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ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online


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The ChemSpider database is a free online resource containing information for over 28 million unique chemicals. The platform has been used as the foundation of a number of other resources including ChemSpider SyntheticPages (CSSP), an online “micro-publishing” site serving chemists interested in chemical syntheses. Synthetic chemists are encouraged to publish the details of their experiments in order to communicate the details of their work. Using a template-based entry form, multimedia support including interactive display of spectral data, CSSP provides an environment for students to develop their writing skills in terms of reporting science. The articles are reviewed by the CSSP editorial board, made up of university professors, as well as then being peer-reviewed by the incorporation of public commentary. Each micro-publication includes a digital object identifier (DOI) making the CSSP contribution a citable object on a CV. This presentation will provide an overview of the ChemSpider SyntheticPages platform and demonstrate how chemists can actively expose their work to the community-at-large and can use the ChemSpider platform to access data that could be of value in everyday lab work. We will also discuss our view of a future platform for managing personal, institutional and public chemistry in a shared environment.

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ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online

  1. 1. ChemSpider SyntheticPages – the Benefits of Publishing Chemical Syntheses Online
  2. 2. If it was not just about me…
  3. 3. 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
  4. 4. 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
  5. 5. 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
  6. 6. ChemSpider SyntheticPages
  7. 7. ChemSpider SyntheticPages
  8. 8. Submission process Register as a user Use the Submit button and fill in the fields…
  9. 9. 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.
  10. 10. Recent Submissions
  11. 11. Semantic Markup: Project Prospect
  12. 12. Entity-Extraction, Mark-up, Annotate
  13. 13. Success Depends on Dictionaries Link to a Structure or the Right Structure?
  14. 14. Name-Structure Pairs
  15. 15. Semantic Linking of Structures What would you want to link off a structure?  Chemical suppliers  Other publications  Analytical Data  Related Reactions  Wikipedia  Patents  “Everything”
  16. 16. ChemSpider The Free 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
  17. 17. 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?
  18. 18. I want to know about “Vincristine”
  19. 19. I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name!
  20. 20. Vincristine: Identifiers and Properties
  21. 21. Vincristine: Identifiers and Properties
  22. 22. Vincristine: Vendors and Sources
  23. 23. Vincristine: Patents
  24. 24. Vincristine: Articles
  25. 25. Searches: The INTERNETAll ChemSpider and Internet searches are “simply algorithms”but synonym searching is based on an assertion
  26. 26. InChIs
  27. 27. Validated Names for Searching…
  28. 28. Interactive Data
  29. 29. Most Accessed
  30. 30. 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
  31. 31. Popular Authors
  32. 32. 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?
  33. 33. How will it improve? Participation and contribution
  34. 34. 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
  35. 35. Social Networking Tools A growing number of social networking tools:  Facebook  Twitter  Linked-In  Flickr  YouTube  Blogs  Communities  Collaborative environments
  36. 36. 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
  37. 37. Drivers in the Social Network Anonymity is a choice in the social networks Anonymity in peer-review will likely become less important and may be generational I may want acknowledgment if…  I share my data  I review a paper  I share my expertise
  38. 38. The Alt-Metrics Manifesto
  39. 39. Enabled by ORCID…
  40. 40. The Joint Responsibility of Authors
  41. 41. What is my ImpactStory?
  42. 42. ImpactStory
  43. 43. The Linked Network
  44. 44. Imperial College Data repository activities initiated with Imperial  Storage of research data from electronic lab notebook  Chemicals  Reactions  Analytical data – spectra  Experimental data points  Open Data with CC licenses of NC-SA
  45. 45. Feeding ELN Data into ChemSpider Integrate e-Notebooks into ChemSpider  IDBS e-Workbook plug-in allows direct deposition of chemical structures  Can be extended to more ELN content  Spectra  Reactions  Properties etc.  Integration Video
  46. 46. Feeding ELN Data into ChemSpider
  47. 47. What is already in testing… ChemSpider Google  Searching Google Scholar, Google Books and Google Patents by chemical structure ChemSpider reactions – alpha version  300,000 reactions extracted from US patents  ChemSpider SyntheticPages container  Container for future RSC Archive reactions  Accepting Electronic Lab Notebook depositions  Successful AND Failed Reactions
  48. 48. Work in Progress – 300k Reactions
  49. 49. 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
  50. 50. EPSRC National Chemical Database RSC is preferred bidder for the EPSRC national chemical database tender – presently completing legal documentation etc. Will deliver federated access to a series of commercial databases plus data repository – personal, group and institutional Citable data objects for papers, supplementary info, non-published work
  51. 51. A model for data segregation Integrate to Institutional repositories Access to Theses and Dissertations
  52. 52. 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
  53. 53. 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
  54. 54. Benefits of PublishingChemical Syntheses Online Not all syntheses will be “published” Publishing is changing and has many forms Online exposure develops reputation, benefits the community, engages discussion and collaboration. Peer review in the open. CSSP offers a platform for exposure, linking to ChemSpider, interactive visualization and is a feed to ChemSpider reactions ELNs are a natural feed to the CSSP micro- publishing platform
  55. 55. Acknowledgments RSC|ChemSpider team CSSP Editorial Team All data source providers Curators and annotators Service providers:  ACD/Labs  OpenEye  GGA Software Services  Many others….
  56. 56. Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: