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Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
 

Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?

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This presentation was given at the Wolfram Data Summit in Washington DC on Sept 9th 2010 as part of a panel series of presentations and discussions on crowdsourcing approaches for data. It was a rant ...

This presentation was given at the Wolfram Data Summit in Washington DC on Sept 9th 2010 as part of a panel series of presentations and discussions on crowdsourcing approaches for data. It was a rant by me on the quality of what's online and questioning "who cares".

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    Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data? Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data? Presentation Transcript

    • Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data? Antony Williams Wolfram Summit, September 2010
    • A Pragmatic Vision
        • “ Build a Structure Centric Community”
      • Integrate chemistry across the internet based on “chemical structure”
        • A “structure-based hub” to information and data
        • Let chemists contribute their own data
        • Allow the community to curate/correct data
    • www.chemspider.com
    • We Answer Questions for Chemists
      • Questions a chemist might ask…
        • What is the melting point of n-heptanol?
        • 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 Aspirin?
        • What is the NMR spectrum of Benzoic Acid?
        • What are the safety handling issues for toluene?
    • Search for a Chemical…by name
    • Available Information…
      • Linked to vendors, safety data, toxicity, metabolism
    • Available Information….
    • Search for chemicals
    • ChemSpider Today
      • 24.8 million structures
      • 400 data sources
      • Grows daily
      • Community annotation and curation
      • We curate, edit, change, enhance data daily
    • Linked Data on the Web
    • Three Years of Experience
      • Internet-based chemistry is a mess !
      • Most public compound databases on the web are contaminated . Including ours !
      • The annotation/curation of data online is difficult
      • Most database hosts are non-responsive to feedback – “We are a host/repository of data”
      • Who cares ?
    • Where is chemistry online?
      • Encyclopedic articles (Wikipedia)
      • Chemical vendor databases
      • Metabolic pathway databases
      • Property databases
      • Patents with chemical structures
      • Drug Discovery data
      • Scientific publications
      • Compound aggregators
      • Blogs/Wikis and Open Notebook Science
    • What is the Structure of Vitamin K?
    • MeSH – Medical Subject Headings
      • A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants , VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K
    • What is the Structure of Vitamin K1?
    • What is the Structure of Vitamin K1?
    • Chemical Abstracts “Common Chemistry” Database
    • Wikipedia
    •  
    • Incorrect Structures
    • Wow!
    • Lack of Stereochemistry
    • Does stereochemistry matter?
      • Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
    •  
    •  
    •  
    • PubChem
    •  
      • “ 2-methyl-3-(3,7,11,15-tetramethyl hexadec-2-enyl)naphthalene-1,4-dione”
      • Variants of systematic names on PubChem
      • 2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
      • 2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
      • 2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
      • 2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
      • 2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
      • 2-methyl-3-[(E)-3,7,11,15-tetramethyl
      • 2-methyl-3-(3,7,11,15-tetramethyl
      • 2-methyl-3-[(E)-3,7,11,15-tetramethyl
    • ChEBI – Manual Curation
    •  
    •  
    •  
    • What’s Methane?
    • What’s Methane?
    • What ELSE is Methane???
    • The EXPERTS must get it right?!
    • Wikipedia, C&E News, PubChem
      • C&E News (from ACS)
    • Internet-Based Chemistry is a Mess
      • Algorithms can get you so far
      • Human curation is necessary
      • Only the crowds can help with big data… ChemSpider is approaching 25 million compounds
    • Search “Vitamin H”
    • Search “Vitamin H”
    • “ Curate” Identifiers
    • “ Curate” Identifiers
    • “ Curate” Identifiers
    • “ Curate” Identifiers
      • General curation activities
        • Remove incorrect names
        • Correct spellings
        • Add multilingual names
        • Add alternative names
      • In 3 years over 1 million structure-identifier relationships have been validated – robotically and manually
      • 130 people have participated in validation or annotation. “ Crowds ” can be quite small!
    • Crowdsourced “Annotations”
      • Registered Users can add
        • Descriptions/Syntheses/Commentaries
        • Links to articles, blogs, wikis etc
        • Add spectral data
        • Add photos
        • Add MP3 files
        • Add Videos
    • Data Validation – Not Vitamin K1
    • Data Validation – Not Beclamethasone Dipropionate DailyMed Article
    • Data Validation …NOT Cholesterol
    • Data Validation – ONE Cymarin Question Quality in Big Databases
    • First request to Database Hosts!
      • Every public compound database host should add ONE feature – “Leave Comments”
    • Second request to Database Hosts! Show Comments
    • Always Question Online Chemistry
    • Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams