Metabo

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Chemoinformatics and Metabolism

Abstract

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.

Technical Summary

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.

Planned Impact

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.

Publications

10 25 50
publication icon
Acharjee A (2017) The translation of lipid profiles to nutritional biomarkers in the study of infant metabolism. in Metabolomics : Official journal of the Metabolomic Society

publication icon
Ament Z (2016) Metabolomics dataset of PPAR-pan treated rat liver. in Data in brief

publication icon
Atzori L (2017) How to bridge metabolomics and genomics. in The international journal of biochemistry & cell biology

publication icon
Beisken S (2015) SpeckTackle: JavaScript charts for spectroscopy. in Journal of cheminformatics

publication icon
Bond NJ (2017) : an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics. in Metabolomics : Official journal of the Metabolomic Society

publication icon
Charidemou E (2017) The use of stable isotopes in the study of human pathophysiology. in The international journal of biochemistry & cell biology

 
Description In this 2nd MetaboLights grant, and we are mainly focusing on the developments around:
- Online curation of submitted studies
- Online staging area (MetaboLights LABS)
- API for ISA-Tab creation, from LIMS and raw data
- Online validations
- Online analysis tools integration (through workflows)
- Visualisations of research data
- Parsing of open source files, mzML and nmrML (mzml2ISA software package)
- Ongoing curation of studies and compounds
Exploitation Route All software and data used is open source and available for any purpose. Software components are being developed such that other interested parties can build upon or customise the existing code to fit their needs. We have also industry partners downloading and evaluation our software for internal use.
Sectors Chemicals,Education,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.ebi.ac.uk/metabolights/
 
Description The MetaboLights repository data is frequently accessed from all over the world and users include industry companies as well as academics. The MetaboLights software suite has been downloaded and is currently being evaluated, and we assume used, internally in Bayer as part of their metabolomics pipeline. The METASPACE H2020 project are now using MetaboLights as the main Metabolomics repository for imaging mass spectrometry data. Additionally our collaboration in developing the new ISA-Tab API has resulted in the setting up an automated submissions pipeline between METASPACE (EMBL-Heidelberg) and MetaboLights and a decision to redevelop our submission procedure to incorporate the API in an wraparound fashion to improve usability for our community. It is also being used in a new prototype pipeline with Metabolon which will greatly increase the data available in MetaboLights and improve reusability. In the time since the above report, we have reutilised the API to provide a service for Metabolon, one of the most successful metabolomics companies, for the deposition of the raw data in MetaboLights and the online editor tool then allows the original submitter to complete the deposition for the benefit of all involved. Previously this data was not available to the public.
Sector Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Description Technology Development Grant, MetaboFlow - the development of standardised workflows for processing metabolomics data to aid reproducible data sharing and big data initiatives
Amount £900,000 (GBP)
Funding ID 202952/B/16/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2016 
End 11/2019
 
Title MetaboLights automatic online validations 
Description The ISA Tool Suite serves as the main study submission platform for MetaboLights. In order to ease the process of correction of incorrect and/or missing information, we have implemented a more stringent online study validation scheme, that checks for the overall integrity of the information contained within the submitted studies. The user can now use the MetaboLights website to verify their submitted data, using the following guidelines. 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact This validation scheme greatly aids the overhead for both our curators and submitters, in terms of going back and forth with the individual corrections. A key component of this validation scheme is ISA-Tab based MSI (Metabolomics standards Initiative) validation. This is a deliverable of the current MetaboLights grant. The URL referenced (http://www.ebi.ac.uk/metabolights/MTBLS1#validations) show the systems for one of our studies, MTBLS1 
URL http://www.ebi.ac.uk/metabolights/MTBLS1#validations
 
