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.
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
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.
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?
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
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
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
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….