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Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry

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    Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry - Presentation Transcript

    1. Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry Antony Williams Bio-IT World 2009
    2. Linked Data Cloud
    3. Chemistry on the Internet
      • Much of the information online is User Beware!
      • The Quality of information is “diverse”
      • Technologies can “link and connect” information but validation and curation is key to providing quality
      • The LinkedData web is of less value when the data linked are “wrong”
    4. Quality Costs
      • Chemical Abstracts Service (CAS), a division of the ACS is “Gold Standard” in Chemistry related information
        • 101 years of content, $260 million revenue (2006), >40 million substances and 60 million sequences
        • But online…
    5. What is “wrong”?
    6. Languages and Links in Chemistry
      • A platform for:
        • Data deposition, curation and annotation
        • Supporting Open Notebook Science efforts
        • Chemistry document mark-up with ChemMantis
        • The Open Access ChemSpider Journal of Chemistry
    8. Search Cholesterol
    9. Search Cholesterol
    10. Search Cholesterol
    11. Search Cholesterol
    12. Search Cholesterol
    13. Search Cholesterol
    14. Complex Data and Information
    15. Online Data
      • Many websites host structure-based information
      • Question quality!!!
    16.  
    17. Wikipedia, C&E News, PubChem
      • C&E News (from ACS)
    18. Does one stereocenter matter?
    19. Vancomycin
      • Who will curate?
      • PubChem is not resourced to clean these errors 
      • How would you clean such a large dataset?
    20. Vancomycin ChemSpider: 1 compound – 3 days
    21. Question Everything www.dhmo.org
    22. DailyMed
        • “ DailyMed provides high quality information about marketed drugs.
        • This information includes FDA approved labels (package inserts).”
    23. The FDA’s DailyMed
    24. Structures on DailyMed Poor Representations
    25. Structures on DailyMed Lack of Stereochemisty
    26. Incorrect Structures Scanning (?) Issues
    27. Incorrect Structures
    28. Does it Matter?
      • Does it matter to the consumer that the structures are wrong? No…what matters is what is in the bottle is the right medication!
      • To make DailyMed structure searchable it DOES matter
      • To data mine DailyMed it matters
      • To mark up DailyMed it matters
    29. Collaborative Knowledge Management for Chemists
    30. Wikipedia Links to Drugbank
    31. Taxol on PubChem
    32. Taxol on Daily Med
    33. The InChI Identifier
    34. Multiple Layers
      • Source: Unofficial InChI FAQ page
    35. InChIStrings Hash to InChIKeys
    36. InChIs for Taxol
    37. Back to Taxol
      • DrugBank: RCINICONZNJXQF-CLDWUXIMDD
      • ChEBI: RCINICONZNJXQF-GXKQXQCDDN
      • Wikipedia: RCINICONZNJXQF-MZXODVADBJ
      • Which one is correct???
    38. InChIKeys for Taxol
      • DrugBank: RCINICONZNJXQF-CLDWUXIMDD
      • ChEBI: RCINICONZNJXQF-GXKQXQCDDN
      • Wikipedia: RCINICONZNJXQF-MZXODVADBJ
      • ChEBI and Wikipedia are the SAME structure
      • Drugbank is a DIFFERENT structure – ONE stereocenter
    39. The InChI Resolver
    40.  
    41. Coming Soon…Linked Articles
    42. How bad can it get??? And who is right????
    43. ChemMantis
      • Chem ical M arkup A nd N omenclature T ransformation I ntegrated S ystem – ChemMantis
      • A platform for entity extraction for chemistry documents, markup and integration to online information sources – Wikipedia, ChemSpider, Entrez…
      • Web-based submission, markup and publishing platform now hosting the ChemSpider Journal of Chemistry
    44. ChemMantis Markup
    45. Enable Electronic Articles…
      • Structures are the language of chemistry
      • Show structures to chemists and search/link from there…
    46. Species Markup
    47. Dictionaries are Easily Enhanced
      • Copy-Paste into appropriate Entity Dictionary
      • Impacts all future markups
      • Expanding knowledgebases of information
      • Linked out to rich sources of information
    48. Build Dictionaries Ontologies Next
    49. Outlinks…
    50. Publishers and Document Mark-Up
    51. ChemSpider Everywhere
      • Linked from Wikipedia
      • Linked from Open Notebook Science sites using EMBED
      • Linked from Blogs using Structure/Spectra EMBED
      • Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
      • Integrated to software offerings from Thermo, Waters, Agilent, Bruker
    52. ChemSpider Everywhere Embed Functionality (like YouTube)
    53. ChemSpider Everywhere www.spectralgame.com
    54. ChemSpider Everywhere Crowdsourced Curation of Spectra
    55. ChemSpider Everywhere RSC Compounds
    56. ChemSpider Everywhere Nature Chemistry
      • Nature Chemistry articles are annotated to identify all of the chemical compounds mentioned throughout the text.
      • Those compounds are linked out to other information resources including PubChem and ChemSpider .
    57. ChemSpider Everywhere ChemMobi
    58. Structure RSS Feeds with InChIs
    59.  
    60. Acknowledgments
      • Richard Kidd, Royal Society of Chemistry
      • Jason Wilde, Nature Publishing Group
      • Martin Walker and the Wikipedia Chemistry team
      • Microsoft – Rudy Potenzone
      • Symyx – Keith Taylor and James Jack
      • SureChem – Nicko Goncharoff
      • Spectral game - Andrew Lang and Jean-Claude Bradley
      • “ The InChI team and Advisory Group”
    61. Conclusions
      • www.chemspider.com
      • www.chemspider.com/journal
      • InChIs and Internet Chemistry
      • http://inchis.chemspider.com

    + Antony Williams, ChemSpidermanAntony Williams, ChemSpiderman, 6 months ago

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