ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community

ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community OpenSciNY, New York, May 2010,

Once Upon a Time Over a “Coffee”

Which is better for Plants? Vodka, Sprite or Viagra?

It Works – Viagra Wins the Day

Now Which is Better?
Viagra or Cialis?
Images sourced from Wikipedia

Cialis
I want…
The structure
Any patent information
Related publications
Where can I buy it?
Metabolic pathway info
What else is easy to find…

Cialis on Google?

What is Cialis?

What is Cialis? Can we trust Wikipedia?

What is Cialis? 6 hits on PubChem

What is Cialis?

Search by Trade Name

Are there other names???

PubMed hits:
736 Tadalafil
744 Cialis

Are There Other Names?

IC351 on PubChem? 5 HITS for IC351 ZERO HITS for IC 351

Chemistry on the Web
Text searching the web is far from optimal
The quality of data on the web is a problem
It may be hard to find but it is “out there”
What was once locked up behind an expensive license can generally be found
Structure searching the web is already possible!

Text Searching the Web
Text searching the web for chemical compounds is an enormous challenge
RSC has multiple databases, >500,000 articles and a lot of other resources. How do we do?

The RSC Publishing Platform (Beta)

2+2 = 4 Articles?

CAS Number Search

Text Searching the Web
Disambiguation dictionaries of name-structure relationships would be very enabling.
IC351 = IC 351 = Tadalafil = Cialis = …
Creating validated dictionaries is an enormous challenge to cover chemistry

CAS Registry – LOTS of Chemicals!

The Final Search Strategy A “Disambiguation Query!”

All Those Names, One Structure A problem to solve…

ChemSpider - A Pragmatic Vision
“ Build a Structure Centric Community to
Serve Chemists”
Aggregate and integrate chemical structure data on the web – names, structures, links
Create a “structure-based hub” to information, data and algorithmic predictions
Let chemists contribute their own data
Allow the community to curate/correct data

media.obsessable.com
As few interfaces as possible
What do humans want?

Aggregating Data – Who to Trust???
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

Just “Public Compound” Databases
PubChem
Drugbank
ChEBI/ChEMBL
KEGG
LipidMAPs
ChemIDPlus
eMolecules
ZINC
Lots of chemical vendors

Question Everything online: www.dhmo.org

Di-Hydrogen Monoxide
2H

2H + 1O

H2O

H2O
Water

It’s all on Wikipedia…

What About Gases? Methane…

What’s Methane?

What ELSE is Methane???

Structural Data for Life Sciences DailyMed

Lack of Stereochemisty

Incorrect Structures

Pragmatic Vision Delivered…
Aggregate, integrate and link data from across the internet
Almost 25 million structures from > 300 data sources
Linked to vendors, literature, online databases (open and commercial), open notebook science, patents and….
Robotic and Crowdsourced Curation

Search “OEA”

Search OEA

Linked Patents for OEA

Answering Questions…
Questions a student might ask…
What is the structure of levulinic acid?
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?
How can I synthesize 2,4-dichlorophenol?
What are the safety handling issues for Thymol Blue?

Back to Cialis…

Cialis on ChemSpider : 1 hit
Chemicals are curated/validated on ChemSpider by ourselves and the community
Based on assertions from various sources. Iterative, time-consuming and exacting!
We believe we know the structure now
What is linked and available?

Google Patents

ChemSpider – Patents Linked SURECHEM PATENTS GOOGLE

Google Books

Microsoft Academic Search

Google Scholar – Articles were found by CAS Number !

Identifiers for Tadalafil

How Many Articles in RSC Journals ?
Based on 171596-29-5 there are 13 articles in RSC journals
What about if we VALIDATE identifiers?

Validated Dictionaries Hit APIs This is data curation...

Does this generate more results?

RSC Journals

RSC Journals REMEMBER 2+2 = 4

PubMed

Google Scholar – Expanded Hit Set

Be careful! More mussels than drugs…

Searching Chemistry on the Internet
Do we get complete a result set will we get if we search for “chemicals” only by name?
Is there a better way to link chemistry databases? Linking by “names” is dangerous
Chemists want structure and SUBstructure searching

Structure Searching the Web
We have resources about Tadalafil actively linked to ChemSpider
What about searching the web for Tadalafil by structure…not based on the various identifiers
How?

Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog

The InChI Identifier

Multiple Layers

InChIStrings Hash to InChIKeys

Cialis – Searching the Web by InChI Search Molecular SKELETON Search Full Molecule

InChI Search the Web by Skeleton 78 Hits by Skeleton

InChI Search the Web Exact Match 32 Hits by InChIKey

InChI Search the Web Exact Match 6 Hits by Standard InChIKey

InChifying the Web
There are more than 2X “skeletons” for Cialis than exact matches – different stereo? Mistakes?
Our judgment…MISTAKES

Vancomycin – Search the Internet

Full Molecule Search: 4 Hits

Full Skeleton Search: 104 Hits

InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… But what is the structure???

We need an InChI “Resolver”

InChI Resolver to DOIs Structure Search the Web

Semantic Markup: Project Prospect

Depends on Validated Dictionaries Link to a Structure or the Right Structure?

Name-Structure Pairs

Semantic Linking of Structures
What would you want to link off a structure?
Chemical suppliers
Other publications
Analytical Data
Related Reactions
Wikipedia
Patents
“ Everything”
Through ChemSpider!

Unpublished Chemistry
Only a fraction of chemistry is published
Only a tiny fraction of chemistry is patented
What of the “Lost Chemistry”- never published and cannot be abstracted
Reactions performed
Structures made and studied
Spectra acquired and then disposed of
Available chemicals never found

Org Prep Daily (Blog)

ChemSpider SyntheticPages

Submission process
Register as a user
Use the Submit button and fill in the fields…

Submission Process
Submissions reviewed by editorial board
Published as is or comments sent to author
Online Peer Review process
Data supported include web movies, images, live spectra etc.

Micro- and Nano-publications
Blogs, wiki entries and even Amazon book reviews are micro/nano-publications
ChemSpider SyntheticPages will be DOI’ed – students can add these “micro-publications” to their resume
Structures and spectra are nano-publications – these can be tracked and referenced also. (depositions, curations etc). Students participate in building one of the premier sources of chemistry data.

ChemSpider : Spectra Linked

Spectra Linked

Not Just NMR Data

www.SpectralGame.com http://www.jcheminf.com/content/1/1/9

Spectral Game

Increasing Complexity

Spectral Game

ChemSpider Content
ChemSpider is a container…supports multimedia
Spectra
Crystal structures
Images
MP3s
Videos

Roses’ Crystal Image Collection

MP3s and Videos : Titanium

Periodic Table Images

How Can You Help ChemSpider?
Deposit your data and share with the community
Structures – one or many
Spectra
Links
Syntheses into SyntheticPages
Curate data – most basic level…just add comments
Spread the word – ChemSpider is an untapped resource

Community Contribution
We can make a bigger contribution to the community if the community shares via ChemSpider
Don’t underestimate what others will find of value
ChemSpider wins “Community
contribution” best practice award”

Chemistry on the Internet FUTURE
The semantic web for chemistry is in place
Crowdsourced contributions are commonplace
Chemists will search by structure/substructure
Chemistry articles indexed and searchable
Reduced number of searches to find data
Data are integrated – compounds, vendors, syntheses, data, publications and patents
A world of Open Access and Open Data

Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community

by Antony Williams, ChemConnector on May 14, 2010

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ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community — Presentation Transcript