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Leveraging Transparency and Crowdsourcing in Chemistry
Using Open Notebook Science
Jean-Claude Bradley
October 9, 2009
Northeast Regional Meeting of the American Chemical Society
Associate Professor of ChemistryDrexel University
The NaH oxidation controversy
Information spreads quickly through the blogosphere
15% NMR yield
Khalid Mirza and Marshall Moritz
Top results on a Google search
Motivation: Faster Science, Better Science
Open Notebook Science Logos (Andy Lang, Shirley Wu)
Sharing: how much and when
There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data provenance by
making assumptions explicit
TRUST
PROOF
The solubility of 4-chlorobenzaldehyde
The Log makes Assumptions Explicit
The Rationale of Findings Explicit
Raw Data Made Public
Splatter?
Some liquid
YouTube for demonstrating experimental set-upYouTube for demonstrating experimental set-up
Calculations Made Public on Google Spreadsheets
Link to Docking Results: Link to Docking Results: Lists of SMILES in GoogleDocs Lists of SMILES in GoogleDocs
(Rajarshi Guha)(Rajarshi Guha)
Link to Docking Procedure Link to Docking Procedure (Rajarshi Guha)(Rajarshi Guha)
Revision History on Google Spreadsheets
Wiki Page History
Comparing Wiki Page Versions
Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
Linking to Molecules in Chemistry Databases
Experimental Spectra and User-Deposited Data on ChemSpider
(Andy Lang, Tony Williams)
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams, Robert Lancashire)
Database Curation via Game Playing
Over 50,000 spectrum views so far - worldwide
Link Spectral Game to Open Educational Content
NMR game in Second Life (Andy Lang)
The Ugi reaction: can we predict precipitation?
Can we predict solubility in organic solvents?
Crowdsourcing Solubility Data
ONS Submeta Award Winners
ONS Challenge Judges
Teaching Lab: Brent Friesen (Dominican University)
Solubility Experiment List
Solubilities collected in a Google Spreadsheet
Rajarshi Guha’s Live Web Query using Google Viz API
Rajarshi Guha and Andy Lang: Chemical Space Explorer
WE ARE HEREWE ARE HERE
How can the scientific process become more automated?
The Robot ScientistThe Robot Scientist
Semi-Automated Measurement of Semi-Automated Measurement of solubility via web service analysis solubility via web service analysis
of JCAMP-DX files of JCAMP-DX files
(Andy Lang)(Andy Lang)
Solubility Measurement Requests: DoSol sheet
•Outlier Bot: flags measurements with high standard deviation to mean ratios•Google Analytics queries – new solvent/solute searches•Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study•Application based models – high priority Ugi reactants
Solubility Prediction (Andy Lang’s Model)
Solubility prediction can generate requests for additional measurements
Solvent mixture and temperature: multidimensional solubility data
Actual Data (4-nitrobenzaldehyde)
From quadratic regression of 5D space
Feeds DoSol Sheet the next points to measure to best cover the space
Understanding in addition to empirical modeling
Missed in a prior publication on solubility
for this compound
Data provenance: From Wikipedia to…
…the lab notebook and raw data
Including links to the literature
Pierre Lindenbaum’s Solubility Data as RDF Triples
•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)
How does Open Notebook Science fit with traditional publication?
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
XML reports from MiniMapper robot
GoogleDoc to program and report
Paper written on Wiki
References to papers, blog posts, lab notebook pages, raw data
Paper on Journal of Visualized Experiments (JoVE)
Pre-print on Nature Precedings
ChemSpider Automated Mark-up of Chemical Names
Cameron Neylon’s NotebooksCameron Neylon’s Notebooks
Other Open NotebooksOther Open Notebooks
Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)
Educational “Open Notebooks”Educational “Open Notebooks”
Educational “Open Notebooks”Educational “Open Notebooks”
Educational “Open Notebooks”Educational “Open Notebooks”
Crowdsourcing ChemInfo Resource CollectionCrowdsourcing ChemInfo Resource Collection