Open Notebook Science Web Services - ACS Spring 2011
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Open Notebook Science Web Services - ACS Spring 2011

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Jean-Claude Bradley presents on March 30, 2011 at the American Chemical Society on Rapid Dissemination of Chemical Information for people and machines using Open Notebook Science.

Jean-Claude Bradley presents on March 30, 2011 at the American Chemical Society on Rapid Dissemination of Chemical Information for people and machines using Open Notebook Science.

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Open Notebook Science Web Services - ACS Spring 2011 Open Notebook Science Web Services - ACS Spring 2011 Presentation Transcript

  • Rapid dissemination of chemical information for people and machines using Open Notebook Science
    American Chemical Society Meeting
    Jean-Claude Bradley
    Andrew Lang
    Department of Chemistry
    Drexel University
    Department of Mathematics
    Oral Roberts University
    March 30, 2011
  • 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
  • ONS Challenge Judges
  • ONS Challenge Award Winners
  • 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)
  • The Intersection of Open Notebooks (Bradley/Todd) and IP implications
    Open Notebook could have blocked patent if done earlier
  • 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
  • Decanoic acid
    Water
    NaCl
  • Phrase searching for useful solubility applications
  • The challenge of modeling inorganic solubility openly
  • All ONS web services
  • Dynamic links to private tagged
    Mendeley collections
    (Andrew Lang)
  • For all Formats of ONS Projects
  • Conclusions
    • Abstraction of ONS experimental data into a clear semantic format can be done quickly and easily and greatly leverages the utility of the data
    • No information is lost as long as a link to the Open Notebook is captured