RSC ChemSpider is the online chemistry database where community contributions coun
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RSC ChemSpider is the online chemistry database where community contributions coun

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The ChemSpider database is a resource hosted by the Royal Society of Chemistry. With over 28 million unique chemicals on the database linked out to over 400 data sources the platform provides......

The ChemSpider database is a resource hosted by the Royal Society of Chemistry. With over 28 million unique chemicals on the database linked out to over 400 data sources the platform provides access to experimental and predicted data (properties, spectra etc.), links to publications, patents and a myriad of other resources. The ChemSpider database has been used as the foundation of a number of other resources for chemists including ChemSpider SyntheticPages, the Learn Chemistry Wiki and the Spectral Game. This presentation will provide an overview of ChemSpider and discuss how chemists can both derive value from and contribute to the content available from the database and its related resources. We will also discuss our view of future platform for managing personal, institutional and public chemistry in a shared environment.

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  • 1. RSC|ChemSpider – The Online Chemistry Database WhereCommunity Contributions Count
  • 2. ChemSpider The RSC’s Online Chemical Database A central hub for chemists to source information  >28 million unique chemical records  Aggregated from >400 data sources  Chemicals, spectra, CIF files, movies, images, podcasts, links to patents, publications, predictions A central hub for chemists to deposit & curate data
  • 3. Answer Questions with ChemSpider 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?
  • 4. I want to know about “Vincristine”
  • 5. I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name!
  • 6. Vincristine: Identifiers and Properties
  • 7. Vincristine: Identifiers and Properties
  • 8. Vincristine: Vendors and Sources
  • 9. Vincristine: Patents
  • 10. Vincristine: Articles
  • 11. ChemSpider : Spectra Linked
  • 12. Spectra Linked
  • 13. Multiple Spectra for One Structure
  • 14. ChemSpider ID 24528095 H1 NMR
  • 15. ChemSpider ID 24528095 C13 NMR
  • 16. ChemSpider ID 24528095 HHCOSY
  • 17. ChemSpider ID 24528095 HSQC
  • 18. ChemSpider ID 24528095 HMBC
  • 19. About Structures
  • 20. The InChI Standard
  • 21. InChIKeysSearch the Web by Structure
  • 22. InChIs
  • 23. Searches: The INTERNETAll ChemSpider and Internet searches are “simply algorithms”but synonym searching is based on an assertion
  • 24. Validated Names for Searching…
  • 25. Scientists are measured by… Impact Citations Papers Patents Funding and increasingly by “Alt-Metrics” – what you say, what you contribute, your data depositions, your code in repositories, your voice in the network, your activities on Facebook (be careful!)
  • 26. If it was not just about me…
  • 27. If it was not just about me… We might have a community built encyclopedia I might know where the best restaurants are I might get good advice on books to read I might know which movies to watch I might know which plumber to call Data might just be Open
  • 28. If it was not just about me… We might have a community built encyclopedia I might know where the best restaurants are I might get good advice on books to read I might know which movies to watch I might know which plumber to call Data might just be Open
  • 29. The Social Network Career-wise NOT having a personal presence online will be a detriment  Self-marketing  Establishing a profile  Getting on the record  Collaborative Science  Demonstrating a skill set  Measured using alternative metrics  Contributing to the public peer review process
  • 30. Social Networking Tools A growing number of social networking tools:  Facebook  Twitter  Linked-In  Flickr  YouTube  Blogs  Communities  Collaborative environments
  • 31. Chemistry Social Networking Methods of sharing MY chemistry online include:  Wikis or blogs  Slideshare for presentations  YouTube for videos  Flickr, Wikimedia etc. for images  PubChem for assay data  NMRShiftDB for NMR assignments  GoogleDocs for data
  • 32. Your profile online…
  • 33. Establish a Mendeley Accounthttp://www.mendeley.com/profiles/antony-williams/
  • 34. ResearchGatehttp://www.researchgate.net/profile/Antony_Williams/
  • 35. Microsoft Academic Searchhttp://academic.research.microsoft.com/Author/12789419
  • 36. The Alt-Metrics Manifesto http://altmetrics.org/manifesto/
  • 37. What is my ImpactStory?
  • 38. ImpactStory
  • 39. Enabled by ORCID…
  • 40. The Linked Network
  • 41. There is much to be linked
  • 42. The World of Contribution Times have changed  Immediacy of social networks  Commenting on articles/data is here  The “participating scientist” has high profile  And who can be a scientist now???
  • 43. A Ten Year Old Scientist
  • 44. Share Science!!! Not Just Yourself If you have time, and the inclination, become a community contributor Share your expertise in the new world of openness  Share your Open Source code  Share your data and your model  Share your Figures  Contribute to Wikis – Wikipedia and others  Become an Open Notebook Scientist
  • 45. Expose Data and Figures on FigShare
  • 46. Expose Data and Figures on FigShare
  • 47. ChemSpider SyntheticPages Many syntheses are not published but are of value A database of synthesis procedures built for the community, by the community. Peer-reviewed by the community Each contribution DOI’ed. Develop online scientific reputation at a time of “micro-publications” Integrates semantic mark-up and visualization tools
  • 48. ChemSpider SyntheticPageshttp://cssp.chemspider.com
  • 49. ChemSpider SyntheticPages
  • 50. Submission process Register as a user Use the Submit button and fill in the fields…
  • 51. Submission Process Submissions reviewed by editorial board Published as is or comments sent to author Online Peer Review process – engage chemists in ongoing discussions and feedback loop Data supported include web movies, images, live spectra etc.
  • 52. Recent Submissions
  • 53. Interactive Data
  • 54. Most Accessed
  • 55. Is it working? Show of hands…  How many of you know ChemSpider?  How many of you know CSSP?  Have any of you submitted to CSSP? Low submissions but some dedicated authors
  • 56. Popular Authors
  • 57. Is it working? Show of hands…  How many of you know CSSP?  Have any of you submitted to CSSP? Low submissions but some dedicated authors What reasons are there you would not publish?  Time  Approval from supervisor  Need to keep the science quiet  Publishing on CSSP prevents future publishing?
  • 58. Contributing to The Quality of DataWhat is the Structure of Vitamin K?
  • 59. Contributing to The Quality of Data What is the Structure of Vitamin K?A lipid cofactor that is required for normal bloodclotting. Several forms of vitamin K have beenidentified: VITAMIN K1 (phytomenadione)derived from plants, VITAMIN K2(menaquinone) from bacteria & syntheticnaphthoquinone provitamins, VITAMIN K3(menadione).
  • 60. What is the Structure of Vitamin K1?
  • 61. CAS’s Common Chemistry
  • 62. Wikipedia
  • 63. Wolfram Alpha
  • 64. DailyMed
  • 65. People Use Trusted Resources…
  • 66. Quality police…
  • 67. How will it improve? Participation and contribution
  • 68. ALL Different, ALL “Domoic Acids”
  • 69. The EXPERTS must get it right?!
  • 70. Question Everything Online
  • 71. Deposition, Annotation andValidation ANYBODY can annotate a record on ChemSpider Registered users can deposit new data Registered users can validate existing data
  • 72. CURATION Search “Vitamin H”
  • 73. “Curate” Identifiers
  • 74. “Curate” Identifiers
  • 75. Spectra Linked
  • 76. Spectral Uploading Locate the structure of interest and deposit spectrum
  • 77. Spectral Uploading Various types of NMR spectra supported
  • 78. Regular Updates
  • 79. Web Services
  • 80. www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9
  • 81. Spectral Game
  • 82. Increasing Complexity
  • 83. SpectralGame in the hand
  • 84. Work in Progress – 300k Reactions
  • 85. Data Enabling the RSC Archive An archive going back to 1841. Project underway to “data enable” the archive:  Extract chemistry – chemicals, reactions, experimental data points, complex data  Semantic enriching of the articles for interactive viewing and crowdsourced annotation/curation  Dramatically enables the type of queries possible across the archive
  • 86. A model for data segregation Integrate to Institutional repositories Access to Theses and Dissertations
  • 87. Model Building with Community Data Community data can be the basis of model building  Consume data from available databases, RSC archive, new publications and build predictive algorithms for the community  Accept research data from the community and include into predictions
  • 88. An Open Data-Centric 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
  • 89. Wikipediahttp://en.wikipedia.org/wiki/Antony_John_Williams
  • 90. An Interesting Readhttp://tinyurl.com/7e3l6rz
  • 91. ScientistsDBhttp://tinyurl.com/7cqylsp
  • 92. ScientistsDB Write your OWN article about yourself on ScientistsDB It is a community-policed site so any comments you write might be challenged/edited. It is “your” page but edited by all An article, once approved by the community, can, in theory, be moved to Wikipedia All content is licensed under standard CC-BY-SA 3.0 licensing provided by Wikipedia
  • 93. Acknowledgments RSC|ChemSpider team CSSP Editorial Team All data source providers Curators and annotators Service providers:  ACD/Labs  OpenEye  GGA Software Services  Many others….
  • 94. Communicating Science As scientists one of our primary roles is contribution The internet enables contribution in different ways, benefitting the scientist and the community Share your data and experience – it can enhance your public profile as a scientist, make you more discoverable and contribute data to the community AltMetrics will be a measure of scientists…
  • 95. Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams