Award details

Metabo

Reference	BB/L024152/1
Principal Investigator / Supervisor	Ms Claire O'Donovan
Co-Investigators / Co-Supervisors	Professor Julian Griffin, Professor Christoph Steinbeck
Institution	EMBL - European Bioinformatics Institute
Department	Chemoinformatics and Metabolism
Funding type	Research
Value (£)	840,689
Status	Completed
Type	Research Grant
Start date	15/07/2014
End date	14/01/2018
Duration	42 months

Abstract

In the past three years, the MetaboLights database at the European Bioinformatics Institute has been established as the first open-access, general-purpose, cross-species database and study repository in Metabolomics world-wide. Here, we now propose significant new developments which will lead to more and better metabolomics data openly available to the scientific community and will allow researchers to better visualise and analyse the data in MetaboLights and to contribute more efficiently: We will add new database interfaces to support the data flow from local LIMS. We will provide a JAVA API to create valid ISA-tab data structures to be used by developers and vendors, labs and individual researchers We will extend our set of online analysis tools and develop a) 'MetaboLights Labs' for people to upload data and run key data processing or analysis task inside MetaboLights, b) pipelines for producing a datasets annotated with identified and semi-quantified metabolites. c) an integration the Risa package, which allows access to metadata/data in ISA-Tab format and build Bioconductor data structures. d) All raw MS and NMR data uploaded for analysis will be transformed into a MSI-compliant study for MetaboLights integration. We will develop visualisation tools and methods for many data types (including raw spectra, chromatograms, compound collection, multivariate study metadata ...). Identified metabolites will be mapped onto pathways. We will provide tools for enrichment analysis for researchers to determine whether a pattern of metabolic changes are associated with particular metabolic pathways. The reference collections will be significantly extended and enriched with data focus areas, grouped and visualised based on information on a model organism or biological interest area. Through developing a MetaboLights curation tool, we will allow online editing after the submission has gone online, with tracked changes allowing rigorous auditing and versioning.

Summary

Metabolomics is an important phenotyping technique for molecular biology and medicine. It assesses the molecular state of an organism or collections of organisms through the comprehensive quantitative and qualitative analysis of all small molecules in cells, tissues, and body fluids such as urine and blood. Metabolic processes are at the core of physiology. Consequently, metabolomics is ideally suited as a tool to characterize disease states in organisms, as a tool to assessment of organism for their suitability in, for example, renewable energy production or for biotechnological applications in general. In addition application of metabolomics in environmental science, toxicology, food and medical industry is well established, growing and documented. The production of metabolomics data is labour- and cost-intensive. There is therefore a strong incentive for a society to encourage the broadest and most open imaginable access to data produced in publically funded research. This has now been widely recognized by funders, publishers and governments for applications throughout the biosciences and beyond. During the initial 3-year funding period (2011-2013), MetaboLights has been widely publicised and recognised throughout the community as the first general purpose, cross-species, cross-application database for metabolomics. This is exemplified by the central role of MetaboLights in the European COSMOS consortium for metabolomics standards development and as part of the recently founded expert centre for metabolomics in the European Biobanks Infrastructure BBMRI. We are now proposing significant new and crucial enhancements for the next three years of MetaboLights development. Specifically, we propose to work on: * Large metabolomics lab submission interfaces/integration (API): We will develop new database interfaces to support the data flow from large Laboratory Information Management Systems (LIMS). Specifically we will provide a JAVA library (API) to create valid ISA-tab data structures. We will provide online MSI compliant validation methods for generated ISA-tab structures. These tools allows participating labs to generate valid studies inside their compute infrastructure. * Analysis tools (online): Despite significant improvements in the software for metabolomics studies these tools are in general fragmented across laboratories or specific to a particular workflow. To address this we will collect open access tools and investigate workflows for the most common approaches used in metabolomics, acting as a portal. * Tools for visualisation of metabolomics data: We will develop visualisation tools and methods for as many different data types as possible, deposited by our users, so that primary data and study results can be visualised online without the need for download and local analysis. * Enrichment and extension to the reference layer: Our curators will continue to add richly annotated compounds to the reference layer. This will be partly be driven through compound identification data in the repository layer and partly by our efforts to create complete reference collections for metabolomes of important model organisms. The reference collections will be grouped and visualised based on information on a model organism or biological interest area. * A curation tool for MetaboLights submissions: This allows for the versioned online editing of MetaboLights studies, eliminating the need to for offline editing and re-upload. * Metabolite identification assistant: We will use information of identified compounds within a dataset as prior information for identifying known unknowns, one of the biggest problems associated with metabolomic datasets. We are confident that those developments will greatly enhance the utility of MetaboLights for the metabolomics and systems biology community and contribute to the visibility of the strong UK metabolomics community in the world.

Impact Summary

Metabolomics is an important phenotyping technique for molecular biology and medicine. It assesses the molecular state of an organism or collections of organisms through the comprehensive quantitative and qualitative analysis of all small molecules in cells, tissues, and body fluids such as urine and blood. Metabolic processes are at the core of physiology. Consequently, metabolomics is ideally suited as a tool to characterise disease states in organisms, as a tool to assess organism suitability, for example, in renewable energy production or for biotechnological applications in general. In addition application of metabolomics in environmental science, toxicology, food and medical industry is well established, growing and documented. Production of metabolomics data is labours and costly. There is therefore a strong incentive for a community to encourage the broadest and most open imaginable access to data produced in publicly funded research. This has now been widely recognised by funders, publishers and governments for applications throughout the biosciences and beyond. During the initial 3-year funding period (2011-2013), MetaboLights has been widely publicised and recognised throughout the community as the first general purpose, cross-species, cross-application database for metabolomics. This is exemplified by the central role of MetaboLights in the European COSMOS consortium for metabolomics standards development and as part of the recently founded expert centre for metabolomics in the European Biobanks Infrastructure BBMRI. We further demonstrate the utility of the MetaboLights resource through a substantial number of letters of support from all across the globe. The MetaboLights resource benefits a number of significant communities performing biological research and development in metabolomics, proteomics and functional genomics. This is in congruence with virtually all of the strategic research priorities of the BBSRC: The metabolome is ideally suited to fingerprint a food item in food security monitoring. Many products of industrial biotechnology and bioenergy production are metabolites, and the optimisation of their yield is done through engineering of metabolic pathways and monitored through metabolome analysis. The last three years have seen a substantial increase of scientific publications on the use metabolomics in ageing research, with an emphasis of areas affecting live-long health and well-being. MetaboLights is already serving datasets on diabetes and obesity research to the scientific community. Last but not least, metabolomics plays an important role as a hypothesis generator in data-driven biology and as one of the building blocks of cross-omics studies. Metabolomics it is an irreplaceable building block to systems approaches in the biosciences. For government agencies and ministries, MetaboLights serves as a portal for information about small molecule biomarkers and their significance for a particular diagnostic tool or method. MetaboLights has been widely recognised in industry and is, for instance, an important bioinformatic resources for a number of major companies in the UK such as GlaxoSmithKline, Syngenta, AstraZeneca and Unilever. As a unique and general metabolomics resource based in the UK we are strengthening the standing of the UK biomedical community through our strong and growing networks within Europe and across the globe, as MetaboLights will be one of the core nodes of the emerging global network for omics data exchange. The biological community surely benefits from MetaboLights because like all other EBI resources, the databases is completely open to the public, including open access to the data. Data is available in publicly accepted open standards. We also provide training material and courses about MetaboLights which are open and accessible to everyone.

Committee	Research Committee D (Molecules, cells and industrial biotechnology)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	Bioinformatics and Biological Resources Fund (BBR) [2007-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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