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ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences
 

ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences

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ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it ...

ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.

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    ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences Presentation Transcript

    • ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences
    • Chemistry on the Internet 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
    • Chemistry on the Internet 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
    •  
    •  
    • The Final Search Strategy
    • All Those Names, One Structure A problem to solve…
    • Chemistry on the Internet 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
    • Trustworthy Chemistry?
      • 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
    • Where Would You look? What Do You Trust?
    • Question Everything online: www.dhmo.org
    • Di-Hydrogen Monoxide
      • 2H
    • Di-Hydrogen Monoxide
      • 2H + 1O
    • Di-Hydrogen Monoxide
      • H2O
    • Di-Hydrogen Monoxide
      • H2O
      • Water
    • It’s all on Wikipedia…
    • Chemistry on The Internet Is Messy
    • It’s Methane…
    • What’s Methane?
    • What’s Methane?
    • What ELSE is Methane???
    • Drugs are REALLY Messy
    • Vancomycin
      • Who will curate?
      • How would you clean such a large dataset?
      • Assertions!!!
    • The EXPERTS must get it right?!
    • Wikipedia, C&E News, PubChem
      • C&E News (from ACS)
    • Feedback from C&E Senior Editor
      • “ Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access , strangely enough.”
      • “ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”
    • Structural Data for LifeSciences DailyMed
    • Lack of Stereochemisty
    • Incorrect Structures
    • Ugh…
    • Chemistry on the Internet 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
    • Just “Public Compound” Databases
      • PubChem
      • Drugbank
      • ChEBI/ChEMBL
      • KEGG
      • LipidMAPs
      • ChemIDPlus
      • eMolecules
      • ZINC
      • Lots of chemical vendors
      • ChemSpider
    • media.obsessable.com
      • As few interfaces as possible
      What do humans want?
    • A Pragmatic Vision
        • “ Build a Structure Centric Community to
        • Serve Chemists”
      • December 2006 – A hobby project initiated to connect chemistry on the web
        • 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
    • Answer Questions
      • 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 Ketoconazole?
        • What is the NMR spectrum of Aspirin?
        • What are the safety handling issues for Thymol Blue?
    • ChemSpider Searches
    • Search Cholesterol
    • Search Cholesterol
    • Search Cholesterol
    • Search Cholesterol
    • Search Cholesterol
    • A Link Farm to Content
    • Linked across the internet
    • Kyoto Encyclopedia of Genes and Genomes
    • Linking SMPDB
    • Links to Patents based on structure
    • Articles Linked
    •  
    • Search “OEA”
    • Search OEA
    • Search OEA
    • Search OEA
    • Linked Patents for OEA
    •  
    • Statistics for Today
        • >23 million compounds from >300 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
    • Searching Chemistry on the 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
    • The InChI Identifier
    • Multiple Layers
    • InChIStrings Hash to InChIKeys
    • Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog
    • Vancomycin – Search the Internet
    • Vancomycin Search Molecular SKELETON Search Full Molecule
    • Full Molecule Search: 4 Hits
    • Full Skeleton Search: 104 Hits
    •  
    •  
    •  
    • Vancomycin
    • Vancomycin on ChemSpider 1 compound – 3 days
    • InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now…
    • InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… is what???
    • The InChI “Resolver”
    • InChI Resolver to DOIs Structure Search the Web
    • Most Chemistry is NOT 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
    • The CAS Registry
    • CAS Registry
    • Crowd-sourcing Curation and Deposition
      • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
    • Multi-level Curation and Approval Building a Structure Centric Community for Chemists
    • Entity-Extraction, Mark-up, Annotate
    • Semantic Markup: Project Prospect
    • Success Depends on Dictionaries Link to a Structure or the Right Structure?
    • Name-Structure Pairs
    • Semantic Linking of Structures
      • What would you want to link off a structure?
        • Chemical suppliers
        • Other publications
        • Analytical Data
        • Related Reactions
        • Wikipedia
        • Patents
        • “ Everything”
    • Org Prep Daily (Blog)
    • ChemSpider SyntheticPages
    • Chemistry on the Internet 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
      • Classical business models will have to morph
    • ChemSpider Web Services
    •  
    • Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams