International Year of Chemistry: Perils and Promises of Modern Communication

in the Sciences The Role of Trust

June 14, 2011

Special Libraries Association

Jean-Claude Bradley

Department of ChemistryDrexel University

Unknown Perils of the Past

Before online databases (early 90s) searching for properties like melting

points using ONE “trusted source” was practical

• CRC Handbook•Merck Index• Chemical Vendor Catalogs (e.g. Sigma-Aldrich)• Peer-Reviewed Journals

Known Perils of the Present

Today, many librarians discourage the use of new online sources (like Wikipedia) for the

searching of chemical data and recommend using only “trusted sources”

The problem is that the “trusted source” model is - and always was – fundamentally

flawed.

Ironically most of Wikipedia’s chemical information is problematic BECAUSE it is based

on “trusted sources”!

Promises for the Future

Using technology, we can begin to replace the “trusted source”

model with one based on transparency and provenance

The current state of transparency in scientific communication

Case study of melting point data

The Chemical Information Validation Sheet

567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

The Chemical Information Validation Explorer

(Andrew Lang)

Discovering outliers for melting points (stdev/average)

Investigating the m.p. inconsistencies of EGCG

Investigating the m.p. inconsistencies of cyclohexanone

Most popular data sources

Alfa Aesar donates melting points to the public

Open Melting Point Explorer

(Andrew Lang)

OutliersMDPI

datasetEPI (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

Open Melting Point DatasetsCurrently 20,000 compounds with Open MPs

Live curation on a public Google Spreadsheet of compounds with highest mp ranges

(collaboration with Andrew Lang and Antony Williams)

Some melting points can’t be resolved only with literature: 4-benzyltoluene

The quest to resolve the melting point of 4-benzyltoluene: liquid at room temp

and can be frozen <-30C

The quest to resolve the melting point of 4-benzyltoluene: ambiguous results upon heating

but clearly remains a liquid at -15 C for 2 days in freezer

Further investigation into the literature for the melting point of 4-benzyltoluene

Although a general description of method is provided the raw data are

not

Because of broken provenance errors cascade through the literature

Calculations in patent based on incorrect data

Open Random Forest modeling of Open Melting Point data using CDK descriptors

(Andrew Lang)

R2 = 0.78, TPSA and nHdon most important

Melting point prediction service

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

Using melting point for temperature dependent solubility prediction

Motivation: Faster Science, Better Science

There are NO FACTS, only measurements embedded

within assumptions

Open Notebook Science maintains the integrity of data

provenance by making assumptions explicit

TRUST

PROOF

First record then abstract structure

In order to be discoverable use Google friendly formats (simple HTML, no login)

In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets)

Strategy for an Open Notebook:

Crowdsourcing Solubility Data

Data provenance: From Wikipedia to…

…the lab notebook and raw data

Calculations Made Public on Google Spreadsheets

Interactive NMR spectra using JSpecView and JCAMP-DX

Raw Data As Images

Splatter?

Some liquid

YouTube for demonstrating experimental set-up

Solubilities collected in a Google Spreadsheet

Rajarshi Guha’s Live Web Query using Google Viz API

Web services for summary data

(Andrew Lang)

Web service calls from within a Google Spreadsheet for solubility measurement and

prediction

(Andrew Lang)

Integration of Multiple Web Services to Recommend Solvents for Reactions

(Andrew Lang)

Reaction Attempts Book

Reaction Attempts Book: Reactants listed Alphabetically

ONS Challenge Solubility Book cited for nanotechnology application

Lulu.com Data Disks

All ONS web services

For all Formats of ONS Projects

Conclusions

• 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