Chemspider hosting linking and curating chemistry data for the community

ChemSpider – Hosting, Linking and Curating Chemistry Data for the Community Valery Tkachenko SLA Meeting, June 2011

Chemistry on the Internet
100s of websites hosting chemistry-related data
Chemistry information is generally “compound-based”
Chemical “structures”
Identifiers, names and synonyms
Properties
Analytical data
How to synthesize
Articles, patents, safety information
Chemistry “language and dialects”

Dialects describing chemicals

A Pragmatic Vision
“ Build a Structure Centric Community”
Integrate chemistry across the internet based on “chemical structure”
A “structure-based hub” to information and data
Let chemists contribute their own data
Allow the community to curate & annotate data

www.chemspider.com

Answering Questions for Chemists
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 Aspirin?
What is the NMR spectrum of Benzoic Acid?
What are the safety handling issues for toluene?

Search for a Chemical…by name

Available Information…
Linked to chemical vendors, safety data, toxicity, metabolism…

Available Information….

ChemSpider Today
Over 26 million unique chemicals
Over 420 data sources
Grows daily – community and RSC depositions
Community annotation and curation
We curate, edit, change, enhance data daily

Three Years of Experience
Internet-based chemistry is a mess !
Public compound databases are contaminated
The annotation/curation of data online is difficult
Most database hosts are non-responsive to feedback – “We are a host/repository of data”
Who cares ? We all should!!!

Linked Data on the Web

Where is chemistry online?
Encyclopedic articles (Wikipedia)
Chemical vendor databases
Metabolic pathway databases
Property databases
Patents with chemical structures
Drug Discovery data
Scientific publications
Compound aggregators
Blogs/Wikis and Open Notebook Science

What is the Structure of Vitamin K1?

Chemical Abstracts “Common Chemistry” Database

Wikipedia

Internet-Based Chemistry is a Mess
Algorithms can get you so far
Human curation is necessary
Only the crowds can help with big data… ChemSpider is over 26 million compounds
Imagine if we worked together to create a centralized validated structure-name dictionary! Enhances text-mining, searching, linking…

Search “Vitamin H”

“ Curate” Identifiers

Crowd-sourcing Chemistry Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate

“ Curate” Identifiers
General curation activities
Remove incorrect names
Correct spellings
Add multilingual names
Add alternative names
In 3 years over 1 million structure-identifier relationships have been validated – robotically and manually
130 people have participated in validation or annotation. “ Crowds ” can be quite small!

Vancomycin – Curate This!!!

Vancomycin on ChemSpider 1 compound – 3 days

Crowdsourced “Annotations”
Users can add
Descriptions/Syntheses/Commentaries
Links to articles
Spectral data
Photos
MP3 files
Videos

Multimedia Content Holder

Gaming for Validation of Spectra

Crowdsourced Validation of Spectra

“ Game-based” Validation of Data

ChemSpider SyntheticPages

Sharing Our Activities
Presently defining approaches with other public compound databases to share results of curation activities
Member of large European project to link data from the Life Sciences. Sharing results of curation is essential
Making curation and contribution interfaces Mobile.

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

Chemspider hosting linking and curating chemistry data for the community

by Royal Society of Chemistry

Accessibility

Categories

Upload Details

Usage Rights

Statistics

Chemspider hosting linking and curating chemistry data for the community Presentation Transcript