Download Cheminformatics and metabolism resources

Cheminformatics and
Metabolism Resources
Janna Hastings
Group coordinator
Cheminformatics
and
Metabolism
Team
Metabolomics
Measures occurrence and
concentrations of many
small molecules
(metabolites) in an organism
at once.
http://www.ebi.ac.uk/metabolights
MetaboLights
open-access, cross-species, crossapplication
The EBI’s Metabolomics Database
Christoph Steinbeck, Jules Griffin
BBSRC BBR grant BB/I000933/1
Species
Nomenclature
GC
Crossrefs
MS
NMR
Disease
Structure
LC
Identifier
Reference
Spectroscopy
Publication
Experimental Repository
MetaboLights
Organs
Pathways
Reference
Chemistry
Tissues
Cell Types
Reference
Biology
Repository Layer
www.ebi.ac.uk/metabolights
(metabolights.org, metabolights.eu)
Reference Layer
Reference Layer
Reference Layer
Reference Layer
ChEBI: Chemical Entities of Biological
Interest
Names and synonyms
Ontology –
classifications
caffeine
1,3,7-trimethylxanthine
methyltheobromine
metabolite
CNS stimulant
trimethylxanthines
Chemical data
Formula: C8H10N4O2
Charge: 0
Mass: 194.19
Chemical Informatics
InChI=1/C8H10N4O2/c1-10-4-9-65(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
SMILES CN1C(=O)N(C)c2ncn(C)c2C1=O
Links to more
information in
other databases
MSDchem: CFF
KEGG DRUG: D00528
Chemical structures and
visualisations
Increasing focus on natural products
Global Collaboration
in Metabolomics and
the BioSciences
COSMOS
COrdination of Standards in MetabolOmicS
• 2 mio Euros for meetings and
coordination
• 90.000 Euros for travel for global
stakeholders
INFRA-2012-3.3. "Coordination actions, conferences and
studies supporting policy development, including
international cooperation, for e-Infrastructures".
Research
PAMELA pipeline for
metabolome inference
DB integration
Text Mining
Enumeration
Validation
Moreno P, PhD thesis, U Cambridge, 2012
Computer-Assisted
Structure Elucidation
(CASE)
Steinbeck C (2004) Recent developments in
automated structure elucidation of natural
products. Nat. Prod. Rep. 21, 512–518.
The Chemistry Development Kit (CDK):
An Open Source Java Library for
Structural Cheminformatics
http://cdk.sourceforge.net
Feature Extraction and Spectrum
Processing
Beisken, S., Meinl, T., Wiswedel, B.,
de Figueiredo, L. F., Berthold, M., &
Steinbeck, C. (2013). KNIME-CDK:
Workflow-driven cheminformatics.
BMC Bioinformatics, 14(1), 257
Stephan
Beisken, EBI
Stochastic Searching for
Structure Elucidation
Crossover
Fitness Evaluation (Scoring)
Stotal = SNMR-HMBC + SNMR-HHCOSY +
SNMR-Shift + SSymmetry + SMassSpec...
+ SFeatures
Polycarpol (C30H48O2).
Mutation
Han YQ & Steinbeck C (2004) Evolutionary-algorithm-based
strategy for computer-assisted structure elucidation. Journal
of Chemical Information & Computer Sciences 44, 489–498.
• Natural Product-likeness classification and integrated it into
Taverna workflow tool
• (http://sourceforge.net/projects/np-likeness/).
• Included in second version of SENECA CASE
Jayaseelan KV, Moreno P, Truszkowski A, Ertl P & Steinbeck C (2012) Natural product-likeness
score revisited: an open-source, open-data implementation. BMC Bioinformatics 13, 106.
http://johnmay.github.io/metingear/
John
May
Desktop Application
• Simplify editing of genome-scale metabolic model
• Backed by the CDK providing structure representation
• Database free, access to common resources resolved
automatically through web and local instances
• Export to annotated SBML
• Use the structure to rapidly merge, compare and
complete models (wip)
Thank You