    Thanks
Tony Hey, Lee Dirks, Alex Wade, Savas Parastatidis,
   Oscar Naim, Pablo Fernicola, Geraldine Wade,
  Murray Sargent, Rudy Potenzone, Tim Haughton,
      Mike Galos, Tola Chhoeun, Jim McGill

        Peter Murray-Rust, Jim Downing,
            Sam Adams, Daniel Lowe
      http://research.microsoft.com/chem4word
           http://chem4word.codeplex.com

				
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