Skolnik symposium ACS Meeting Philadelphia 2016
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Transcript of Skolnik symposium ACS Meeting Philadelphia 2016
Steve Bryant Evan Bolton
Thanks, Steve!
Thanks, Steve!
The Software Years
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
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
Successful Science requires
Data and Software to be
Free and Open
1990
16 Years of the Chemistry Development Kit (CDK)
Christoph Steinbeck and the CDK Developers
http://cdk.sourceforge.net
The Chemistry Development Kit (CDK) Open Source Cheminformatics in Java
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
Bibliometrics
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
The Database Years
16
NMRShiftDB.org
The European Bioinformatics Institute
(EBI)
The European Bioinformatics Institute
(EBI)
The European Bioinformatics Institute
(EBI)
The European Bioinformatics Institute
(EBI)
The European Molecular Biology Laboratory
(EMBL)
A basic research institute funded by public research monies from 20 member states.
The European Bioinformatics Institute
(EBI)
Intermission
Chris Steinbeck David Wild
Rajarshi Guha Egon Willighagen
Documenting the metabolomes of all
species on the planet
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
Chemical Entities of Biological Interest (ChEBI)
Chemical Entities of Biological Interest (ChEBI)
Additional data items for natural products
Species Variety Tissue
Links to ontologies and taxonomies
Links to citations, where available
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
The PubChem Collaboration
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)
•8.7 mio eukaryotic species on earth (+- 1.3mio)
•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified
•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
•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?
•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?
Species Metabolomes are being assembled on the fly
right now through data sharing in Metabolomics
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
Repository Entry
Repository Entry
Reference Layer
7 most annotated metabolomes in MetaboLights
30 most annotated metabolomes in MetaboLights
1600 metabolome sizes in MetaboLights on a log scale
Slides athttps://www.slideshare.net/csteinbeck
Funding
Steve Bryant Evan Bolton
Thanks for your attention