1. Steve Bryant Evan Bolton

3. Thanks, Steve!

4. Thanks, Steve!

5. The SoftwareYears

6. 1992
• CAS (and meters of books)
• Access through STN via IBM 3270
terminal emulation and cryptic
commands
• Beilstein Database (and meters of books)
• No open source software libraries for
cheminformatics

7. Computer-Assisted
Structure Elucidation
(CASE)
Steinbeck, C.; Angewandte Chemie. International
Ed. in English 1996, 35, 1984-1986
Steinbeck, C.: J. Chem. Inf. Comput. Sci. 2001,
41, 6, 1500
1992 - now

8. Successful Science
requires
Data and Software
to be
Free and Open

9. 1990

11. 16 Years of the
Chemistry Development Kit
(CDK)
Christoph Steinbeck
and the CDK Developers

12. http://cdk.sourceforge.net
The Chemistry Development Kit (CDK)
Open Source Cheminformatics in Java

13. The CDK after 16 years
•16,521 commits made by 115 contributors
•564,171 lines of code
•mostly written in Java
•well established, mature codebase
•maintained by a large development team
•with stable Y-O-Y commits
•estimated 151 years of effort (COCOMO model)
•first commit in October, 2000
•most recent commit 1 day ago
The Chemistry Development Kit (CDK)
Open Source Cheminformatics in Java

14. Bibliometrics

15. Try it: http://cdkdepict-openchem.rhcloud.com/
Error
1.4.x1.5.x
Examples 1-4: Clark A, et al, 2D structure depiction. JCIM, 46, 1107-1123 (2006)
1.5.x: Cleaner, More Efficient, More Robust, More Stable
Molecule 2D layout and rendering from SMILES

16. The DatabaseYears

17. 16
NMRShiftDB.org

18. The
European Bioinformatics Institute
(EBI)

19. The
European Bioinformatics Institute
(EBI)

20. The
European Bioinformatics Institute
(EBI)

21. The
European Bioinformatics Institute
(EBI)

22. The
European
Molecular
Biology
Laboratory
(EMBL)
A basic research
institute funded by
public research
monies from 20
member states.

23. The
European
Bioinformatics
Institute
(EBI)

24. Intermission

25. Chris Steinbeck David Wild

26. Rajarshi Guha Egon Willighagen

27. Documenting the
metabolomes of all
species on the planet

28. There are known knowns; there are things we know
we know.
We also know there are known unknowns; that is to
say, we know there are some things we do not know.
But there are also unknown unknowns – the ones we
don’t know we don’t know.
—United States Secretary of Defense,
Donald Rumsfeld

29. Chemical Entities of Biological Interest (ChEBI)

30. Chemical Entities of Biological Interest (ChEBI)

31. Additional data items for natural products
Species Variety Tissue
Links to ontologies
and taxonomies
Links to citations,
where available

33. ChEMBL – Data for Drug Discovery
Bioactivity
Compou
Assay/
>Thrombin
MAHVRGLQLPGCLALAALCSLVHSQHVFLAPQQARSLLQRVRRANTFLEEVRKGN
LERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRDKLAACLEGNCAE
GLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSSTT
GPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQ
YQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCY
VAGKPGDFGYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFG
SGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKS
PQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEK
3. Insight, tools and resources for translational drug discovery
2. Organization, integration, curation and standardization of pharmacology data
1. Scientific facts
Ki =
APTT = 11

36. The PubChem
Collaboration

38. Building upon extensive genomics research, we argue that the time is
now right to focus intensively on model organism metabolomes. We
propose a grand challenge for metabolomics studies of model
organisms: to identify and map all metabolites onto metabolic
pathways, to develop quantitative metabolic models for model
organisms, and to relate organism metabolic pathways within the
context of evolutionary metabolomics, i.e., phylometabolomics. These
efforts should focus on a series of established model organisms in
microbial, animal and plant research.
Metabolites. 2016 Feb 15;6(1)

40. •8.7 mio eukaryotic species on earth (+- 1.3mio)

41. •8.7 mio eukaryotic species on earth (+- 1.3mio)
•1.2 mio species identified and classified

42. •8.7 mio eukaryotic species on earth (+- 1.3mio)
•1.2 mio species identified and classified
•3000 - 4000 complete species genomes sequenced

43. •8.7 mio eukaryotic species on earth (+- 1.3mio)
•1.2 mio species identified and classified
•3000 - 4000 complete species genomes sequenced

44. •8.7 mio eukaryotic species on earth (+- 1.3mio)
•1.2 mio species identified and classified
•3000 - 4000 complete species genomes sequenced
What about completed metabolomes?

45. •8.7 mio eukaryotic species on earth (+- 1.3mio)
•1.2 mio species identified and classified
•3000 - 4000 complete species genomes sequenced
What about completed metabolomes?

46. Species Metabolomes are
being assembled on the fly
right now through data
sharing in Metabolomics

47. Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
AnalysisTools
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
MetaboLights Database at the EBI

48. Repository Entry

49. Repository Entry

50. Reference Layer

51. 7 most annotated metabolomes
in MetaboLights

52. 30 most annotated
metabolomes in MetaboLights

53. 1600 metabolome sizes in
MetaboLights on a log scale

55. Slides at
https://www.slideshare.net/csteinbeck
Funding

56. Steve Bryant Evan Bolton

58. Thanks for your attention