chemspider as a platform for crowd participation in curating chemistry
DESCRIPTION
This is a presentation I gave at the International Digital Curation Conference in Chicago, December 7th 2010, #idcc10. The presentation discusses the issues of data quality and the need for collective, crowdsourced efforts to improve the quality of chemistry related data on the InternetTRANSCRIPT
ChemSpider as a Platform for Crowd Participation in Curating Chemistry
Antony WilliamsIDCC, Chicago, December 2010
WARNING: Chemistry is Dangerous
Di-Hydrogen Monoxide
Di-Hydrogen Monoxide
2H
Di-Hydrogen Monoxide
2H + 1O
Di-Hydrogen Monoxide
H2O
Di-Hydrogen Monoxide
H2OWater
It’s all on Wikipedia…
Chemistry on the Internet – Not All Bad
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
Almost 25 million unique chemicals Over 400 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?
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 K?
MeSH – Medical Subject Headings
Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione).
What is the Structure of Vitamin K1?
What is the Structure of Vitamin K1?
Chemical Abstracts“Common Chemistry” Database
Wikipedia
Incorrect Structures
Lack of Stereochemistry
Does stereochemistry matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
PubChem
What’s Methane?
What’s Methane?
What ELSE is Methane???
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 approaching 25 million compounds
Search “Vitamin H”
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“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!
Crowdsourcing Works
The “crowd” has deposited data (structures, spectra, etc) and participated in data curation
Different level curators check each others work Wikipedia is the modern primary example Some curators are “madmen”…
Crowdsourcing Works
The “crowd” has deposited data (structures, spectra, etc) and participated in data curation
Different level curators check each others work Wikipedia is the modern primary example Some curators are “madmen”… The Oxford English Dictionary
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 Curation of Spectra
ChemSpider EverywhereCrowdsourced Curation of Spectra
Data Curation
True Curation of Data
ChemSpider SyntheticPages
Drug Name Generic Name ChEBI ChemSpiderCAS Com.
Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia
SpirivaTiotropium Bromide
No Hits No Hits 4/0
DepakoteValproate semisodium No
Structure
Basen Voglibose No Hits No Hits 2/1 Symbicort 1) Budesonide 8/1 Symbicort 2) Formoterol WRONG No Hits 6/1 Vytorin 1) Ezetimibe No Hits Vytorin 2) Simvastatin 2/1 Taxol Paclitaxel 44/1 Thalidomid Thalidomide No Hits Zocor Simvastatin 2/1 Crestor Rosuvastatin No Hits 2/1
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
Mobile ChemSpider
First request to Database Hosts!
Every public compound database host should add ONE feature – “Leave Comments”
Second request to Database Hosts! Show Comments
Question Quality
Thank you
Email: [email protected] Twitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams