Citizen Scientists and Their Contributions to Internet Based Chemistry
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Transcript of Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists Enable the Web
Who is writing about chemical compounds on Wikipedia?
Who is writing critical reviews of Chemistry online?
Who is blogging about chemistry on the web?
Org Prep Daily (Blog)
Encyclopedic Articles (Wikipedia)
Chemistry online – An Overview Encyclopedic articles (Wikipedia) Chemical vendor databases Metabolic pathway databases Property databases Chemical Synthesis procedures Scientific publications Chemical vendors Blogs Wikis Open Notebook Science
What and who do you trust?
Compounds and Identifiers
What is ChemSpider? ChemSpider is:
Building a Structure Centric Community for Chemists >23 million compounds, ca. 250 data sources
A deposition and curation platform
A publishing platform for the community
Grows daily – more depositions, more links, more data sources
Search Cholesterol
Search Cholesterol
Perform Real Search on Cholesterol
Link off a structure in ChemSpider
Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “Everything”
Answering Questions for Chemists
Questions a chemist might ask… What is the melting point of n-butanol? 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?
What is Flibanserin?
What is the structure of Flibanserin?
What is the structure of Flibanserin?
Complex Data and Information
Various Searches
Structure searching
Substructure searching
Subset searching – choose from 200 data sources
Property searching
Searches are used in various ways by different types of chemists…
ChemSpider Searches
ChemSpider Searches
Aspirin On Wikipedia
Aspirin names and synonyms
• Text searches depend on correct association
• 335 suggested identifiers for Aspirin just on PubChem!
• Disambiguation dictionaries are necessary
The Final Search Strategy
All Those Names, One Structure
The InChI Identifier
Multiple Layers
InChIStrings Hash to InChIKeys
Oleoylethanolamine
InChI=1S/C20H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-20(23)21-18-19-22/h9-10,22H,2-8,11-19H2,1H3,(H,21,23)/b10-9-
BOWVQLFMWHZBEF-KTKRTIGZSA-N
Search Engine Dependencies
Search Engine Dependencies
Vancomycin
Vancomycin on PubChem
Methane on PubChem
Question Everything online: www.dhmo.org
Vancomycin on ChemSpider
Vancomycin
Vancomycin
Search Molecular SKELETON
Search Full Molecule
The EXPERTS must get it right?!
Wikipedia, C&E News, PubChem C&E News (from ACS)
Citizen Scientists
Crowd-sourcing Chemistry Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
Curate Fostriecin
Search Fostriecin on ChemSpider Curate it
Become a Data Source
Synthesis Procedures
Links to Data or Deposit Data
Upload Spectral Data, OPEN Data?
Semantic Mark-up for Chemistry
Semantic mark-up for chemistry is here
RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies). Based on the OSCAR system
ChemSpider Journal of Chemistry
Nature publishing group compound linking
ChemMantis and CJOC
Name-Structure Pairs
Deposit Structures
Species – linked to Wikipedia
In Development ChemSpider Synthesis
ChemSpider Synthesis will be a home for all things “synthetic”
An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc.
Public peer-review and feedback for synthetic procedures
Online Journals and Live Data
ChemSpider Everywhere : Embed
ChemSpider Everywhere: Spectral Game
ChemSpider EverywhereCrowdsourced Curation of Spectra
ChemSpider EverywhereChemMobi
People Make Change HappenYou are invited.. Curate ChemSpider data and link to us
Deposit your data with us Structures Spectra Synthesis procedures
ChemSpider Synthesis is under development
Thank you
[email protected]: ChemSpidermanwww.chemspider.com/blogSLIDES: www.slideshare.net/AntonyWilliams