ChemSpider hosting linking and curating chemistry data for the community
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ChemSpider is a platform for hosting, linking, and curating chemistry data with over 26 million unique chemicals and 420 data sources. It aims to create a structure-centric community where chemists can contribute their own data while facilitating annotation and curation by the community. The document discusses the challenges of data contamination in public databases and emphasizes the importance of human curation and crowdsourced efforts for improving data accuracy and accessibility in chemistry.
ChemSpider hosting linking and curating chemistry data for the community
- 1. ChemSpider – Hosting, Linking and Curating Chemistry Data for the Community Valery Tkachenko SLA Meeting, June 2011
- 2. Chemistry on the Internet 100s of websites hosting chemistry-related data Chemistry information is generally “compound-based” Chemical “structures” Identifiers, names and synonyms Properties Analytical data How to synthesize Articles, patents, safety information Chemistry “language and dialects”
- 4. A Pragmatic Vision “ Build a Structure Centric Community” Integrate chemistry across the internet based on “chemical structure” A “structure-based hub” to information and data Let chemists contribute their own data Allow the community to curate & annotate data
- 6. Answering Questions for Chemists Questions a chemist might ask… What is the melting point of n-heptanol? 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 Aspirin? What is the NMR spectrum of Benzoic Acid? What are the safety handling issues for toluene?
- 7. Search for a Chemical…by name
- 8. Available Information… Linked to chemical vendors, safety data, toxicity, metabolism…
- 10. ChemSpider Today Over 26 million unique chemicals Over 420 data sources Grows daily – community and RSC depositions Community annotation and curation We curate, edit, change, enhance data daily
- 11. Three Years of Experience Internet-based chemistry is a mess ! Public compound databases are contaminated The annotation/curation of data online is difficult Most database hosts are non-responsive to feedback – “We are a host/repository of data” Who cares ? We all should!!!
- 12. Linked Data on the Web
- 13. Where is chemistry online? 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
- 14. What is the Structure of Vitamin K1?
- 15. What is the Structure of Vitamin K1?
- 16. Chemical Abstracts “Common Chemistry” Database
- 17. Wikipedia
- 20. Internet-Based Chemistry is a Mess Algorithms can get you so far Human curation is necessary Only the crowds can help with big data… ChemSpider is over 26 million compounds Imagine if we worked together to create a centralized validated structure-name dictionary! Enhances text-mining, searching, linking…
- 26. Crowd-sourcing Chemistry Curation Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
- 27. “ Curate” Identifiers General curation activities Remove incorrect names Correct spellings Add multilingual names Add alternative names In 3 years over 1 million structure-identifier relationships have been validated – robotically and manually 130 people have participated in validation or annotation. “ Crowds ” can be quite small!
- 28. Vancomycin – Curate This!!!
- 29. Vancomycin on ChemSpider 1 compound – 3 days
- 30. Crowdsourced “Annotations” Users can add Descriptions/Syntheses/Commentaries Links to articles Spectral data Photos MP3 files Videos
- 32. Gaming for Validation of Spectra
- 33. Crowdsourced Validation of Spectra
- 34. “ Game-based” Validation of Data
- 36. Sharing Our Activities Presently defining approaches with other public compound databases to share results of curation activities Member of large European project to link data from the Life Sciences. Sharing results of curation is essential Making curation and contribution interfaces Mobile.
- 37. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams