cheminfo 2011 class1
DESCRIPTION
Jean-Claude Bradley presents the introductory lecture for Chemical Information Retrieval at Drexel University for Fall 2011 on September 23, 2011. Examples are given to demonstrate how difficult it can be to find and assess chemical information such as melting points. An overview of the class wiki is then givenTRANSCRIPT
![Page 1: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/1.jpg)
Chemical Information Retrieval 2011
Jean-Claude Bradley
September 23, 2011
First Class
Associate Professor of ChemistryDrexel University
CHEM367/767 Drexel University
![Page 2: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/2.jpg)
Finding reliable chemical information
can be really hard
![Page 3: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/3.jpg)
After this class,you should feel that
you can never blindly trust
chemical data sources again
![Page 4: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/4.jpg)
But…You will learn how to do the best you can
with imperfect information
![Page 5: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/5.jpg)
The Chemical Information Validation Sheet
567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
![Page 6: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/6.jpg)
Discovering outliers for melting points (stdev/average)
![Page 7: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/7.jpg)
Investigating the m.p. inconsistencies of EGCG
![Page 8: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/8.jpg)
Investigating the m.p. inconsistencies of cyclohexanone
![Page 9: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/9.jpg)
Most popular data sources
![Page 10: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/10.jpg)
Alfa Aesar donates melting points to the public
![Page 11: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/11.jpg)
Open Melting Point Explorer
(Andrew Lang)
![Page 12: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/12.jpg)
OutliersMDPI
datasetEPI (donated all data to public
also)
![Page 13: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/13.jpg)
Outliers for ethanol: Alfa Aesar and Oxford MSDS
![Page 14: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/14.jpg)
Inconsistencies and SMILES problems within MDPI dataset
![Page 15: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/15.jpg)
MDPI Dataset labeled with High Trust Level
![Page 16: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/16.jpg)
Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs
![Page 17: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/17.jpg)
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?
![Page 18: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/18.jpg)
The quest to resolve the melting point of 4-benzyltoluene: liquid at room temp
and can be frozen <-30C
![Page 19: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/19.jpg)
Open Lab Notebook page measuring the melting point of 4-benzyltoluene
![Page 20: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/20.jpg)
Motivation: Faster Science, Better Science
![Page 21: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/21.jpg)
Ruling out all melting points above -15C?
![Page 22: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/22.jpg)
Oops – 4-benzyltoluene freezes after 16 days at -15C!
![Page 23: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/23.jpg)
Measuring the melting point by slowly heating from -15 C gives 5 C
![Page 24: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/24.jpg)
There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
![Page 25: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/25.jpg)
Open Random Forest modeling of Open Melting Point data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important
![Page 26: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/26.jpg)
Melting point prediction service
![Page 27: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/27.jpg)
Melting point predictions and measurements on iPhone/iPad (Andrew Lang and Alex Clark)
![Page 28: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/28.jpg)
Using melting point for temperature dependent solubility prediction
![Page 29: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/29.jpg)
Web services for summary data
(Andrew Lang)
![Page 30: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/30.jpg)
Web service calls from within a Google Spreadsheet for solubility measurement
and prediction
(Andrew Lang)
![Page 31: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/31.jpg)
Integration of Multiple Web Services to Recommend Solvents
for Reactions
(Andrew Lang)
![Page 32: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/32.jpg)
Publication of double+ validated melting point dataset to Nature
Precedings and LuLu
![Page 33: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/33.jpg)
![Page 34: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/34.jpg)
![Page 35: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/35.jpg)
Reaction Attempts Book
![Page 36: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/36.jpg)
Reaction Attempts Book: Reactants listed Alphabetically
![Page 37: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/37.jpg)
![Page 38: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/38.jpg)
All ONS web services
![Page 39: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/39.jpg)
Google Apps Scripts web services
![Page 40: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/40.jpg)
Google Apps Scripts for conveniently exploring melting
point data
![Page 41: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/41.jpg)
Straight chain carboxylic acids from 1 to 10 carbons
Straight chain alcohols from 1 to 10 carbons
Comparison of model with triple validated measurements
![Page 42: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/42.jpg)
Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)
![Page 43: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/43.jpg)
Google Apps Scripts for planning reactions and creating schemes
![Page 44: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/44.jpg)
Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)
![Page 45: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/45.jpg)
Web services from data collected in this class will be added here
![Page 46: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/46.jpg)
In this class you will learn
How to search Science1.0 resources
•Peer-Reviewed journals•Commercial databases•Patents•Conference Proceedings
![Page 47: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/47.jpg)
In this class you will learn
How to participate in Science2.0
•wikis (Wikipedia, class wiki)•blogs•interactive databases (ChemSpider)•social software (Twitter, FriendFeed)
![Page 48: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/48.jpg)
In this class you will learnHow to leverage Science3.0
(via collaboration with Andrew Lang)
•machine readable web-services
![Page 49: ChemInfo 2011 class1](https://reader033.vdocuments.net/reader033/viewer/2022061214/549aa3bab479590b098b4574/html5/thumbnails/49.jpg)
Now lets take a look at the class wiki