Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?

Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data? Antony Williams Wolfram Summit, September 2010

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/correct data

www.chemspider.com

We Answer 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 vendors, safety data, toxicity, metabolism

Available Information….

Search for chemicals

ChemSpider Today
24.8 million structures
400 data sources
Grows daily
Community annotation and curation
We curate, edit, change, enhance data daily

Linked Data on the Web

Three Years of Experience
Internet-based chemistry is a mess !
Most public compound databases on the web are contaminated . Including ours !
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 ?

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
A lipid cofactor that is required for normal blood clotting. 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). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K

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

“ 2-methyl-3-(3,7,11,15-tetramethyl hexadec-2-enyl)naphthalene-1,4-dione”
Variants of systematic names on PubChem
2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl
2-methyl-3-(3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl

ChEBI – Manual Curation

What’s Methane?

What ELSE is Methane???

The EXPERTS must get it right?!

Wikipedia, C&E News, PubChem
C&E News (from ACS)

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”

“ Curate” Identifiers

“ 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!

Crowdsourced “Annotations”
Registered Users can add
Descriptions/Syntheses/Commentaries
Links to articles, blogs, wikis etc
Add spectral data
Add photos
Add MP3 files
Add Videos

Data Validation – Not Vitamin K1

Data Validation – Not Beclamethasone Dipropionate DailyMed Article

Data Validation …NOT Cholesterol

Data Validation – ONE Cymarin Question Quality in Big Databases

First request to Database Hosts!
Every public compound database host should add ONE feature – “Leave Comments”

Second request to Database Hosts! Show Comments

Always Question Online Chemistry

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

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Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?

by Antony Williams, ChemConnector

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