Connecting Chemistry Across the Internet Using ChemSpider
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Connecting Chemistry Across the Internet Using ChemSpider

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Connecting Chemistry Across the Internet Using ChemSpider Connecting Chemistry Across the Internet Using ChemSpider Presentation Transcript

  • Connecting Chemistry Across the Internet Using ChemSpider Antony J Williams and Valery Tkachenko SERMACS, November 15th 2012
  • Chemistry Data and the Weeds
  • Tell me about Roundup
  • So what is Round Up?
  • The World’s Encyclopedia
  • Roundup
  • Where do we Round Up data? Where can I find the molfile for Roundup? Papers/Patents about Roundup? What are the side effects of Roundup? Where can I order Roundup? What are the physicochemical properties? Metabolic pathways? Different synonyms of Roundup? Synthesis of Roundup? Side effects of Roundup? Etc….
  • Where do I Round Up Data?
  • In an increasing LinkedData map….
  • But I want to aggregate data? So…
  • ChemSpider Takes on the role of a structure centric hub:  Connecting, validating, qualifying data  Enhancing data with connections to services  Provides access to data and services for others to use (Thermo, Agilent, Bruker, Waters, ACD/Labs, Accelrys, etc.)  Uses available services to integrate, connect and enhance the offering
  • Roundup on ChemSpider
  • What will ChemSpider give us??
  • What will ChemSpider give us??
  • What will ChemSpider give us??
  • What will ChemSpider give us??
  • What will ChemSpider give us??
  • What will ChemSpider give us??
  • ChemSpider is Collapsing Data???
  • What will ChemSpider give us??
  • For Glyphosate itself
  • How did we build it? We deal in Molfiles or SDF files – with coordinates Deposit anything that has an InChI – we support what InChI can handle, good and bad Standardization based on “InChI standardization” InChIs aggregate (certain) tautomers How much of ChemSpider is “on ChemSpider”?
  • Connecting Chemistry across the web So much of what is seen on ChemSpider is retrieved in real time using services
  • Connecting Chemistry across the web
  • Online Predictions
  • A Comment on Quality For >28 million chemical compounds there are some errors:  “Incorrect” structure representations  Mismatched name-structure relationships  Experimental properties (the values, the units)  Real vs. virtual compounds – text-mining and conversion  We have deprecated a LOT of data…
  • Downsides of InChI Good for small molecules – but no polymers, issues with inorganics, organometallics, imperfect stereochemistry. ChemSpider is “small molecules” InChI used as the “deduplicator” – FIRST version of a compound into the database becomes THE structure to deduplicate against…
  • Side Effects of InChI Usage
  • SMILES by comparison…
  • Side Effects of InChI Usage
  • Standardization IssuesDepiction based on molfile
  • Downsides of Overall Approach Meshing data together based on InChIs worked for simple molecules 2D layout errors inherited or limited by algorithm Complex molecules that are meant to be the same thing were NOT deduplicated. Compounds differing by one stereocenter, named the same, meant to be the same, are not the same
  • So much data online is “erroneous”
  • The confusion of name-structures
  • Collapsing Data – Standardization
  • What needs to happen? If we could validate  Catch errors in databases (and clean)  Proactively catch errors in publications/patents  Reduce junk in the ether – improve QUALITY! If we collectively standardized  Interlinking between databases should improve  CVSP – a separate presentation….stick around
  • Crowdsourcing ChemSpider ChemSpider is crowdsourced Community deposition, annotation and curation Anyone can “Leave Feedback” Registered users can add data
  • ChemSpider and Global Chemistry Hub Internet Data Small organic molecules Commercial Software Undefined materials Pre-competitive Data Organometallics Open Science Nanomaterials Open Data Polymers Publishers Minerals Educators Particle bound Open Databases Links to Biologicals Chemical Vendors
  • Delivering a Prediction Platform Experimental data will be used as the basis of model generation – a predictive platform…
  • The Future of ChemSpider Continued focus on quality over quantity – but more data is good too! ChemSpider Reactions – work in progress and includes >300,000 reactions Plugging in a validation and standardization platform Delivering personal and institutional repository capabilities
  • Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams