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ChemSpider – The Vision and Challenges Associated with Building a Free Online Community Resource for Chemists Antony Williams AZ, February 2011
What’s the Status of Chemistry online? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
For Synthesis…TotallySynthetic.com
Org Prep Daily  (Blog)
Molbank (Open Access Journal)
Lots of “Public Compound” Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Where Would You look?  What Do You Trust?
Linked Data on the Web
What is a compound? “ARTAs”
Vision: Connect Chemistry on the Web ,[object Object],[object Object],[object Object],[object Object]
We Have Delivered the Vision ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How Was ChemSpider Built? ,[object Object],[object Object],[object Object],[object Object]
How Did We Build It? ,[object Object],[object Object],[object Object],[object Object]
www.chemspider.com
We Want to Answer Questions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Search for a Chemical…by name
Link off a structure in ChemSpider ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Available Information… ,[object Object]
Available Information….
Clickthrough to Patent (SureChem)
Crowdsourced “Annotations” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
Spectra Linked
Spectra Linked
Search for a chemical…by structure Substructure search coming…
Inherited Errors ,[object Object],[object Object],[object Object],[object Object]
What is the Structure of Vitamin K?
MeSH ,[object Object]
What is the Structure of Vitamin K1?
What is the Structure of Vitamin K1?
Vitamin K1
 
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Question Everything online: www.dhmo.org
It’s all on Wikipedia…
Chemistry on The Internet Is Messy
It’s Methane…
What’s Methane?
What’s Methane?
What  ELSE  is Methane???
 
 
EPA’s DailyMed
EPA’s DailyMed
EPA’s DailyMed
Public Domain Chemistry Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Drug Name Generic Name ChEBI ChemSpider CAS Com. Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia Spiriva Tiotropium Bromide No Hits  No Hits    4/0  Depakote Valproate semisodium        No Structure Basen Voglibose   No Hits  No Hits  2/1  Symbicort 1) Budesonide       8/1  Symbicort 2) Formoterol WRONG  No Hits    6/1  Vytorin 1) Ezetimibe   No Hits      Vytorin 2) Simvastatin       2/1  Taxol Paclitaxel       44/1  Thalidomid Thalidomide No Hits        Zocor Simvastatin       2/1  Crestor Rosuvastatin   No Hits    2/1 
Symbicort: Budesonide + Formoterol
Symbicort: Budesonide + Formoterol ChemIDPlus Wikipedia
DrugBank: Search Symbicort…
Symbicort: Budesonide + Formoterol ,[object Object],[object Object],[object Object],[object Object]
Taxol: Paclitaxel  44  structures
Taxol: Paclitaxel  Bioassay  Data
Taxol: Paclitaxel  Bioassay  Data ,[object Object]
[object Object]
 
 
 
 
The Final Search Strategy
All Those Names, One Structure
Searching Chemistry on the  Internet ,[object Object],[object Object],[object Object]
The InChI Identifier
Multiple Layers
InChIStrings Hash to InChIKeys
Oleoylethanolamine
InChIs have traction…
Vancomycin
Vancomycin
Vancomycin Search Molecular SKELETON Search Full Molecule
Full  Molecule  Search: 4 Hits
Full  Skeleton  Search: 104 Hits
Vancomycin ,[object Object],[object Object]
Vancomycin on ChemSpider
 
 
 
 
 
 
Name Searching is “Easier”
Name Searching is “Easier”
 
 
Content is King and  Quality  Costs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The EXPERTS must get it right?!
Wikipedia, C&E News, PubChem ,[object Object]
Feedback from Steve Ritter ,[object Object],[object Object]
 
Search OEA
Search OEA
Search OEA
Semantic Mark-up for Chemistry ,[object Object],[object Object],[object Object]
Nature Chemistry Compound Pages
Project Prospect
Entity-Extraction, Mark-up, Annotate
Entity-Extraction, Mark-up, Annotate
And linked to STITCH…
Success Depends on Dictionaries
Online Curation ,[object Object],[object Object],[object Object]
Search “Vitamin H”
“ Curate” Identifiers
“ Curate” Identifiers
“ Curate” Identifiers
Crowd-sourcing Chemistry Curation
Crowdsourcing Works ,[object Object],[object Object],[object Object]
ChemSpider and Publishing ,[object Object],[object Object],[object Object]
Crowdsourcing Synthesis ChemSpider SyntheticPages
Crowdsourcing Synthesis ChemSpider SyntheticPages
ChemSpider Everywhere: What do computers want? ,[object Object]
Web Services
ChemSpider Everywhere ,[object Object],[object Object],[object Object],[object Object],[object Object]
ChemSpider Everywhere : Embed
ChemSpider Everywhere: Spectral Game
ChemSpider Everywhere Crowdsourced Curation of Spectra
ChemSpider Everywhere : ChemMobi
Structure Database Lookup
Structure Database Lookup
Reaction Database Look-up
Reaction Database Look-up
There will always be gaps... ,[object Object],[object Object],[object Object],[object Object],[object Object]
Collaborative Data Curation ,[object Object],[object Object],[object Object]
Future Work ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The Future of Chemistry on the Web? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
It’s a long road ahead…
Thank you Email: williamsa@rsc.org  Twitter: ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

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AZ of Chemspider February 2011