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Open Notebook Science: Does Transparency Work? HUBzero Conference Jean-Claude Bradley Department of Chemistry Drexel University April 6, 2011
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
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points
Sigma-Aldrich, Acros and Wolfram Alpha apparently  DO NOT use the same sources for flash points
Most popular data sources
Alfa Aesar donates melting points to the public
Open Melting Point Explorer
Outliers MDPI  dataset EPI (via ChemSpider)
Outliers Alfa Aesar
Inconsistencies and SMILES problems within MDPI dataset
MDPI Dataset labeled with High Trust Level
Open Melting Point Datasets
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
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
Strategy for an Open Notebook: 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)
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
The importance of raw data availability Missed in a prior publication on solubility for this compound
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
Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley) (Don Pellegrino)
All ONS web services
For all Formats of ONS Projects
Conclusions ,[object Object]

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