crowdsourced curation of chemistry data. how bad is online chemistry data?
DESCRIPTION
This presentation was given at the Wolfram Data Summit in Washington DC on Sept 9th 2010 as part of a panel series of presentations and discussions on crowdsourcing approaches for data. It was a rant by me on the quality of what's online and questioning "who cares".TRANSCRIPT
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Antony WilliamsWolfram 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?
What is the Structure of Vitamin K1?
Chemical Abstracts“Common Chemistry” Database
Wikipedia
Incorrect Structures
Wow!
Lack of Stereochemistry
Does stereochemistry matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
PubChem
“2-methyl-3-(3,7,11,15-tetramethylhexadec-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’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”
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
“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 CymarinQuestion 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: [email protected] Twitter: ChemConnectorBlog: www.chemspider.com/blogPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams