Citizen Scientists and Their Contributions to Internet Based Chemistry
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Citizen Scientists and Their Contributions to Internet Based Chemistry

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This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online ...

This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online databases. The movie of the presentation is online at SciVee here: http://www.scivee.tv/node/14770

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Citizen Scientists and Their Contributions to Internet Based Chemistry Citizen Scientists and Their Contributions to Internet Based Chemistry Presentation Transcript

  • Citizen Scientists and Their Contributions to Internet Based Chemistry
  • Citizen Scientists Enable the Web
    • Who is writing about chemical compounds on Wikipedia?
    • Who is writing critical reviews of Chemistry online?
    • Who is blogging about chemistry on the web?
  • Org Prep Daily (Blog)
  • Encyclopedic Articles (Wikipedia)
  • Chemistry online – An Overview
    • Encyclopedic articles (Wikipedia)
    • Chemical vendor databases
    • Metabolic pathway databases
    • Property databases
    • Chemical Synthesis procedures
    • Scientific publications
    • Chemical vendors
    • Blogs
    • Wikis
    • Open Notebook Science
  • What and who do you trust?
  • Compounds and Identifiers
  • What is ChemSpider?
    • ChemSpider is:
      • Building a Structure Centric Community for Chemists
      • >23 million compounds, ca. 250 data sources
      • A deposition and curation platform
      • A publishing platform for the community
      • Grows daily – more depositions, more links, more data sources
  • Search Cholesterol
  • Search Cholesterol
    • Perform Real Search on Cholesterol
  • Link off a structure in ChemSpider
      • Chemical suppliers
      • Other publications
      • Analytical Data
      • Related Reactions
      • Wikipedia
      • Patents
      • “ Everything”
  • Answering Questions for Chemists
    • Questions a chemist might ask…
      • What is the melting point of n-butanol?
      • What is the chemical structure of Xanax?
      • Chemically, what is phenolphthalein?
      • What are the stereocenters of cholesterol?
      • Where can I find publications about xylene?
      • What are the different trade names for Ketoconazole?
      • What is the NMR spectrum of Aspirin?
      • What are the safety handling issues for Thymol Blue?
  • What is Flibanserin?
  • What is the structure of Flibanserin?
  • What is the structure of Flibanserin?
  • Complex Data and Information
  • Various Searches
    • Structure searching
    • Substructure searching
    • Subset searching – choose from 200 data sources
    • Property searching
    • Searches are used in various ways by different types of chemists…
  • ChemSpider Searches
  • ChemSpider Searches
  • Aspirin On Wikipedia
  • Aspirin names and synonyms
    • Text searches depend on correct association
    • 335 suggested identifiers for Aspirin just on PubChem!
    • Disambiguation dictionaries are necessary
  •  
  •  
  •  
  • The Final Search Strategy
  • All Those Names, One Structure
  • The InChI Identifier
  • Multiple Layers
  • InChIStrings Hash to InChIKeys
  • Oleoylethanolamine
  • Search Engine Dependencies
  • Search Engine Dependencies
  • Vancomycin
  • Vancomycin on PubChem
  • Methane on PubChem
  • Question Everything online: www.dhmo.org
  • Vancomycin on ChemSpider
  • Vancomycin
  • Vancomycin Search Molecular SKELETON Search Full Molecule
  • The EXPERTS must get it right?!
  • Wikipedia, C&E News, PubChem
    • C&E News (from ACS)
  • Citizen Scientists
  • Crowd-sourcing Chemistry Curation
    • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  • Curate Fostriecin
    • Search Fostriecin on ChemSpider
    • Curate it
  • Become a Data Source
  •  
  • Synthesis Procedures
  • Links to Data or Deposit Data
  • Upload Spectral Data, OPEN Data?
  • Semantic Mark-up for Chemistry
    • Semantic mark-up for chemistry is here
      • RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies). Based on the OSCAR system
      • ChemSpider Journal of Chemistry
      • Nature publishing group compound linking
  • ChemMantis and CJOC
  • Name-Structure Pairs
  • Deposit Structures
  • Species – linked to Wikipedia
  • In Development ChemSpider Synthesis
    • ChemSpider Synthesis will be a home for all things “synthetic”
    • An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc.
    • Public peer-review and feedback for synthetic procedures
  • Online Journals and Live Data
  • ChemSpider Everywhere : Embed
  • ChemSpider Everywhere: Spectral Game
  • ChemSpider Everywhere Crowdsourced Curation of Spectra
  • ChemSpider Everywhere ChemMobi
  • People Make Change Happen You are invited..
    • Curate ChemSpider data and link to us
    • Deposit your data with us
      • Structures
      • Spectra
      • Synthesis procedures
    • ChemSpider Synthesis is under development
  • Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams