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The collection, curation and modeling of Open Melting Point measurements. 5 th Meeting on U.S. Government Chemical Databases and Open Chemistry. Jean-Claude Bradley. Andrew Lang. Antony Williams. Department of Chemistry Drexel University. ChemSpider Royal Society of Chemistry.

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The collection, curation and modeling of Open Melting Point measurements

5th Meeting on U.S. Government Chemical Databases and Open Chemistry

Jean-Claude Bradley

Andrew Lang

Antony Williams

Department of Chemistry

Drexel University

ChemSpider

Royal Society of Chemistry

Department of Mathematics

Oral Roberts University

August 26, 2011


The Problem of Data Quality in Chemistry

  • Lack of provenance

  • Reliance on a system of “trusted sources”

In the case of melting points:

  • CRC Handbook

  • Merck Index

  • Chemical Vendor Catalogs (e.g. Sigma-Aldrich)

  • Peer-Reviewed Journals


Strategy for the curation of melting points

Rely on redundancy when possible

Provide the maximum level of provenance when necessary (Open Notebook Science)

Adhere to Open Data, Open Descriptors and Open Algorithms for measurements and modeling

Using technology, we can begin to replace the “trusted source” model with one based on transparency and provenance


The Chemical Information Validation Sheet

567 curated and referenced measurements from

Fall 2010 Chemical Information Retrieval course




Alfa Aesar donates melting points to the public



Outliers

EPA/PhysProp (donated all data to public also)

MDPI

dataset


Outliers for ethanol: Alfa Aesar and Oxford MSDS




EPA/PHYSPROP Structure Errors (Incorrect Valence): 2315 out of 43543 were contained pentavalentnitrogens


EPA/PHYSPROP of 43543 were contained Errors: Structure displayed is for the neutral compound dopamine but the associated CAS Number and chemical name in the file are for the hydrobromidesalt.


Common errors in datasets
Common errors in datasets of 43543 were contained

multiple melting points for the same compound in the same database

stereochemistry issues

sign inversion

conversion errors (Kelvin/CelciusFahrenheit/Celcius)

bad SMILES (non-rendering)

salts associated with SMILES for free base

using boiling point for melting point


Open melting point datasets
Open melting point of 43543 were contained datasets

Double+ validated: 2706 compounds (7413 highly curated measurements. range: 0.01-5 C. Compounds that had at least one chiral center, possessed cis/trans isomerism, were inorganic or a salt removed.)

Entire dataset: 19933 unique compounds (27684 measurements – no inorganics or salts)


Open models with open data using open descriptors cdk
Open of 43543 were contained Models with Open Data Using Open Descriptors (CDK)


Modeling results
Modeling Results of 43543 were contained


Melting point prediction service of 43543 were contained


Melting point predictions and measurements on of 43543 were contained iPhone/iPad(Alex Clark)




Open Melting Point Datasets Nature

Currently 20,000 compounds with Open MPs


Some melting points can’t be resolved Nature

only with literature: 4-benzyltoluene


Motivation: Nature Faster Science,Better Science


Open Lab Nature Notebook page measuring the melting point of 4-benzyltoluene





All ONS web services for Reactions




Comparison of model with triple validated measurements data

Straight chain carboxylic acids from 1 to 10 carbons

Straight chain alcohols from 1 to 10 carbons


Cyclic primary amines from 3 to 6 carbons ( datacyclobutylamine flagged for validation – only single source available)




Conclusions (Martin Walker)

  • For science to progress quickly there is great benefit in moving away from a “trusted source” model to one based on transparency and data provenance

  • Open Notebook Science offers an efficient way to make research transparent and discoverable


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