How Internet Resources Are Providing a Collaborative Community for Chemistry
Download as PPT, PDF1 like1,462 views
The document discusses how internet resources are providing a collaborative community for chemistry. It describes how chemistry articles and structures can now be searched online through databases and services. It highlights the InChI identifier system which allows structures to be linked and searched across different databases. The document advocates that crowdsourcing could help expand and integrate online chemistry resources through activities like deposition, curation, and semantic linking of structures.
![[email_address] Twitter: ChemSpiderman www.chemspider.com/blog](https://image.slidesharecdn.com/howinternetresourcesareprovidingacollaborativecommunityforchemistry101909final-091019090956-phpapp02/85/How-Internet-Resources-Are-Providing-a-Collaborative-Community-for-Chemistry-61-320.jpg)
How Internet Resources Are Providing a Collaborative Community for Chemistry
- 1. How Internet Resources Are Providing a Collaborative Community for Chemistry 60 slides in 20 minutes
- 2. Imagine a time when …. The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar) Chemistry articles are indexed and searchable by a free online service The web is linked together through the “language of chemistry”
- 3. It’s Coming…Linked Data Cloud
- 4. Thanks to the Organizers…
- 5. Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .
- 6. Aspirin vs Chemical Identifiers
- 7. Aspirin names and synonyms Text searches depend on correct association 335 suggested identifiers for Aspirin just on PubChem! Disambiguation dictionaries are necessary
- 11. The Final Search Strategy
- 12. All Those Names, One Structure
- 13. Searching Chemistry on the Internet How complete a result set will we get if we search for “chemicals” by name? Is there a better way to link chemistry databases? Linking by “names” is dangerous Chemists want structure and SUBstructure searching
- 15. Multiple Layers
- 16. InChIStrings Hash to InChIKeys
- 21. RDF Linking of Structures
- 22. PubChem
- 23. The Simplest Organic Molecule
- 24. Vancomycin
- 26. Vancomycin Who will curate? How would you clean such a large dataset?
- 28. Vancomycin
- 29. Vancomycin Search Molecular SKELETON Search Full Molecule
- 30. Full Skeleton Search: 104 Hits
- 31. Full Molecule Search: 4 Hits
- 33. Content is King and Quality Costs Curated Chemistry “content” is expensive to create Patent searching Structures and properties Drug databases Literature databases Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information 102 years of content >50 million substances Proprietary platform
- 34. The EXPERTS must get it right?!
- 35. Wikipedia, C&E News, PubChem C&E News (from ACS)
- 36. Feedback from Steve Ritter “ Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.” “ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”
- 37. Maybe it will be ChemSpider? What is ChemSpider? A database of almost 23 million compounds, >200 data sources A deposition and curation platform A publishing platform for the community Grows daily – more depositions, more links, more data sources
- 38. Search OEA
- 39. Search OEA
- 40. Search OEA
- 41. Search OEA
- 42. Linked Patents for OEA
- 44. Linked resources Vendor sites – Aldrich, Alfa Aesar, TCI and 100s of others Government databases – PubChem, DSSTox, FDA databases, ChemIDPlus,… Biological Databases – Protein Database, Stitch, KEGG, ChEBI,… Analytical databases –NMRShiftDB,…
- 45. Linked across the internet
- 46. Kyoto Encyclopedia of Genes and Genomes
- 47. Complex Data and Information
- 48. Remember – QUALITY ISSUES
- 50. Incorrect Structures
- 52. The Currency of Recognition We need to build a platform for recognition ….
- 53. Chemistry – A Deposition Platform CAS indexes published literature, patents and chemical vendors CAS indexes ChemSpider – >303,000 records “ Lost Chemistry” – syntheses in theses, lab notebooks? Compounds in private collections? ChemSpider accepts public depositions, linking to websites, hosting of details etc. Accepts structures, text, spectra, images.
- 54. Blogs should be searchable too…
- 55. Use Intelligent Structures : ChemSpider Embed Web Service
- 57. Semantic Linking of Structures What would you want to link off a structure? Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “ Everything” See Richard Kidd’s Talk
- 58. Conclusions Internet resources provide a collaborative community for chemistry Crowdsourcing to expand, curate and integrate to the benefit of chemists Searching the web for chemistry is arriving InChIs are enabling chemistry on the internet Question Quality!
- 60. Acknowledgments Valery Tkachenko and Sergey Golotvin RSC infrastructure team The ChemSpider advisory group The Wikipedia Chemistry team
- 61. [email_address] Twitter: ChemSpiderman www.chemspider.com/blog