chemistry add-in for word or 10 joe townsend university of cambridge [email protected]
TRANSCRIPT
The World
Publication
The World (2003)
The Scientist
The Lab Journals
Web Pages
Sad
Front Matter
Abstract
Introduction
Discussion
Experimental
References
Results
Article Structure
Synthesis
Set up
Analysis
Compound Name
(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
(S) (S)
(S) (S)
Br
Br
Br
NH2
NH
HN
HN
NH
NH
OH
O
OO
O O
O
O
S
H H
H H
(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
O
NH
O
O O-
O
O
NH
O
O
O O-
O
O
NH
O
O
O O-
O
O
NH
O
O
O O-
O
O
NH
O
O
O O-
O
O
NH
O
O
O O-
O
O
NH
OOH
O
OS
O
O
HO
O
S
O
O
OH
HH
H
H
O
S
O
OOH
HHO
S
O
O
OH
H
H
H
O
O
S
O
O
HO
O
S
O
OOH
HH
H H
H
O
S
O
O
OHH
H
O
S
O
OOH
H
H H
O
O
S
O
O
HO
O
S
O
O
OH
HH
H H
H
O
S
O
OOHH
H
O
S
O
OOH
H
H H
O
O
S
O
OHO
O
S
O
OOH
HH
H
H
H
O
S
O
O
OH
HHO
S
O
O
OH
H
H
H
O
O
S
O
O
HO
O
S
O
O
OH
HH
H H
H
O
S
O
OOHH
H
O
S
O
OOH
H
H H
O
O
S
O
OHO
O
S
O
OOH
H
H
H H
H
O
S
O
O
OHH
H
O
S
O
OOH
H
H H
O
O
S
O
O
HO
O
S
O
O
OH
HO
O
O
S
O
O
OH
H
H
O
S
O
OOH
O O-
HH
H
H
H
HamburgersPaper 1
Communication 2
Supplementary Information 2
[1] Org. Biomol. Chem., 2010, 8, 3149 - 3156, DOI: 10.1039/c003511d
[2] Org. Biomol. Chem., 2010, 8, 3130 - 3132, DOI: 10.1039/c004556j
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
[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
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
Validation
Chemistry Zone
ChemistryZone
CML
Properties
Function&
OPC
Package Structure
APP.SPECIFIC
UIMANIPUL-
LATIONDOMAINMODEL
NUMBO
ChemicalIntelligence
Zone
CML
Properties
List ofDepictions
Show List
CIDZone’ Properties’
Linked Zones
CML
Properties 1
Properties 2
Properties 3
154
CML
Properties
154CML
Properties
154
CML’
Properties
155
COPY
Fn
Copied Zones
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
The Scientist
The Lab
Journals
Web Pages
Repositories
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/chem4wordhttp://chem4word.codeplex.com
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