chemical information retrieval class 1
DESCRIPTION
Jean-Claude Bradley presents the first lecture of Chemical Information Retrieval in the Fall of 2012 at Drexel University.TRANSCRIPT
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Chemical Information Retrieval 2012
Jean-Claude Bradley
September 28, 2012
First Class
Associate Professor of ChemistryDrexel University
CHEM367/767 Drexel University
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Finding reliable chemical information
can be really hard
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After this class,you should feel that
you can never blindly trust
chemical data sources again
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But…You will learn how to do the best you can
with imperfect information
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The Chemical Information Validation Sheet
567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
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Discovering outliers for melting points (stdev/average)
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Investigating the m.p. inconsistencies of EGCG
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Investigating the m.p. inconsistencies of cyclohexanone
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Most popular data sources
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Alfa Aesar donates melting points to the public
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Open Melting Point Explorer
(Andrew Lang)
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OutliersMDPI
datasetEPI (donated all data to public
also)
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Outliers for ethanol: Alfa Aesar and Oxford MSDS
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Inconsistencies and SMILES problems within MDPI dataset
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MDPI Dataset labeled with High Trust Level
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Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs
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American Petroleum Institute 5 CPHYSPROP -30 CPHYSPROP 125 Cpeer reviewed journal (2008) 97.5 Cgovernment database -30 Cgovernment database 4.58 C
What is the melting point of 4-benzyltoluene?
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The quest to resolve the melting point of 4-benzyltoluene: liquid at room temp
and can be frozen <-30C
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Open Lab Notebook page measuring the melting point of 4-benzyltoluene
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Motivation: Faster Science, Better Science
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Ruling out all melting points above -15C?
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Oops – 4-benzyltoluene freezes after 16 days at -15C!
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Measuring the melting point by slowly heating from -15 C gives 5 C
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There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
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“Simple” aldol condensation synthesis
Top Hit(no reports of synthesis)
In top ten(a few reports of synthesis)(Andrew Lang)
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Information from the literature on the target synthesis
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Information from the literature on the target synthesis
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An example of a “failed experiment” in an Open Notebook with useful
information
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A successful synthesis by avoiding water, dramatically increasing NaOH and long reaction
time
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Open Random Forest modeling of Open Melting Point data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important
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Melting point prediction service
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Web services for summary data
(Andrew Lang)
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Using a Google Spreadsheet as a “dashboard interface” for reaction planning and analysis
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Calling Google App Scripts
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Calling Google App Scripts
(Andrew Lang and Rich Apodaca)
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Google Apps Scripts for conveniently exploring melting
point data
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Straight chain carboxylic acids from 1 to 10 carbons
Straight chain alcohols from 1 to 10 carbons
Comparison of model with triple validated measurements
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Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)
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Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
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Google Apps Scripts web services
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Integration of Multiple Web Services to Recommend Solvents
for Reactions
(Andrew Lang)
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What are good solvents to recrystallize benzoic acid?
(Andrew Lang)
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Click on the solvent to see temp curve
(Andrew Lang)
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Deliver melting point data via App
(Andrew Lang)
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Web services from data collected in this class will be added here
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In this class you will learn
How to search Science1.0 resources
•Peer-Reviewed journals•Commercial databases•Patents•Conference Proceedings
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In this class you will learn
How to participate in Science2.0
•wikis (Wikipedia, class wiki)•blogs•interactive databases (ChemSpider)•social software (Twitter, FriendFeed)
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In this class you will learnHow to leverage Science3.0
(via collaboration with Andrew Lang)
•machine readable web-services
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Now lets take a look at the class wiki