Title MetaboLights new online help and guide 
Description After feedback from submitters and users of the database it was apparent that the Metabolights documentation was inadequate. Submitters were confused about the study production and submission process and a number of basic errors were often made during the process. So it was decided to overhaul and re­write the MetaboLights documentation. It was decided to focus on providing a succession of step­by­step, easy to follow, with clear illustrations, of how to setup, curate, validate, your Metabolights study for the three main types of study assay: NMR, GC/MS. and LC­MS. Advice was provided, as to what parameters to provide, ontology terms to use, along with workaround solutions, to known issues and limitations with the inherent ISAcreator software and the accompanying ISA­Tab metadata capture format. 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact Improved documentation ensures better quality metadata reporting, which in the long term aids both our team and the submitters. We also provide a copy of the tutorials in PDF form for our submitters in China who do not have access to Google Docs. These are currently available here: ftp://ftp.ebi.ac.uk/pub/databases/metabolights/documentation/ 
URL http://www.ebi.ac.uk/metabolights/help
 
Title New AngularJS and VUE frameworks for MetaboLights user interface 
Description We have replaced the older JSP framework with AngularJS. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact Angular is a modern responsive JavaScript framework developed and use by Google. This new framework brings a more responsive page layout that works across multiple devices, browsers and platform. Additionally this also brings a fresh/crisp look to MetaboLights. 
URL http://www.ebi.ac.uk/metabolights/
 
Title New search engine for MetaboLights 
Description Replaced the older direct Lucene based search with Elastic. 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact MetaboLights use to maintain a local Lucene search index based in extracting data from our database schema. With the addition of our new web services, we switched the search engine to Elastic. In elastic we index the complete study based in the same JSON objects we use to display the study and compound pages online. This enable a more consistent search result, and offer a much easier technical infrastructure. Elastic search is still based on an underlaying Lucene index, but it's abstracted away. 
URL http://www.ebi.ac.uk/metabolights
 
Description BioCrates to MetaboLights submission pipeline 
Organisation Biocrates Life Sciences
Country Austria 
Sector Private 
PI Contribution University of Oxford, EMBL-EBI and Biocrates have worked together to make a deposition process from Biocrates. Users can contact Biocrates or give consent/permission to export the XML document from the MetIDQ software solution for their datasets. The data disclosure practice strongly encourages deposition of raw data files (the mass spectrometry files generated during the data acquisition) alongside the Biocrates XML document and metabolites identified as well as additional metadata, when possible. The MetaboLights team processed the data to allow loading and long term preservation in the repository. The dataset will be issued an citable accession number, therefore increasing the visibility of the research. Part of the MetaboLights curation process may require further interaction to clarify annotations, but overall, the burden on submitters is minimal.
Collaborator Contribution This work was initiated from University of Oxford, Dr. Philippe Rocca-Serra. Philippe developed the XML parser that converts the data from Biocrates proprietary format to ISA-Tab.
Impact More study submissions to MetaboLights from Biocrates MetIDQ users
Start Year 2014
 
Description BioCrates to MetaboLights submission pipeline 
Organisation University of Oxford
Department Oxford E-Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution University of Oxford, EMBL-EBI and Biocrates have worked together to make a deposition process from Biocrates. Users can contact Biocrates or give consent/permission to export the XML document from the MetIDQ software solution for their datasets. The data disclosure practice strongly encourages deposition of raw data files (the mass spectrometry files generated during the data acquisition) alongside the Biocrates XML document and metabolites identified as well as additional metadata, when possible. The MetaboLights team processed the data to allow loading and long term preservation in the repository. The dataset will be issued an citable accession number, therefore increasing the visibility of the research. Part of the MetaboLights curation process may require further interaction to clarify annotations, but overall, the burden on submitters is minimal.
Collaborator Contribution This work was initiated from University of Oxford, Dr. Philippe Rocca-Serra. Philippe developed the XML parser that converts the data from Biocrates proprietary format to ISA-Tab.
Impact More study submissions to MetaboLights from Biocrates MetIDQ users
Start Year 2014
 
Description ISA-Tab API 
Organisation University of Oxford
Department Oxford E-Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Our goal is to provide an API to enable institutes and their laboratory information management systems (LIMS) to output metadata in ISA-Tab format. These tools allow participating labs to generate valid metadata studies within their compute infrastructure. We wish to point out that we do not plan to write code for any particular number of LIMS integrations. Rather, we are providing one and only one Application Programming Interface (API) on the MetaboLights side. This will enable interested laboratories to online interface their existing LIMS system with MetaboLights. We developed an API, for reading data only, in Java. This read-only API is currently supplying our web services with all the metadata elements contained in the respective studies metadata. Our work in this area prompted our collaborators in Oxford introduce the group at TGAC to the MetaboLights team.
Collaborator Contribution The Oxford e-Research Centre at the University of Oxford has for some time worked together with TGAC in Norwich, which is implementing a new system for multi-omics data capture based on ISA-Tab for metadata capture. TGAC is trying to achieve the same features as EMBL-EBI in terms of an API for ISA-Tab manipulation. TGAC and Oxford started working on a Phyton based approach, and this would support traditional CRUD (Create, Read, Update and Delete). Their choice was also influences by similar efforts at TGAC, how was already working on a Phyton based approach. It became apparent that there were clear synergies for EMBL-EBI, TGAC and Oxford. Our team at EMBL-EBI decided to collaborate on this version of the API, which will clearly help in the future development of a ISA-Tab API with more features than we initially anticipated.
Impact Key building block for our approach to edit ISA-Tab files online.
Start Year 2015
 
Description MetaboLights and MetaboAnalyst Collaboration 
Organisation University of Alberta
Country Canada 
Sector Academic/University 
PI Contribution MetaboAnalyst is a web application for doing comprehensive metabolomic data analysis. It is developed and hosted by Dr. Wishart's lab in University of Alberta. The analysis tool is very popular and would benefit from powerful compute resources at the EBI to meet its user load. We are in the process of migrating the current R backend of the tool to EBI in-house R-backend, to improve the overall resource usage. Further, the Metabolights users will benefit from having a integrated analysis tool to perform easy and comprehensive analysis of a metabolomic dataset.
Collaborator Contribution Dr. Wishart's lab has provided the Metabolights team with the code base for MetaboAnalyst and has a dedicated resource for combined development of MetaboAnalyst.
Impact - Shared code repository of MetaboAnalyst
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation Beijing Genomics Institute
Country China 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation University of Birmingham
Department College of Engineering and Physical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation University of Cambridge
Department The Sainsbury Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Description UK and China collaborative partnership 
Organisation University of Oxford
Department Oxford E-Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We host training workshops to support scientists in the UK and China in managing and sharing their metabolomics data and analyses workflows.
Collaborator Contribution Provide metabolomics dataset as well as contributing to training workshops supporting the sharing of data and their analyses in metabolomics.
Impact Several metabolomics dataset shared via thishttp://www.ebi.ac.uk/metabolights/MTBLS146 collaboration via MetaboLights repository e.g: http://www.ebi.ac.uk/metabolights/MTBLS79 http://www.ebi.ac.uk/metabolights/MTBLS146 http://www.ebi.ac.uk/metabolights/MTBLS91
Start Year 2014
 
Title ISA-Tab API 
Description Variability in the studies being submitted to MetaboLights basically come from two sides: First, the submitters using different in-house or commercial Laboratory Information Information Systems (LIMS) with dissimilar features and exporting file formats. Second, the intrinsic nature of the new methods and techniques (Mass Spectrometry imaging, MSI) require different sets of data and metadata matrixes, which must be adapted to the ISA-Tab format. Currently, we are participating in the definition and implementation of a new Python-based ISA-API library, which will support the programmatic creation of ISA objects, multiple ISA serializations (e.g. tabular and JSON representations) and conversions between ISA and other formats (e.g. SRA xml). 
Type Of Technology Webtool/Application 
Year Produced 2015 
Impact Data files within metabolomics studies can become rather large, taking to much time in the process of online submission, sometimes producing connection time outs. In order to prevent this we are providing a mechanism for failsafe and resumable online transfer of large study data to MetaboLights, benefiting small or large labs equally. Submitters can use the ftp protocol, with longer connection time that regular http, or use an Aspera client application. Aspera is being assumed as the general procedure for the future. We are actively participating in the new ISA-Tab developments, leaded by the ISATeam at Oxford, are being done on JSON schemas and JSON representation for ISA-Tab. A python-based ISA-API with components for parsing and converting between ISA-Tab and ISA-JSON, will be available soon and a working prototype is being tested now. The conversion from Metabolomics Workbench to ISA-tab will be carried out by a python script that relies on BeautifulSoup parser. This script is being developed to produce ISA objects, that way the actual serialization mechanism can be decided later. In addition, the ISAconverter tool has implemented ISA-Tab to SRA-xml and a opposite conversion from SRA-xml to ISA-Tab. 
URL https://github.com/ISA-tools/isa-api
 
