• Representation of Chemical Structures
• 37 min
  1. Basics in cheminformatics: representation of chemical structures 1

  • Dr. Thomas Engel
• 28 min
  2. Basics in cheminformatics: representation of chemical structures 2

  • Dr. Thomas Engel
• 35 min
  3. Chemical file formats and line notations

  • Prof. Achim Zielesny
• Visualization of Chemical Structure
• 17 min
  4. Common types of visualization of chemical structure

  • Prof. Robert M. Hanson
• Basic Algorithms in Cheminformatics
• 40 min
  5. Ring searching and aromaticity detection

  • Prof. Dr. Christoph Steinbeck
• 44 min
  6. Substructure searching, similarity calculations and fingerprints

  • Mr. Mark Rijnbeek
• 36 min
  7. Canonization, Morgan algorithm, equivalence classes

  • Dr. Markus Meringer
• Structure Databases
• 46 min
  8. Storing, searching and dissemination of chemical information

  • Prof. Achim Zielesny
• 42 min
  9. Databases, indices and structure-related queries

  • Dr. Wolf-Dietrich Ihlenfeldt
• Quantitative Structure-Activity/Property Relationships
• 40 min
  10. Overview of descriptors

  • Dr. Jörg Kurt Wegner
• Machine Learning in Cheminformatics
• 44 min
  11. Introduction to machine learning and its application in chemistry

  • Dr. Nikolas Fechner
• Cheminformatics in Drug Discovery
• 38 min
  12. Virtual screening

  • Dr. John H. Van Drie
• 47 min
  13. Pharmacophore methods in drug discovery

  • Dr. John H. Van Drie
• 65 min
  14. Pragmatic virtual fragment-based ligand design

  • Dr. Marcus Gastreich
• 44 min
  15. Chemogenomics

  • Dr. John P. Overington
• Molecular Modelling
• 62 min
  16. Molecular modelling: empirical methods

  • Prof. Tim Clark
• 59 min
  17. Molecular modelling: electronic structure methods

  • Prof. Tim Clark
• Computer-Assisted Structure Elucidation
• 53 min
  18. Methods for NMR-spectrum prediction

  • Dr. Wolfgang Robien
• 44 min
  19. Cyber-based structure elucidation

  • Prof. Morton E. Munk
• The Chemical Semantic Web
• 41 min
  20. Semantic chemistry: an overview

  • Dr. Nico Adams
• Open Notebook Science and the Open Access Movement in Chemistry
• 34 min
  21. Open research: motivation, theory, and practice

  • Dr. Cameron Neylon
• Archived Lectures *These may not cover the latest advances in the field
• 48 min
  22. Representation of chemical structures

  • Dr. Thomas Engel

Printable Handouts

PDF

Navigable Slide Index

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.