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The collection, curation and modeling of Open Melting Point measurements PowerPoint PPT Presentation

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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

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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


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

Investigating the m.p. inconsistencies of EGCG

Most popular data sources

Alfa Aesar donates melting points to the public

Open Melting Point Explorer


EPA/PhysProp (donated all data to public also)



Outliers for ethanol: Alfa Aesar and Oxford MSDS

Inconsistencies and SMILES problems within MDPI dataset

MDPI Dataset labeled with High Trust Level

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

EPA/PHYSPROP 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

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

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)

Modeling Results

Melting point prediction service

Melting point predictions and measurements on iPhone/iPad(Alex Clark)

Publication of double+ validated melting point dataset to Nature Precedings and LuLu

For all Formats of ONS Projects

Open Melting Point Datasets

Currently 20,000 compounds with Open MPs

Some melting points can’t be resolved

only with literature: 4-benzyltoluene

Motivation: Faster Science,Better Science

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

Using melting point for temperature dependent solubility prediction

Crowdsourcing Solubility Data

Integration of Multiple Web Services to Recommend Solvents for Reactions

All ONS web services

Google Apps Scripts web services

Google Apps Scripts for conveniently exploring melting point data

Comparison of model with triple validated measurements

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 (cyclobutylamine flagged for validation – only single source available)

Google Apps Scripts for planning reactions and creating schemes

Open Melting Points in Supplementary Data Pages of Wikipedia (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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