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eScience at the Royal Society of Chemistry and our current initiatives
 

eScience at the Royal Society of Chemistry and our current initiatives

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Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and ...

Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this eScience cheminformatics platform and the nature of the solutions that it helps to enable including structure validation, text mining and semantic markup, the National Chemical Database Service for the United Kingdom and the development of a chemistry data repository. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.

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    eScience at the Royal Society of Chemistry and our current initiatives eScience at the Royal Society of Chemistry and our current initiatives Presentation Transcript

    • eScience at the Royal Society ofChemistry: Current InitiativesAntony WilliamsCornell University, May 14th2013
    • We Have …Too Much Data!!!
    • The World of Online Chemistry• Property databases• Compound aggregators• Screening assay results• Scientific publications• Encyclopedic articles (Wikipedia)• Metabolic pathway databases• ADME/Tox data – eTOX for example• Blogs/Wikis and Open Notebook Science
    • e-Science and Primary Data• How much data generated in a lab, that COULD go public, islost forever?
    • e-Science and Primary Data• How much data generated in a lab, that COULD go public, islost forever?• Public Domain reference databases of value?– Syntheses– Properties– Spectra– CIFs– Images
    • e-Science and Primary Data• How much data generated in a lab, that COULD go public, islost forever?• Public Domain reference databases of value?– Syntheses– Properties– Spectra– CIFs– Images• Much of chemistry is chemical structure-based – where andhow could we host these data?
    • RSC’s ChemSpider
    • ChemSpider• >28.5 million unique chemicals from >400data sources• Focus on improving data quality, enhancingfunctionality, integrating and enabling
    • Crowdsourced “Annotations”• Users can add– Descriptions/Syntheses/Commentaries– Links to PubMed articles– Links to articles via DOIs– Add spectral data– Add Crystallographic Information Files– Add photos– Add MP3 files– Add Videos
    • Spectra
    • Chemistry Data online are messy• We have inherited errors• All public compound databases have errors• “Incorrect” structures – assertions, timelines etc• “Incorrect” names associated with structures• Properties• Links• Publications• ENORMOUS CHALLENGE
    • Crowdsourced Curation• Crowd-sourced curation: identify/tag errors,edit names, synonyms, identify records todeprecate
    • Search “Vitamin H”
    • “Curate” Identifiers
    • “Curate” Identifiers
    • “Curate” Identifiers
    • Validated Name-Structure Dictionaries• Chemical name dictionaries are used for:• Text-mining (publications, patents)– Used to index PubMed and link to Google Patents• Linking to other databases – think Biology!– When structures are not available drug names link• Searching the web– Names link to structures link to InChIs
    • I want to know about “Vincristine”
    • Vincristine: Identifiers andProperties
    • Vincristine: Vendors and SourcesLinked by Structure
    • Vincristine: PatentsLinked by Name
    • Vincristine: ArticlesLinked by Name
    • Semantic Mark-up of Articles
    • Linking Names to Structures
    • The InChI Identifier
    • InChIStrings Hash to InChIKeys
    • Vancomycin – Search the Internet
    • VancomycinSearch MolecularSKELETONSearch Full Molecule
    • Full Skeleton Search: 104 Hits
    • Full Molecule Search: 4 Hits
    • ChemSpider Resources for Chemistry
    • Some usage statistics• ca. 200 visitors at any one time, ~30,000 visits per day• Mar 4-Apr 3, 2013– Visits = 731,656– Unique Visitors = 527,008• Independent servers to support other projects
    • Access ChemSpider• APIs– Programmatic access used by Mobile Apps, FundedConsortia projects, many Academic groups• Widgets– UI components for embedding in other websites• Data– Data access, downloads, reuse, licensing
    • Flexible ChemSpider APIhttp://www.chemspider.com/google/
    • Flexible ChemSpider API
    • Publications - a summary of work• Scientific publications are a summary of work– Is all work reported?– How much science is lost to pruning?– What of value sits in notebooks and is lost?• How much data is lost?– How many compounds never reported?– How many syntheses fail or succeed?– How many characterization measurements?
    • Micropublishing Syntheses
    • ChemSpider SyntheticPages
    • Olympicene
    • So you Want a Profile???
    • Interactive Data
    • Integrate to instruments and software• Integration to analytical instrumentation vendorsalready in place– Agilent, Bruker, Thermo, Waters• Also, Cheminformatics vendors link to ChemSpider– Accelrys, ACD/Labs, ChemAxon, iChemLabs, and…
    • PharmaSea• Dereplication via ChemSpider• Segregation of natural products datasets• Analytical data algorithms & integration– Mass spec searching – predicted fragmentation– NMR feature searching – NMR prediction– Computer-assisted structure elucidation
    • It is so difficult to navigate…What’s thestructure?What’s thestructure?Are they inour file?Are they inour file?What’ssimilar?What’ssimilar?What’s thetarget?What’s thetarget?Pharmacologydata?Pharmacologydata?KnownPathways?KnownPathways?Working OnNow?Working OnNow?Connections todisease?Connections todisease?Expressed inright cell type?Expressed inright cell type?Competitors?Competitors?IP?IP?
    • • 3-year Innovative Medicines Initiative project• Integrating chemistry and biology data using semanticweb technologies• Open source code, open data and open standards• Academics, Pharma companies, Publishers….
    • ChemSpider Contributions• The host of the chemistry services– Supplier of “standardized” chemical data files– Chemistry searching (structure, substructure etc)– Curator and data quality checking• Now building the Open PHACTS chemicalregistration system
    • Natural Products Updates• Names hard, Structures“Obvious”• New content based onmonthly updates of thedatabase• Click through to the NaturalProducts Updates entry
    • National Chemical Database Service
    • Chemical DatabaseService• National Chemical Database Servicefor UK Academics• Integrating Commercial Databasesand Services• Chemicals, analytical data,prediction algorithms• Development of data repository
    • Community Repository for Data• Funding agencies encourage sharing of data• Increasing availability of “Open Data”• Institutional repositories no specific domainsupport• Develop a community repository for chemistrydata – private, public, embargoed• Provides data to develop models/algorithms
    • Community Repository for Data• Automated depositions of data• DOI’ed data objects for citation purposes• A database of reference data, but validated bythe community• National services feeding the repository –crystallography, mass spectrometry• Integrate to blogging tools for chemistry• Integrate to Electronic Lab Notebooks as feeds
    • Model Building with Community Data• Community data as a basis of model building– Consume data from available databases, communitydata, new publications and build predictivealgorithms for the community– How many algorithms are reported and lost? Howmuch repeat work is done in the domain ofalgorithmic development?
    • Support for Chemical Reactions• Integrating mined reaction data from patents• Will also incorporate and integrate RSCDatabases: Methods of Organic Synthesis,Catalysts and Catalyzed Reactions and…
    • Inside our Publication Archive• How much data is in the archive, in thepublications and in the supplementary info?– How many compounds for ChemSpider?– How many syntheses for ChemSpider reactions?– How many characterization measurements?• Property Data• Spectral Data• Graphs and charts to be used for modeling?
    • What if we could capture it all?Digitally Enhancing the RSC Archive
    • Start with data in publications
    • Data Validation and Curation RequiredEncouraging Participation withRewards and RECOGNITION
    • Manual Curation• Integrated commenting, curating and validationplatform across ALL eScience and publishingplatforms• All integrated to a central RSC profile andfeeding the AltMetrics tools
    • Structure Review
    • Future Recognition in AltMetrics?ChemSpider
    • Internet DataThe FutureCommercial SoftwarePre-competitive DataOpen ScienceOpen DataPublishersEducatorsOpen DatabasesChemical VendorsSmall organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks to Biologicals
    • The Future of Chemistry on the Web?• Public compound databases federate & build alinked environment of validated data!• Data validation needs are not ignored• Publishers layer on information to makepublications discoverable• Open Data proliferate• The “Semantic Web” will continue to develop…
    • Thank youEmail: williamsa@rsc.orgTwitter: @ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams