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ChemSpider SyntheticPages –
    the Benefits of Publishing
   Chemical Syntheses Online
If it was not just about me…
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
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
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
ChemSpider SyntheticPages
http://cssp.chemspider.com
ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online
ChemSpider SyntheticPages
Submission process
 Register as a user
 Use the Submit button and fill in the fields…
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.
Recent Submissions
Semantic Markup: Project Prospect
Entity-Extraction, Mark-up, Annotate
Success Depends on Dictionaries




 Link to a Structure or the Right Structure?
Name-Structure Pairs
Semantic Linking of Structures
 What would you want
  to link off a structure?
     Chemical suppliers
     Other publications
     Analytical Data
     Related Reactions
     Wikipedia
     Patents
     “Everything”
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
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?
I want to know about “Vincristine”
I want to know about “Vincristine”




                       If all algorithms work then
                       everything on the page is
                       correct by default except
                       the name!
Vincristine: Identifiers and Properties
Vincristine: Identifiers and Properties
Vincristine: Vendors and Sources
Vincristine: Patents
Vincristine: Articles
Searches: The INTERNET




All ChemSpider and Internet searches are “simply algorithms”
but synonym searching is based on an assertion
InChIs
Validated Names for Searching…
ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online
ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online
Interactive Data
ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online
Most Accessed
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
Popular Authors
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?
How will it improve?

          Participation
              and
          contribution
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
Social Networking Tools
 A growing number of social networking tools:

     Facebook
     Twitter
     Linked-In
     Flickr
     YouTube
     Blogs
     Communities
     Collaborative environments
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
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
The Alt-Metrics Manifesto
 http://altmetrics.org/manifesto/
Enabled by ORCID…
The Joint Responsibility of Authors
What is my ImpactStory?
ImpactStory
The Linked Network
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
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 http://tinyurl.com/9xnprqr
Feeding ELN Data into ChemSpider
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
Work in Progress – 300k Reactions
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
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
A model for data segregation




     Integrate to Institutional repositories
     Access to Theses and Dissertations
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
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
Benefits of Publishing
Chemical 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
Acknowledgments
   RSC|ChemSpider team
   CSSP Editorial Team
   All data source providers
   Curators and annotators
   Service providers:
     ACD/Labs
     OpenEye
     GGA Software Services
     Many others….
Thank you

Email: williamsa@rsc.org
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams

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ChemSpider SyntheticPages and the benefits of publishing chemical syntheses online

  • 1. ChemSpider SyntheticPages – the Benefits of Publishing Chemical Syntheses Online
  • 2. If it was not just about me…
  • 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. 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. 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
  • 9. Submission process  Register as a user  Use the Submit button and fill in the fields…
  • 10. 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.
  • 14. Success Depends on Dictionaries Link to a Structure or the Right Structure?
  • 16. Semantic Linking of Structures  What would you want to link off a structure?  Chemical suppliers  Other publications  Analytical Data  Related Reactions  Wikipedia  Patents  “Everything”
  • 17. 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
  • 18. 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?
  • 19. I want to know about “Vincristine”
  • 20. I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name!
  • 26. Searches: The INTERNET All ChemSpider and Internet searches are “simply algorithms” but synonym searching is based on an assertion
  • 28. Validated Names for Searching…
  • 34. 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
  • 36. 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?
  • 37. How will it improve? Participation and contribution
  • 38. 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
  • 39. Social Networking Tools  A growing number of social networking tools:  Facebook  Twitter  Linked-In  Flickr  YouTube  Blogs  Communities  Collaborative environments
  • 40. 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
  • 41. 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
  • 42. The Alt-Metrics Manifesto  http://altmetrics.org/manifesto/
  • 45. What is my ImpactStory?
  • 48. 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
  • 49. 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 http://tinyurl.com/9xnprqr
  • 50. Feeding ELN Data into ChemSpider
  • 51. 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
  • 52. Work in Progress – 300k Reactions
  • 53. 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
  • 54. 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
  • 55. A model for data segregation Integrate to Institutional repositories Access to Theses and Dissertations
  • 56. 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
  • 57. 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
  • 58. Benefits of Publishing Chemical 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
  • 59. Acknowledgments  RSC|ChemSpider team  CSSP Editorial Team  All data source providers  Curators and annotators  Service providers:  ACD/Labs  OpenEye  GGA Software Services  Many others….
  • 60. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams