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, cross- application The EBI’s Metabolomics Database Christoph Steinbeck, Jules Griffin BBSRC BBR grant BB/I000933/1 Nomenclature Species Tissues GC Disease NMR MS Crossrefs Organs Structure LC Cell Types Identifier Pathways Reference Reference Reference Spectroscopy Chemistry Biology Publication Experimental Repository MetaboLights 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 Ontology – Names and synonyms classifications caffeine metabolite 1,3,7-trimethylxanthine CNS stimulant methyltheobromine trimethylxanthines Links to more Chemical data information in Formula: C8H10N4O2 other databases Charge: 0 Mass: 194.19 MSDchem: CFF KEGG DRUG: D00528 Chemical Informatics Chemical structures and InChI=1/C8H10N4O2/c1-10-4-9-6- visualisations 5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 SMILES CN1C(=O)N(C)c2ncn(C)c2C1=O 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: Stephan Workflow-driven cheminformatics. Beisken, EBI BMC Bioinformatics, 14(1), 257 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. John May http://johnmay.github.io/metingear/ 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.