The document discusses the potential impact of an online chemistry resource encompassing searchable chemical data, spectra, and methodologies, similar to advancements in bioinformatics. It emphasizes the need for quality validation and curation in the linked data web to ensure reliable information for chemists. Additionally, it highlights the integration of databases and services like ChemSpider to enhance accessibility and usability for researchers in the field.

1. How an Online Chemistry Resource Could Change Our World Antony Williams Triangle Chromatography Discussion Group, Raleigh, NC, May 2009

2. Imagine a time when …. The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar) When there is an online database of NMR, IR, MS spectra and chromatography methods built by available to the community Chemistry articles are indexed and searchable by “chemistry” The web is linked together through the “language of chemistry” Publicly funded research data can be shared and discussed in the Open, maybe as Open Notebook Science Cheminformatics has as much of a public face and success as bioinformatics (Protein DataBank, Genbank, etc)

3. The Language of Chemistry My language….

4. And its dialects….

5. As a chemist… I look for information about chemicals/chemistry What is a particular structure ? What alternative names/identifiers? Reaction synthesis? Physical properties? Analytical data? Purchase? Tell me more? Similar stuff – what other compounds are “like” mine?

6. Linked Data Cloud

7. Chemistry on the Internet Much of the information online is User Beware! The Quality of information is “diverse” Technologies can “link and connect” information but validation and curation is key to providing quality The LinkedData web is of less value when the data linked are “wrong”

8. “ Good Stuff” TotallySynthetic.com

9. PubChem

10. 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?

11. Search Cholesterol

12. Search Cholesterol

13. Search Cholesterol

14. Search Cholesterol

15. Search Cholesterol

16. Link outs

17. Complex Data and Information

18. Online Analytical Data

19. Various Searches Structure searching Substructure searching Subset searching – choose from 200 data sources Property searching Value for Mass Spectrometrists and Chromatographers?

20. ChemSpider for MS Spectrometrists What would an MS spectrometrist want to do? Search the database based on mass (various forms) Search selected subsets of the database based on mass Search based on mass and substructure(s) Search for structure based on name(s) or database IDs Search for structures based on elements/not elements Download the structure/structures in standard format Search literature for information Identify related data sources – chemical vendors, pathway databases, etc

21. Search Database Based on Mass

22. Mass Based Searches? What compounds have a mass of 300+/-0.001?

23. 59 hits/1.3 seconds from 21.5 MILLION

24. Substructure and Property

26. Elemental Constraints

27. Search based on Data Sources

28. Outlinks – to vendors and other databases Example databases of interest to MS Spectrometrists: HMDB – Human Metabolome Database KEGG – Kyoto Encyclopedia of Genes and Genomes BioCyc - collection of Pathway/Genome Databases Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds WikiPathways – new initiative to build crowdsourced pathway data management

29. Links out to KEGG Kyoto Encyclopedia of Genes and Genomes

30. WikiPathways Link

31. Download Structure(s) Download individual record – molfile Download SDF file (group of structures)

32. Web Service Integration ChemSpider integration presently integrated to Bruker, Waters and Thermo – more vendors coming… Direct integration to vendor data processing tools

33. MassSpec API Web Services http:// www.chemspider.com/MassSpecAPI.asmx

34. Web Services

35. Test Web Services for MassSpec http:// www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx

36. Test results

37. Waters Integration

38. Waters Integration

39. Outlinks from Table

40. For Chromatographers? “ Structure-based methods” being linked Structure-centric searching of methods We can host chromatograms for display LogPs and LogDs (pH5.5 and 7.4) calculated for >21 million compounds using ACD/Labs software We’d love to host collections from the column vendors! [email_address]

41. From 21.5 MILLION molecules… Data are gathered/deposited from >200 data sources Government databases Chemical vendors Wikipedia There are “imperfections” in all online data sources How bad can it get????

42. What is “wrong”?

43. Quality is a Major Issue- Search Butanol OLD EXAMPLE..now fixed

44. Vancomycin Who will curate? PubChem is not resourced to clean these errors  How would you clean such a large dataset?

45. Wikipedia, C&E News, PubChem C&E News (from ACS)

47. Does one stereocenter matter? Thalidomide

48. Question Everything www.dhmo.org

49. DailyMed “ DailyMed provides high quality information about marketed drugs. This information includes FDA approved labels (package inserts).”

50. The FDA’s DailyMed

51. Structures on DailyMed Poor Representations

52. Incorrect Structures Scanning (?) Issues

53. Incorrect Structures

54. Wikis for Science Who in the room hasn’t used Wikipedia? Is it trustworthy? What are the advantages and disadvantages of the Wiki environment? How suitable is it for Chemistry?

55. Collaborative Knowledge Management for Chemists

56. Wikipedia Curation Looking for self-consistency across a Wikipedia Page Primary key is the article TITLE The chemical shown needs to match the title Cyclic self-consistency – and decisions must get made

57. Taxol on PubChem

58. When are things “wrong”? Structures have a timeline…..

62. Creating a trusted source… Small databases can be curated by the hosts – EPA’s DSSTox, Wikipedia, etc. Who will curate an enormous database?

63. Crowdsourcing

64. Curating ChemSpider Anyone can “Post Comments” associated with a structure. To curate data we require login to track

65. Multi-level Curation and Approval

66. ChemMantis Chem ical M arkup A nd N omenclature T ransformation I ntegrated S ystem

67. On the fly conversion

68. Nature Publications

69. Integrations Out to Other Sources

70. Reactions

71. ChemSpider Everywhere RSC Compounds

72. ChemSpider Everywhere Nature Chemistry Nature Chemistry articles are annotated to identify all of the chemical compounds mentioned throughout the text. Those compounds are linked out to other information resources including PubChem and ChemSpider .

73. ChemSpider Everywhere ChemMobi

75. It Happened in a Basement!! Homebuilt servers Cable internet Software donations Lots of hard work >8000 users per day >80,000 transactions per day

76. And now… The Royal Society of Chemistry announced on May 11th that it has acquired ChemSpider , heralding a breakthrough investment for the organisation and for the Chemistry Community. This acquisition reflects RSC's commitment to providing access to rich resources of chemistry data and information.