Evolution of open chemical information
Valery Tkachenko
Royal Society of Chemistry
ACS Fall 2016
Philadelphia, PA

The Short History of Time
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~1992

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Compounds
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Text and References

Reaction 1: NextMove reaction text-mined
from RSC archive – original article

Reaction 1: NextMove reaction text-
mined from RSC archive – cml output
<?xml version="1.0" encoding="UTF-8"?>
<reactionList xmlns="http://www.xml-cml.org/schema" xmlns:cmlDict="http://www.xml-cml.org/dictionary/cml/" xmlns:nameDict="http://www.xml-cml.org/dictionary/cml/name/"
xmlns:unit="http://www.xml-cml.org/unit/" xmlns:cml="http://www.xml-cml.org/schema" xmlns:dl="http://bitbucket.org/dan2097">
<reaction>
<dl:source>
<dl:documentId>c3ra45871g</dl:documentId>
<dl:paragraphText>Diisobutylaluminium hydride (1.1 M in cyclohexane, 2.93 mL, 3.23 mmol) was added dropwise to the solution of 9 (500 mg, 1.29 mmol) and dichloromethane (20 mL)
at −78 °C. The reaction mixture was stirred at −78 °C for another 2 h, warmed up to rt, quenched with methanol (3 mL) and citric acid(aq) (w/w, 10%, 5 mL), concentrated. The residue
was added with water (10 mL) and extracted with dichloromethane (12 mL × 3). The organic layers were combined, dried over Na2SO4, filtered and concentrated. The crude product
was further purified by column chromatography (SiO2, EtOAc–hexanes, 1 : 7; Rf 0.33) to give 10 (308 mg, 1.02 mmol, 79%) as a colourless liquid. [α]D20 −24.2 (c 1.1, CHCl3); 1H NMR
(CDCl3, 300 MHz) δ 0.04 (s, 3H), 0.07 (s, 3H), 0.85 (s, 9H), 1.34 (s, 3H), 1.44 (s, 3H), 2.16 (br, 1H), 3.68–3.81 (m, 3H), 4.16 (t, J = 13.8 Hz, J = 13.8 Hz, 1H), 4.59 (t, J = 6.6 Hz, J = 6.6
Hz, 1H), 5.22 (d, J = 10.7 Hz, 1H), 5.34 (d, J = 17.1 Hz, 1H), 5.90 (ddd, J = 7.2 Hz, J = 10.2 Hz, J = 17.2 Hz, 1H); 13C NMR (CDCl3, 75 MHz) δ 134.1, 118.4, 108.5, 79.5, 78.8, 70.8,
65.0, 27.8, 25.9, 25.4, 18.1, −3.7, −4.4. HRMS (ESI) calcd for [M + Na]+ (C15H30O4SiNa) 325.1811, found 325.1807.</dl:paragraphText>
</dl:source>
<dl:reactionSmiles>[H-
].C([Al+]CC(C)C)C(C)C.C([O:17][CH2:18][C@@H:19]([O:29][Si:30]([C:33]([CH3:36])([CH3:35])[CH3:34])([CH3:32])[CH3:31])[C@@H:20]1[C@H:24]([CH:25]=[CH2:26])[O:23][C:22]([CH3
:28])([CH3:27])[O:21]1)(=O)C(C)(C)C&gt;ClCCl&gt;[C:33]([Si:30]([CH3:32])([CH3:31])[O:29][C@@H:19]([C@@H:20]1[C@H:24]([CH:25]=[CH2:26])[O:23][C:22]([CH3:28])([CH3:27])[O:21
]1)[CH2:18][OH:17])([CH3:36])([CH3:35])[CH3:34] |f:0.1|</dl:reactionSmiles>
<productList>
<product role="product">
<molecule id="m0">
<name dictRef="nameDict:unknown">10</name>
<dl:nameResolved>(R)-2-((tert-Butyldimethylsilyl)oxy)-2-((4S,5S)-2,2-dimethyl-5-vinyl-1,3-dioxolan-4-yl)ethanol</dl:nameResolved>
</molecule>
<amount dl:propertyType="AMOUNT" dl:normalizedValue="0.00102">1.02 mmol</amount>
<amount dl:propertyType="MASS" dl:normalizedValue="0.308">308 mg</amount>
<amount dl:propertyType="PERCENTYIELD" dl:normalizedValue="79">79%</amount>
<amount dl:propertyType="CALCULATEDPERCENTYIELD" dl:normalizedValue="79.1" units="unit:percentYield">79.1</amount>
<identifier dictRef="cml:smiles" value="C(C)(C)(C)[Si](O[C@H](CO)[C@H]1OC(O[C@H]1C=C)(C)C)(C)C"/>
<identifier dictRef="cml:inchi" value="InChI=1S/C15H30O4Si/c1-9-11-13(18-15(5,6)17-11)12(10-16)19-20(7,8)14(2,3)4/h9,11-13,16H,1,10H2,2-8H3/t11-,12+,13-/m0/s1"/>
<dl:entityType>definiteReference</dl:entityType>
<dl:appearance>colourless</dl:appearance>
<dl:state>liquid</dl:state>
</product>
</productList>
<reactantList>
<reactant role="reactant">
<molecule id="m1">
<name dictRef="nameDict:unknown">Diisobutylaluminium hydride</name>
</molecule>
<amount dl:propertyType="AMOUNT" dl:normalizedValue="0.00323">3.23 mmol</amount>

