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Taming The Wild West Of Internet Based Chemistry You Can Help
 

Taming The Wild West Of Internet Based Chemistry You Can Help

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I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I ...

I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I had 20 minutes to prepare and assembled a mish-mash of information that might be of value to Citizen Chemists, those who might want to contribute to chemistry on the internet

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    Taming The Wild West Of Internet Based Chemistry You Can Help Taming The Wild West Of Internet Based Chemistry You Can Help Presentation Transcript

    • Taming the Wild, Wild West of Chemistry on the Internet. Maybe YOU Can Help?
    • 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?
    • For Synthesis…TotallySynthetic.com
    • Org Prep Daily (Blog)
    • Molbank (Open Access Journal)
    • Synthetic Pages (Website)
    • 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
    • Search Cholesterol
    • Search Cholesterol
    • Search Cholesterol
    • Linked across the internet
    • Link off a structure in ChemSpider
        • Chemical suppliers
        • Other publications
        • Analytical Data
        • Related Reactions
        • Wikipedia
        • Patents
        • “ Everything”
    • Linked to Millions of Articles
    • 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 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
    • Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .
    • Aspirin vs Chemical Identifiers
    • 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
    • Connections Can Lead Anywhere
    • The InChI Identifier
    • Multiple Layers
    • InChIStrings Hash to InChIKeys
    • Oleoylethanolamine
    • Search Engine Dependencies
    • Search Engine Dependencies
    • Vancomycin
    • Vancomycin
      • Who will curate?
      • How would you clean such a large dataset?
    • Chemistry on the Internet
      • Much of the information is based on assertions and User Beware!
      • The Quality of information available is diverse and how does the user know what is and is not “correct”?
    • Caution! Question Everything!
    • Question Everything online: www.dhmo.org
    • Vancomycin on ChemSpider
    • Vancomycin
    • Vancomycin Search Molecular SKELETON Search Full Molecule
    • Full Skeleton Search: 104 Hits
    • Full Molecule Search: 4 Hits
    • The EXPERTS must get it right?!
    • Wikipedia, C&E News, PubChem
      • C&E News (from ACS)
    • “ Lathosterol”
    • “ Lathosterol”
    • “ Lathosterol”
    • “ Lathosterol” Removed
    •  
    • “ Lathosterol” on PubChem
    • Crowd-sourcing Chemistry Curation
      • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
    • Citizen Scientists
    • Become a Data Source
    •  
    • Synthesis Procedures
    • Links to Data or Deposit Data
    • Your Blog Posted Online?
    • 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 Building a Structure Centric Community for Chemists
    • ChemSpider Everywhere
      • Linked from Wikipedia
      • Linked from Open Notebook Science sites
      • Linked from Blogs using Structure/Spectra
      • Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
    • Where is ChemSpider Lacking?
      • ChemSpider is limited to “defined chemicals”. No support for:
        • Polymers
        • Minerals
        • Markush structures
      • ChemSpider is very dependent on InChIs
        • Stereochemistry around non-carbon centers
        • Organometallics are not correctly represented
      • There are millions of errors on ChemSpider
    • What’s next?
      • Keep cleaning and depositing data
      • Enable discovery via the semantic web (RDF)
      • Integrate software: Symyx Jdraw, NMRShiftDB
      • Integrate RSC content – a massive archive!
      • Integrate RSC publishing workflows and databases
      • Continue Building Community for Chemistry
      • Building a Public ADME/Tox database
      • Delivering ChemSpider Synthetic Pages
      • Delivering ChemSpider Analytical Data
      • Delivering ChemSpider Education
      Project Focus
    • 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
    • People Make Change Happen
      • ChemSpider was a “hobby project”
      • Housed in a basement and running off three servers – one bought, two built
      • Sensitive to weather and power stability
      • Went live at ACS Spring 2007 in Chicago
      • ca. 6000 visitors a day, >50,000 transactions daily
    • Organizations Scale Innovation
    • Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams