ChemSpider Overview SLides August 2007
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ChemSpider Overview SLides August 2007

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ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and ...

ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.

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    ChemSpider Overview SLides August 2007 ChemSpider Overview SLides August 2007 Presentation Transcript

    • An Introduction to ChemSpider Antony Williams
    • The ChemSpider Mission ChemSpider intends to build a structure centric community for chemists by: Providing an environment for chemical structure drawing, manipulation, visualization, modeling & databasing Providing methods by which to deposit, curate and enhance data associated with chemical structures Providing structure-based access to federated Chemistry databases representing chemical vendors, literature, online data, patents and other forms of Chemistry data Building a Structure Centric Community for Chemists
    • Every Journey Starts with a Single Step March 2007 ChemSpider Beta opened to the public for exposure at the Spring ACS (March 2007) Initial database exposed only PubChem Data as a proof of concept (10.5 Million compounds) Structure/substructure searching available Online prediction services available Accompanying Spinneret Blog released Building a Structure Centric Community for Chemists
    • Execution of the Mission August 2007 An online database of over 16.5 million structures Systems in place for: Single structure and data collection depositions Association of analytical data with structures Ability to curate data for each individual record Indexing of and Integration to: Over 70 individual databases Patents from the US, European and Asian Patent offices Text-based searching of over 50,000 Open Access articles Over a thousand unique users access ChemSpider per day Building a Structure Centric Community for Chemists
    • Search Text “Prozac” Building a Structure Centric Community for Chemists
    • Predicted Properties Details “Prozac” Building a Structure Centric Community for Chemists
    • Flexible Boolean Searching Building a Structure Centric Community for Chemists
    • Integrated Searching from Online Applet or Desktop Drawing Packages Building a Structure Centric Community for Chemists
    • Integrated Structure/Substructure and Property Searches Building a Structure Centric Community for Chemists
    • Search result: 49 hits in 2.8 seconds Building a Structure Centric Community for Chemists
    • Integrated Visualization Tools Building a Structure Centric Community for Chemists
    • Integrated Analytical Data Management for Public Domain Data Building a Structure Centric Community for Chemists
    • Integrated Prediction Engines Input a chemical structure and predict the properties in real time using server- based transactions. Predictions furnished by ACD/Labs at present. Building a Structure Centric Community for Chemists
    • Integrated Access to Open Access Literature Text-based searching of over 50,000 Open Access Chemistry Articles Building a Structure Centric Community for Chemists
    • External Integrations - Wikipedia The links between Wikipedia and ChemSpider are formed automatically Building a Structure Centric Community for Chemists
    • External Integrations - Google Search Across Google Using InChI string Building a Structure Centric Community for Chemists
    • External Integrations – Patents Reel Two Surechem Portal Building a Structure Centric Community for Chemists
    • External Integrations – Plug-ins Building a Structure Centric Community for Chemists
    • How do people generally use ChemSpider? Searching for chemical structures, in rank order, via: Registry numbers, trade names and synonyms. Structure identifiers such as SMILES or InChI Intrinsic properties: commonly mass-based searches executed by mass spectrometrists Systematic names: IUPAC or CAS Index name Generation of physicochemical properties Text-based searching of Open Access articles Structure-based searching of Patents Building a Structure Centric Community for Chemists
    • Some Initial Feedback “I must say that this site is excellent because it is the only place I can drop the name of a published molecule like a bile acid or steroid metabolite and actually get a hit.” Department of Animal Sciences, University of Wisconsin-Madison “I saw the ChemSpider release today - looks like an awesome service!” Stanford University “We encourage our students to use the chemspider services for looking up chemical structures and their properties. My collaborators use it to find company information. Your services are very valuable for us.” Faculty of Pharmaceutical Sciences, University of Leuven (Belgium) Building a Structure Centric Community for Chemists
    • Curators - An Active Community Building a Structure Centric Community for Chemists
    • The ChemSpider Platform ChemSpider is developed using a series of components and programming languages. The core is C/C++ The database engine is Microsoft SQL Server Web interface is ASP.NET and C# Server-side scripting is Perl. ChemSpider is hosted on x86 PCs on Windows 2003 Server Building a Structure Centric Community for Chemists
    • The ChemSpider Platform Building a Structure Centric Community for Chemists
    • ChemSpider – The Entity The team consists of five people including 3 developers The team has almost 40 years of experience in developing modern cheminformatics software applications for the desktop and the enterprise ChemSpider has been built in off-hours only and with personal funding ChemSpider has an active Advisory Group Building a Structure Centric Community for Chemists
    • The Advisory Group The Advisory Group has been built from industry experts in the fields of: Pharmaceutical sciences Analytical Sciences Academia and Public Chemistry Efforts Forensic Sciences Open Standards Open Source/Open Access Spectroscopy Software Development Chemistry Databases Natural Products Chemical Informatics and Statistics Media, web skills and public relations Building a Structure Centric Community for Chemists
    • Targets for 2007 End of year intentions for ChemSpider include Adding more databases to the index to expand database to 20 million unique structures Enhance integrations to other structure drawing packages Include additional property prediction algorithms as provided Extend integrations to synergistic software offerings Expand the Public Domain analytical data handling Enhance the Patent integration Expand the Open Access article index to >100,000 articles Building a Structure Centric Community for Chemists
    • ChemSpider in the Landscape Common questions include: How does ChemSpider compare with PubChem? Is ChemSpider a competitor to eMolecules? PubChem and CAS collided. Do ChemSpider and CAS collide? Building a Structure Centric Community for Chemists
    • ChemSpider and PubChem Pubchem was built to support the National Screening Libraries Initiative. The system is delivering very well on managing and providing access to associated data ChemSpider HAS taken advantage of the PubChem data sets – PubChem data is only a subset of ChemSpider Aspects of PubChem’s approach to manage and display structure data are worth emulating – so ChemSpider does ChemSpider is in the process of curating data and submitting back to PubChem ChemSpider will make submissions to the PubChem dataset and provide input, guidance and feedback The relationship is synergistic Building a Structure Centric Community for Chemists
    • ChemSpider and eMolecules ChemSpider and eMolecules are similar efforts to deliver access to structure-related information Both groups are developing new cheminformatic technologies to facilitate their systems ChemSpider is actively delivering on a wiki-like environment for expansion and curation of the database Building a Structure Centric Community for Chemists
    • ChemSpider and CAS CAS is the gold standard in many domains – the Registry is a highly curated and controlled assembly of chemical structures and related information connected to publications, patents and vendors. ChemSpider is primarily an algorithmically curated database with manual curation enabled. ChemSpider is a system facilitating the deposition and association of chemical structures and related information including, but not limited to public and commercial databases, chemical vendor catalogs, patents and individual chemists CAS is not yet concerned with providing capabilities to manage chemistry depositions submitted by individual scientists, research groups, with the management of analytical data and the provision of APIs to provide integration to other Open Access systems Building a Structure Centric Community for Chemists
    • Conclusion ChemSpider is successfully building a structure centric community for chemists Over 1000 chemists per day utilize ChemSpider to help answer questions and solve their problems A well-defined path forward to enhance the service has been defined Building a Structure Centric Community for Chemists
    • Acknowledgments Thousands of users for their feedback and ongoing encouragement The “naysayers” – criticism, when taken constructively, can drive creative actions Our advisory group of scientists, specialists and friends The bloggers coming to the ChemSpider Blog and ChemSpider News Building a Structure Centric Community for Chemists