Reaction 1: procedure steps
Diisobutylaluminium hydride (1.1 M in
cyclohexane, 2.93 mL, 3.23 mmol) was added
dropwise to the solution of 9 (500 mg, 1.29
mmol) and dichloromethane (20 mL) at −78 °C.
The reaction mixture was stirred at −78 °C for
another 2 h, warmed up to rt, quenched with
methanol (3 mL) and citric acid (aq) (w/w, 10%,
5 mL), concentrated. The residue was added
with water (10 mL) and extracted with
dichloromethane (12 mL × 3). The organic
layers were combined, dried over Na2SO4,
filtered and concentrated. The crude product
was further purified by column chromatography
(SiO2, EtOAc–hexanes, 1 : 7; Rf 0.33) to give
10 (308 mg, 1.02 mmol, 79%) as a colourless
liquid.
Text mining breaks down procedure summary into steps:
<dl:reactionActionList/dl:reactionActions> dl:phraseTexts
• action="Add“: Diisobutylaluminium hydride (1.1 M in
cyclohexane, 2.93 mL, 3.23 mmol) was added dropwise to
the solution of 9 (500 mg, 1.29 mmol) and
dichloromethane (20 mL) at −78 °C
• action=" Stir“: The reaction mixture was stirred at −78 °C
for another 2 h
• action="Heat“: warmed up to rt
• action="Quench“: quenched with methanol (3 mL) and
citric acid(aq) (w/w, 10%, 5 mL)
• action="Concentrate“: concentrated
• action="Add“: The residue was added with water (10 mL)
• action="Extract“: extracted with dichloromethane (12 mL ×
3)
• action="Dry“: dried over Na2SO4
• action="Filter“: filtered
• action="Concentrate“: concentrated
• action="Purify“: The crude product was further purified by
column chromatography (SiO2, EtOAc–hexanes, 1 : 7; Rf
0.33)
• action="Yield“: to give 10 (308 mg, 1.02 mmol, 79%) as a
colourless liquid

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Our World is hyperconnected

Standards?

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Robochemistry
Proliferation of errors in public and
private databases
Automated quality control system

CVSP

CVSP – submission details

CVSP – issues review

J. Brechner, IUPAC
Graphical Representation of
stereochem. configurations
Section: ST-1.1.10
DB06287

CVSP - mapping

CVSP – rules

Dimensions and complexity of science

D2I2K2W

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Technical University of Denmark
University of Hamburg, Center for
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Consorci Mar Parc de Salut de Barcelona
Leiden University Medical Centre
Royal Society of Chemistry
Vrije Universiteit Amsterdam
Novartis
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Swiss Institute of Bioinformatics
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Janssen Esteve Almirall
OpenLink Scibite
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AstraZeneca
Pfizer

Why is it so hard to….
Competitors?
What’s the
structure?
Are they in our
file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?
Connections to
disease?
Expressed in right
cell type?
IP?

@gray_alasdair Big Data Integration 30
Knowledge is federated

Publishing – then…

…and now?

http://ec.europa.eu/research/press/2016/pdf/opendata-infographic_072016.pdf

Data Market

Publishers - the guardians of knowledge
This is a poster for Guardians of the Galaxy. The poster art copyright is believed to belong to the distributor of the Film, Walt Disney Studios Motion
Pictures, the publisher, Marvel Studios, or the graphic artist.

Data Publishing
Original artist: Joseph Ferdinand Keppler (1838-1894) Restoration: Adam Cuerden - http://www.loc.gov/pictures/item/2011661385/ by way
ofhttp://adamcuerden.deviantart.com/gallery/#/d5onmxh

The World we live in

Moore’s Law

"Internet host count history". Internet Systems Consortium. Retrieved May 16,2012.

We are on a verge of a new technical revolution
and it feels great to anticipate it and be ready to ride!
Image from surfline.com by Mike Cianciulli

Data Science @ RSC
The team. From left to right: Valery Tkachenko and Alexey Pshenichnov, based in the United States;
Aileen Day, based in Southampton; John Boyle, Peter Corbett, Colin Batchelor, Jeff White, Nicholas
Bailey and Val the plant, based at TGH

Thank you
Email: tkachenkov@rsc.org
Slides:
http://www.slideshare.net/valerytkachenko16