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ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community
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Transcript of ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community
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ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Community OpenSciNY, New York, May 2010,
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Once Upon a Time Over a “Coffee”
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Which is better for Plants?Vodka, Sprite or Viagra?
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It Works – Viagra Wins the Day
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Now Which is Better?
Viagra or Cialis?
Images sourced from Wikipedia
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Cialis
I want…The structureAny patent informationRelated publicationsWhere can I buy it?Metabolic pathway infoWhat else is easy to find…
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Cialis on Google?
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What is Cialis?
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What is Cialis? Can we trust Wikipedia?
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What is Cialis?
6 hits on PubChem
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What is Cialis?
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Search by Trade Name
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Are there other names???
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Are there other names???
PubMed hits: 736 Tadalafil 744 Cialis
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Are there other names???
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Are There Other Names?
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IC351 on PubChem?
5 HITS for IC351
ZERO HITS for IC 351
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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!
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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?
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The RSC Publishing Platform (Beta)
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2+2 = 4 Articles?
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CAS Number Search
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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
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CAS Registry – LOTS of Chemicals!
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The Final Search StrategyA “Disambiguation Query!”
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All Those Names, One StructureA problem to solve…
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ChemSpider - A Pragmatic Vision
“Build a Structure Centric Community toServe 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
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media.obsessable.com
As few interfaces as possible
What do humans want?
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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
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Just “Public Compound” Databases
PubChem Drugbank ChEBI/ChEMBL KEGG LipidMAPs ChemIDPlus eMolecules ZINC Lots of chemical vendors
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Question Everything online: www.dhmo.org
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Di-Hydrogen Monoxide
2H
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Di-Hydrogen Monoxide
2H + 1O
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Di-Hydrogen Monoxide
H2O
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Di-Hydrogen Monoxide
H2OWater
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It’s all on Wikipedia…
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What About Gases? Methane…
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What’s Methane?
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What’s Methane?
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What ELSE is Methane???
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Structural Data for Life SciencesDailyMed
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Lack of Stereochemisty
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Incorrect Structures
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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
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Search “OEA”
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Search OEA
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Search OEA
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Search OEA
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Linked Patents for OEA
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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?
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Back to Cialis…
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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?
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Google Patents
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ChemSpider – Patents Linked
SURECHEM PATENTS GOOGLE
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Google Books
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Microsoft Academic Search
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Google Scholar – Articles were found by CAS Number!
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Identifiers for Tadalafil
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How Many Articles in RSC Journals?
Based on 171596-29 -5 there are 13 articles in RSC journals
What about if we VALIDATE identifiers?
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Validated Dictionaries Hit APIsThis is data curation...
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Does this generate more results?
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RSC Journals
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RSC Journals
REMEMBER 2+2 = 4
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PubMed
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Google Scholar – Expanded Hit Set
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Microsoft Academic Search
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Microsoft Academic Search
Be careful! More mussels than drugs…
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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
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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?
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Link the Internet with InChIKeys!
Taken from: Rafael Sidis’ Blog
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The InChI Identifier
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Multiple Layers
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InChIStrings Hash to InChIKeys
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Cialis – Searching the Web by InChI
Search Molecular SKELETON
Search Full Molecule
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InChI Search the Web by Skeleton78 Hits by Skeleton
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InChI Search the Web Exact Match32 Hits by InChIKey
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InChI Search the Web Exact Match6 Hits by Standard InChIKey
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InChifying the Web
There are more than 2X “skeletons” for Cialis than exact matches – different stereo? Mistakes?
Our judgment…MISTAKES
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Vancomycin – Search the Internet
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Full Molecule Search: 4 Hits
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Full Skeleton Search: 104 Hits
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InChIKeys
RCINICONZNJXQF-MZXODVADSA-N
Make the internet searchable by adding InChIKeys
Publishers add InChIKeys to papers now…
But what is the structure???
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We need an InChI “Resolver”
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InChI Resolver to DOIsStructure Search the Web
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Semantic Markup: Project Prospect
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Depends on Validated Dictionaries
Link to a Structure or the Right Structure?
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Name-Structure Pairs
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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!
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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
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Org Prep Daily (Blog)
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ChemSpider SyntheticPages
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Submission process Register as a user Use the Submit button and fill in the fields…
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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.
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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.
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ChemSpider : Spectra Linked
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Spectra Linked
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Spectra Linked
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Not Just NMR Data
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Spectral Game
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Increasing Complexity
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Spectral Game
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ChemSpider Content
ChemSpider is a container…supports multimedia Spectra Crystal structures Images MP3s Videos
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Roses’ Crystal Image Collection
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MP3s and Videos : Titanium
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Periodic Table Images
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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
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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 “Communitycontribution” best practice award”
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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
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Thank you
[email protected]: ChemSpidermanwww.chemspider.com/blogSLIDES: www.slideshare.net/AntonyWilliams