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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 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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RSC|ChemSpider – The Online Chemistry Database Where
Community Contributions Count
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
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
ChemSpider : Spectra Linked
Spectra Linked
Multiple Spectra for One Structure
ChemSpider ID 24528095 H1 NMR
ChemSpider ID 24528095 C13 NMR
ChemSpider ID 24528095 HHCOSY
ChemSpider ID 24528095 HSQC
ChemSpider ID 24528095 HMBC
About Structures
The InChI Standard
InChIKeysSearch the Web by Structure
InChIs
Searches: The INTERNET
All ChemSpider and Internet searches are “simply algorithms” but synonym searching is based on an assertion
Validated Names for Searching…
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!)
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
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
Your profile online…
Establish a Mendeley Accounthttp://www.mendeley.com/profiles/antony-williams/
ResearchGatehttp://www.researchgate.net/profile/Antony_Williams/
Microsoft Academic Searchhttp://academic.research.microsoft.com/Author/12789419
The Alt-Metrics Manifesto
http://altmetrics.org/manifesto/
What is my ImpactStory?
ImpactStory
Enabled by ORCID…
The Linked Network
There is much to be linked
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???
The World of Contribution
A Ten Year Old Scientist
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
Expose Data and Figures on FigShare
Expose Data and Figures on FigShare
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
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
Interactive Data
Most Accessed
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
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?
Contributing to The Quality of DataWhat is the Structure of Vitamin K?
Contributing to The Quality of DataWhat is the Structure of Vitamin K?
A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K1 (phytomenadione) derived from plants, VITAMIN K2 (menaquinone) from bacteria & synthetic naphthoquinone provitamins, VITAMIN K3 (menadione).
What is the Structure of Vitamin K1?
CAS’s Common Chemistry
Wikipedia
Wolfram Alpha
DailyMed
People Use Trusted Resources…
Quality police…
How will it improve?
Participation and
contribution
ALL Different, ALL “Domoic Acids”
The EXPERTS must get it right?!
Question Everything Online
ANYBODY can annotate a record on ChemSpider
Registered users can deposit new data
Registered users can validate existing data
Deposition, Annotation and Validation
CURATION Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
Spectra Linked
Spectral Uploading
Locate the structure of interest and deposit spectrum
Spectral Uploading Various types of NMR spectra supported
Regular Updates
Web Services
www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9
Spectral Game
Increasing Complexity
SpectralGame in the hand
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
A model for data segregation
Integrate to Institutional repositoriesAccess 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
Internet Data
An Open Data-Centric Chemistry Hub
Commercial SoftwarePre-competitive Data
Open ScienceOpen DataPublishersEducators
Open DatabasesChemical Vendors
Small organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks to Biologicals
Wikipediahttp://en.wikipedia.org/wiki/Antony_John_Williams
An Interesting Readhttp://tinyurl.com/7e3l6rz
ScientistsDBhttp://tinyurl.com/7cqylsp
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
Acknowledgments
RSC|ChemSpider team CSSP Editorial Team All data source providers Curators and annotators Service providers:
ACD/Labs OpenEye GGA Software Services Many others….
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…
Thank you
Email: [email protected] Twitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams
