crowdsourcing chemistry for the community – 5 years of experiences antony williams nfais, february...
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Crowdsourcing Chemistry for the Community – 5 Years of Experiences
Antony WilliamsNFAIS, February 28th 2012
The World of Online Chemistry Safety data Toxicity data Blogs and Wikis Property databases Experimental results Scientific publications Compound aggregators Open Notebook Science Metabolic pathway databases Encyclopedic articles (Wikipedia)
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
Collaborative Knowledge Management
QUESTION
Are you involved with assisting chemists, pharmaceutical scientists, etc. in sourcing information about Chemistry?
1. Yes
2. No
Chemistry Databases on the Internet Public databases are “trusted” as primary sources
Trust is granted without investigation of the content
Online data vary dramatically in quality!
Examples…
With Great Fanfare…
NPC Browser http://tripod.nih.gov/npc/
NPC Browser http://tripod.nih.gov/npc/
How many contribute to clean-up?
Less than a dozen contributors to data
The majority are project members
The crowd is small…
What you might not know about Chemistry Databases on the Internet Data-sharing between the databases is cyclic –
proliferating errors – “Linked Data”
What is the Structure of Vitamin K?
MeSH
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).
What is the Structure of Vitamin K1?
QUESTION
Who has heard of ChemSpider as a chemistry database?
1. Yes
2. No
ChemSpider
We Want to Answer Questions
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?
Available Information…
Linked to vendors, safety data, toxicity, metabolism
Available Information….
Crowdsourced “Annotations”
Users can add Descriptions/Syntheses/Commentaries Links to PubMed articles Links to articles via DOIs Add spectral data Add Crystallographic Information Files Add photos Add MP3 files Add Videos
QUESTION
Did you know that ChemSpider was OWNED by the Royal Society of Chemistry?
1. Yes
2. No
Public Domain Databases
Our databases are a mess…
Non-curated databases are proliferating errors
We source and deposit data between databases
Original sources of errors hard to determine
Curation is time-consuming and challenging
Stop Whining – Fix it
Crowdsourced Curation
Crowdsourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
Search “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
Validated Name-Structure Dictionaries
Chemical name dictionaries are used for: Text-mining (publications, patents)
Used to index PubMed and link to Google Patents
Linking to other databases – think Biology! When structures are not available drug names link
Searching the web Names link to structures link to InChIs
Why are Dictionaries important?
The Final Search Strategy
Many Names, One Structure
I want to know about “Vincristine”
Vincristine: Identifiers and Properties
Vincristine: PatentsLinked by Name
Text-Mining Depends on Dictionaries
Curated Dictionaries Matter
Originally 15 compounds “called” Yohimbine54 Skeletons for Yohimbine
Sharing Chemspider curation
Data Curation Sharing - Proof of Concept
Identifier Dictionaries
Reciprocal curation processes…share curation
A series of “added” and “removed” synonyms against structures for matching.
Announced 9 months ago – only one consumer
Who will participate???
Community Contribution to ChemSpider
Curation through “gaming”
Data Curation
Reversed Spectrum
True Curation of Data
ChemSpider SyntheticPages
ChemSpider SyntheticPages
Submission Process Simple template-based submission process
Submissions reviewed by editorial board.
Online Peer Review process
Crowdsourced expansion? A few regular dedicated authors only Online peer review and feedback small but useful
Crowdsourcing – does it work?
192 people EVER have deposited or curated data
ChemSpider SyntheticPages small group of authors
Database hosts make the largest contributions
ChemSpider staff tend to do the most curation
Contributions
Curations
2009 – 8255 curations by 43 people
2010 – 10014 curations by 66 people
2011 – 16025 curations by 116 people
“Crowdsourcing” – the crowd is small!
www.SciMobileApps.com
8 contributors only…in 7 months
www.SciDBs.com
7 contributors only…in 6 months
www.ScientistsDB.com
38 contributors …in 6 weeks
What encourages participation?
“Interested” parties contribute
Marketing and self-promotion are primary reasons for participation
There are very few “selfless” participants
Relationships garner contributions…
Crowdsourcing across drug discovery
Open PHACTS : partnership between European Community and European Pharma Companies
Freely accessible for knowledge discovery and verification. Data on chemistry and biology Pharmacological profiles Proprietary and public data sources.
How will it improve?
Participation and
contribution
Conclusions For chemistry - crowdsourced deposition, annotation,
and curation works but low engagement to date
Primary challenge – engaging the community to help create what they want. Rewards and recognition?
MORE collaboration can benefit us all
Indicators are good for small but continued growth
Thank you
Email: [email protected] Twitter: ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams