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Navigating the Complex Web of Chemistry Using ChemSpider

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US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 200 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the ChemSpider platform and how it is fast becoming the centralized hub for resourcing information about chemical entities.

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Navigating the Complex Web of Chemistry Using ChemSpider
Antony Williams vs Identifiers Old Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .
Aspirin vs Chemical Identifiers
Aspirin names and synonyms ,[object Object],[object Object],[object Object]
Linked Data Cloud
[object Object],[object Object]
 
 
The Final Search Strategy
All Those Names, One Structure
Content is King and Quality Costs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Searching Chemistry on the Internet ,[object Object],[object Object],[object Object]
The InChI Identifier
Multiple Layers
InChIStrings Hash to InChIKeys
Oleoylethanolamine
InChIKey Searches Work
Search Engine Dependencies
Search Engine Dependencies
InChIs have traction…
RDF Linking of Structures
PubChem
The Simplest Organic Molecule
Question Everything online: www.dhmo.org
The Structure-Based Data Cloud
Vancomycin
 
Vancomycin ,[object Object],[object Object]
Vancomycin on ChemSpider
Vancomycin
Vancomycin Search Molecular SKELETON Search Full Molecule
Full Skeleton Search: 104 Hits
Full Molecule Search: 4 Hits
What is ChemSpider? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
For Chemical Compounds ,[object Object],[object Object],[object Object],[object Object]
How Was ChemSpider Built? ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Search Cholesterol
Search Cholesterol
Search Cholesterol
Search Cholesterol
Linked across the internet
Kyoto Encyclopedia of Genes and Genomes
Links to Patents based on structure
 
Answering Questions for Chemists ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Complex Data and Information
Remember – QUALITY ISSUES
The FDA’s DailyMed
Incorrect Structures
Does one stereocenter matter? ,[object Object]
Crowd-sourcing Chemistry Curation
We Need Recognition and Rewards
Master Curators, Curators, Depositors
Collaborating with Wikipedia ,[object Object],[object Object],[object Object]
Blogs need InChIs too!
Blogs need InChIs too!
Use Intelligent Structures : ChemSpider Embed Web Service
ChemSpider Web Services
Semantic Mark-up for Chemistry ,[object Object],[object Object],[object Object],[object Object]
Nature Chemistry Compound Pages
Project Prospect
ChemMantis
Deposit Structures
Species – linked to Wikipedia
Semantic Linking of Structures ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The InChI “Resolver”
InChI Resolver to DOIs Structure Search the Web
 
Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object]
[email_address] Twitter: ChemSpiderman www.chemspider.com/blog

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