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Steve Bryant Evan Bolton
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Thanks, Steve!
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Thanks, Steve!
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The Software Years
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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
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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
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Successful Science requires
Data and Software to be
Free and Open
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1990
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16 Years of the Chemistry Development Kit (CDK)
Christoph Steinbeck and the CDK Developers
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http://cdk.sourceforge.net
The Chemistry Development Kit (CDK) Open Source Cheminformatics in Java
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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
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Bibliometrics
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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
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The Database Years
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16
NMRShiftDB.org
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Molecular Biology Laboratory
(EMBL)
A basic research institute funded by public research monies from 20 member states.
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The European Bioinformatics Institute
(EBI)
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Intermission
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Chris Steinbeck David Wild
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Rajarshi Guha Egon Willighagen
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Documenting the metabolomes of all
species on the planet
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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
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Chemical Entities of Biological Interest (ChEBI)
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Chemical Entities of Biological Interest (ChEBI)
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Additional data items for natural products
Species Variety Tissue
Links to ontologies and taxonomies
Links to citations, where available
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ChEMBL–DataforDrugDiscovery
Bioactivity
Compou
Assay/
>Thrombin MAHVRGLQLPGCLALAALCSLVHSQHVFLAPQQARSLLQRVRRANTFLEEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRDKLAACLEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSSTTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQGRLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEK
3. Insight, tools and resources for translational drug discovery
2. Organization, integration, curation and standardization of pharmacology data
1. Scientific facts
Ki =
APTT = 11
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The PubChem Collaboration
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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)
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•8.7 mio eukaryotic species on earth (+- 1.3mio)
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
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•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?
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•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?
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Species Metabolomes are being assembled on the fly
right now through data sharing in Metabolomics
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Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
Ana
lysi
s To
ols
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
MetaboLights Database at the EBI
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Repository Entry
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Repository Entry
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Reference Layer
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7 most annotated metabolomes in MetaboLights
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30 most annotated metabolomes in MetaboLights
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1600 metabolome sizes in MetaboLights on a log scale
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Slides athttps://www.slideshare.net/csteinbeck
Funding
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Steve Bryant Evan Bolton
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Thanks for your attention