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1. Introduction
2. Chemistry
3. Data is central
4. Work flow
5. Unstructured data and destructive public. formats
6. Structured "vernacular"
7. Object management
8. What are "objects"
9. The world wide web
10. Semantic web
11. Semantic web layer cake
12. On the semantic web
13. XML
14. MDL mol format
15. Chemical markup language
16. Polymer markup language
17. Examples of markup languages
18. RDF
19. Making graphs with RDF
20. Example: Benzene chemical data
21. Linking open data cloud diagram
22. Sources of chemical data in RDF
23. What's a molecule?
24. Ontology definition
25. Ontology in computer sciences
26. Definition from the RNA ontology
27. Example: ebulliometry definition
28. Ontologic frameworks
29. But how do I generate all this markup?
30. A priori and a posteriori
31. A priori - at authoring time
32. Chemistry add-in for word (1)
33. Chemistry add-in for word (2)
34. Word add-in for ontology recognition (1)
35. Word add-in for ontology recognition (2)
36. A posteriori - post-authoring time
37. OSCAR1/OSCAR3 - chemical entity extraction
38. OSCAR1/OSCAR3 - example
39. Identification work-flow
40. Interannotator study
41. Results expressed as RDF
42. Applications
43. Chem2Bio2RDF
44. Web engine for non-obvious drug information
45. SADI - interoperable semantic web services
46. Web services in SADI's service registry
47. SADI's a log p calculation service
48. Summary
49. Acknowledgements

Topics Covered

• Data is central
• Work flow
• Unstructured data and destructive publication formats
• Object management
• Semantic web
• XML
• MDL mol format
• Chemical markup language
• RDF
• Linking open data cloud diagram
• Sources of chemical data in RDF
• What's a molecule?
• Ontology definition
• ebulliometry definition
• Ontologic frameworks
• A priori and a posteriori
• Chemistry add-in for word
• OSCAR1/OSCAR3
• chemical entity extraction
• Identification work-flow
• Interannotator study
• Applications
• Chem2Bio2RDF
• Web engine for non-obvious drug information
• SADI
• interoperable semantic web services

Links

Series:

• Introduction to Cheminformatics

Categories:

• Methods

Talk Citation

Publication History

• Published on June 19, 2011

Financial Disclosures

• Dr. Nico Adams has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.