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Building A Community Resource For The Life Sciences
The document discusses the challenges of finding trustworthy chemistry data online, highlighting issues such as data quality and the limitations of text-based searches. It advocates for building a community platform where chemists can share, curate, and access structure-centric data to improve resource discovery. The future vision includes crowdsourced contributions, enhanced searching capabilities through InChI identifiers, and an integrated semantic web framework for chemistry that facilitates open access to information.
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Building A Community Resource For The Life Sciences
- 1. Building A CommunityPlatform to Support Chemistry and the Life Sciences
- 2. Where Would Youlook? What Do You Trust?
- 3. Chemistry on theInternet TODAY Chemistry searches are generally limited to text-based searches across the internet Data are dirty: sorting the wheat from the chaff. Who can you trust? Too many searches required to resource data
- 4. Chemistry on theInternet TODAY Chemistry searches are generally limited to text-based searches across the internet Data are dirty: sorting the wheat from the chaff. Who can you trust? Too many searches required to resource data
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- 7. The Final SearchStrategy
- 8. All Those Names,One Structure A problem to solve…
- 9. Chemistry on theInternet TODAY Chemistry searches are generally limited to text-based searches across the internet Data are dirty: sorting the wheat from the chaff. Who can you trust? Too many searches required to resource data
- 10. Trustworthy Chemistry? Encyclopedicarticles (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
- 11. Where Would Youlook? What Do You Trust?
- 12. Structural Data forLifeSciences DailyMed
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- 14. IncorrectStructures
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- 16. Drugs are REALLYMessy
- 17. Vancomycin Who willcurate? How would you clean such a large dataset? Assertions!!!
- 18. The EXPERTS mustget it right?!
- 19. Wikipedia, C&E News,PubChem C&E News (from ACS)
- 20. Chemistry on theInternet TODAY Chemistry searches are generally limited to text-based searches across the internet Data are dirty: sorting the wheat from the chaff. Who can you trust? Too many searches required to resource data
- 21. Just “PublicCompound” Databases PubChem Drugbank ChEBI/ChEMBL KEGG LipidMAPs ChemIDPlus eMolecules ZINC Lots of chemical vendors ChemSpider
- 22. media.obsessable.com As fewinterfaces as possible What do humans want?
- 23. A Pragmatic Vision“ Build a Structure Centric Community to Serve Chemists” Integrate chemical structure data on the web Create a “structure-based hub” to information and data Provide access to structure-based “algorithms” Let chemists contribute their own data Allow the community to curate/correct data
- 24. Answer Questions Questionsa 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 Ketoconazole? What is the NMR spectrum of Aspirin? What are the safety handling issues for Thymol Blue?
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- 41. Statistics for TodayAlmost 25 million compounds from >350 data sources About 7000 unique users per day and up to ½ million transactions per day A crowdsourced deposition and curation platform Grows daily – more depositions, more links, more data
- 42. Searching Chemistry onthe Internet How complete a result set will we get if we search for “chemicals” by name? Is there a better way to link chemistry databases? Linking by “names” is dangerous Chemists want structure and SUBstructure searching
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- 45. InChIStrings Hash toInChIKeys
- 46. Link the Internetwith InChIKeys! Taken from: Rafael Sidis’ Blog
- 47. Vancomycin – Search the Internet
- 48. Vancomycin Search MolecularSKELETON Search Full Molecule
- 49. Full Molecule Search: 4 Hits
- 50. Full Skeleton Search: 104 Hits
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- 55. Vancomycin on ChemSpider 1 compound – 3 days
- 56. InChIKeys Make theinternet searchable by adding InChIKeys Publishers add InChIKeys to papers now…
- 57. InChIKeys Make theinternet searchable by adding InChIKeys Publishers add InChIKeys to papers now… is what???
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- 59. InChI Resolver toDOIs Structure Search the Web
- 60. Most Chemistry isNOT Published Only a fraction of chemistry is published Only a tiny fraction of chemistry is patented What of the “Lost Chemistry”- never published and cannot be abstracted Reactions performed Structures made and studied Spectra acquired and then disposed of Available chemicals never found
- 61. Crowd-sourcing Curation andDeposition Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
- 62. Multi-level Curation andApproval Building a Structure Centric Community for Chemists
- 63. Semantic Markup: ProjectProspect
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- 65. Semantic Linking ofStructures What would you want to link off a structure? Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “ Everything”
- 66. Org Prep Daily (Blog)
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- 68. Chemistry on theInternet FUTURE The semantic web for chemistry is in place Crowdsourced contributions are commonplace Chemists will search by structure/substructure Chemistry articles indexed and searchable Reduced number of searches to find data Data are integrated – compounds, vendors, syntheses, data, publications and patents A world of Open Access and Open Data
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- 71. Thank you [email_address]Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams