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Building global chemistry network at the royal society of chemistry
 

Building global chemistry network at the royal society of chemistry

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The Royal Society of Chemistry is building a Global Chemistry Network which will connect chemical resources and chemists across the globe in a single scientific information network dynamically updated ...

The Royal Society of Chemistry is building a Global Chemistry Network which will connect chemical resources and chemists across the globe in a single scientific information network dynamically updated in real time. We have been working on a number of the foundation technologies for a number of years including a structure database containing almost 30 million chemicals, a micropublishing environment, a platform for the validation and standardization of chemical structure representations and a text-mining and semantic markup platform for data enabling our published articles. Our goal is to provide seamless tools for researchers, librarians, publishers, informational technology specialists and government agencies to facilitate scientific research by providing a free flow of information. This talk will review our work to date to provide a chemistry data platform for the community and will highlight some of the challenges we face as we expand the architecture for our Global Chemistry Network platform.

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    Building global chemistry network at the royal society of chemistry Building global chemistry network at the royal society of chemistry Presentation Transcript

    • Building Global Chemistry Network at the Royal Society of Chemistry Valery Tkachenko ICSTI Workshop Data and Non-Data Integration – A Journey Across Disciplines Ottawa, October 16th 2013
    • The World we live in Internet World 20+ years into the Internet Revolution Web 2.0 -> Web 3.0 Connected World Social Networks Real-time Communications Big Data World Semantic content New Interfaces
    • Big Data challenge RSC/ChemSpider platforms Crowdsourcing and AltMetrics New interfaces Building Global Chemistry Network
    • Science map
    • Chemistry on the Internet
    • Why disproportion? Scientific complexity Conservative nature
    • Big Data challenge RSC/ChemSpider platforms Crowdsourcing and AltMetrics New interfaces Building Global Chemistry Network
    • Royal Society of Chemistry (RSC) Largest European organisation for advancing the chemical sciences Founded 1841 Not-for profit “To be the leading voice and trusted partner for science and humanity” Professional body with a worldwide network of 48,000 members International publisher ~400 employees Education facilitator, Science leader, E-Science leaders
    • About the RSC • Headquarters in London • Offices in Cambridge, Beijing, Shanghai, Philadelphia, Tokyo Bangalore, Sao Paulo
    • STM publisher Knowledge Delivery Magic Our User Interfaces (Desktop, Web, Mobile, etc) Customers 3rd party integrations (our web services)
    • ChemSpider Suite UIs ChemSpider Reactions mobile web app ChemSpider website ChemSpider desktop app Depositions client Components Layer Java Beans JS Components Python widgets ASP.NET Components PHP snippets Google Apps Components SharePoint Components APIs Layer Search API CSC API Export API CSR API DS API Processing API CSS API CSM API CSA API CSAs API CSR BO CSS BO CSM BO CSA BO CSAs BO ChemSpider Reactions ChemSpider Spectra ChemSpider Materials ChemSpider Algorithms ChemSpider Assays Business Objects Layer CSC BO Data Layer ChemSpider Compounds
    • • • • • 29 million chemicals and growing Data sourced from >500 different sources Crowdsourced curation and annotation Ongoing deposition of data from our journals and our collaborators • A structure centric hub for web-searching
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider
    • ChemSpider Reactions
    • ChemSpider Reactions
    • ChemSpider Reactions
    • ChemSpider Reactions
    • RSC Archive – since 1841
    • DERA Digitally Enabling RSC Archive
    • Semantic Mark-up of Articles
    • It is so difficult to navigate… IP? IP? What’s the What’s the structure? structure? Are they in Are they in our file? our file? What’s What’s similar? similar? Pharmacology Pharmacology data? data? What’s the What’s the target? target? Known Known Pathways? Pathways? Competitors? Competitors? Connections Connections to disease? to disease? Working On Working On Now? Now? Expressed in Expressed in right cell type? right cell type?
    • DERA Architecture Structures Reactions DERA (Text Mining) Text, PDF, XML Chemistry Validation and Standardization Platform (CVSP) Spectra Materials Biological Activities
    • Data quality issue and CVSP Robochemistry Proliferation of errors in public and private databases Automated quality control system
    • DrugBank dataset (6516 records) ~60 records that can’t be dearomatized unambiguously DB04283 DB04462
    • ~30 records with bonds that do not make sense DB04283 DDB04009
    • 7 records with 2 stereo bonds at chiral atoms J. Brechner, IUPAC Graphical Representation of stereochem. configurations Section: ST-1.1.10 DB08128 DB06287
    • “Direction of bond makes no sense” – 63%
    • “Stereo types of non-opposite bonds match” – 2%
    • ChemSpider Suite UIs ChemSpider Reactions mobile web app ChemSpider website ChemSpider desktop app Depositions client Components Layer Java Beans JS Components Python widgets ASP.NET Components PHP snippets Google Apps Components SharePoint Components APIs Layer Search API CSC API Export API CSR API DS API Processing API CSS API CSM API CSA API CSAs API CSR BO CSS BO CSM BO CSA BO CSAs BO ChemSpider Reactions ChemSpider Spectra ChemSpider Materials ChemSpider Algorithms ChemSpider Assays Business Objects Layer CSC BO Data Layer ChemSpider Compounds
    • Big Data challenge RSC/ChemSpider platforms Crowdsourcing and AltMetrics New interfaces Building Global Chemistry Network
    • AltMetrics
    • Plum Analytics
    • RSC/Rewards and Recognition The First Step badge is awarded when a user submits (& has published) their 1st CSSP article. Congratulations! Your 1st CSSP article has been published. Philosopher Lao Tzu said “A journey of a thousand miles begins with a single step”. In the same way we hope that this will be the first of many submissions that you make to CSSP.
    • Big Data challenge RSC/ChemSpider platforms Crowdsourcing and AltMetrics New interfaces Building Global Chemistry Network
    • Visualization
    • Navigation
    • ChemSpider APIs
    • Big Data challenge RSC/ChemSpider platforms Crowdsourcing and AltMetrics New interfaces Building Global Chemistry Network
    • We are a part of a larger world
    • National Chemistry Database
    • National Data Repository Scientists Funding bodies External clients Publishers Indexes Data Repository indexed storage Chemically intelligent services Data Data Repository provided data storage University 1 University 2 Data Hub Workstations Company 3 Data Hub Workstations Data Hub Workstations
    • http://www.openphacts.org Open PHACTS is an Innovative Medicines Initiative (IMI) project, aiming to reduce the barriers to drug discovery in industry, academia and for small businesses. Semantic web is one of the corner stones
    • We know about Natural Products
    • Marinlit
    • OSDD
    • The Future Internet Data Small organic molecules Undefined materials Organometallics Nanomaterials Polymers Minerals Particle bound Links to Biologicals Commercial Software Pre-competitive Data Open Science Open Data Publishers Educators Open Databases Chemical Vendors
    • Thank you Email: tkachenkov@rsc.org Slides: http://www.slideshare.net/valerytkachenko16