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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, 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.
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