Title MetaboAnalyst integration in MetaboLights 
Description MetaboAnalyst provides a user-friendly, web-based analytical pipeline for high-throughput metabolomics studies. In particular, MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data processing, normalization, multivariate statistical analysis, as well as data annotation. The tool focuses on exploratory statistical analysis, functional interpretation, and advanced statistics for translational metabolomics studies. 
Type Of Technology Webtool/Application 
Year Produced 2015 
Impact MetaboAnalyst has been modified to run on the EMBL-EBI R-cloud and has been included in MetaboLights as part of ongoing integration of analysis tools into MetaboLights LABS. The MetaboLights team has modified the backend (handling of R-pacakges/sniplets) to run on our extensive R-Cloud. Standard MetaboAnalyst runs on a single R-serve instance, so we added the ability to run in a distributed environment. In a recent survey we conducted, MetaboAnalyst was the most used metabolomics analysis tool amongst the respondents. 
URL http://www.ebi.ac.uk/metabolights/metaboanalyst
 
Title MetaboLights RESTful web services 
Description In our ongoing efforts to enable online editing of submitted metadata, in ISA-Tab format, we have developed a RESTful web service (ws) to enable decoupling of dependencies. Currently all pages related to the study/experimental data, metadata and primary research files (MetaboLights repository) as well as compound pages (MetaboLights Reference Layer) as served by this web service. For public data the WS allows open access, but for private data the user needs to be authenticated and authorised, which is all handled in the WS. 
Type Of Technology Webtool/Application 
Year Produced 2015 
Impact We have moved the underlaying technology stack into a more modular modern design. When MetaboLights was first built, we successfully based the repository on the existing ISA data model. Our experience has been that this was in great need of modernisation and was rather cumbersome to maintain. To enable online edit of the primary metadata files, we also needed to have a system less dependent on the database model and more focused on the main ISA-Tab files. Our current WS reads all the data, but we are still implementing full CRUD (Create, Read, Update and Delete) features. This is currently happening as part of our curation tool and online editing of metadata. Please note that the WS URL in the example gets the metabolite annotation file for the first assay for study MTBLS1 
URL http://www.ebi.ac.uk/metabolights/MTBLS1/assay/1/maf
 
Title MetaboLightsDownloader Docker container 
Description Docker container for downloading, public and private, data from MetaboLights. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact This container offers high throughput, via Aspera command line client, download of MetaboLights data. This is specially useful in a workflow setting where softwares are dependent of raw data for data processing. Together with the MetaboLightsUploader this provides a computational method of pushing and pulling data to/from MetaboLights 
URL https://github.com/phnmnl/container-scp-aspera
 
Title MetaboLightsUploader Docker container 
Description Facilities for downloading studies from MetaboLights Labs, containerised in Docker. Use mainly by the PhenoMeNal project 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Enable users to use a container for uploading data to MetaboLights LABS (online staging area). The intention is to use this to push raw and processed data to MetaboLights LABS for further annotation and submission as a completed study. 
URL https://github.com/phnmnl/container-mtbl-labs-uploader
 
Title Metabolite Identification plugin for ISAcreator 
Description We have developed an ISAcreator plugin to simplify the reporting of metabolites identified in an experiment. We have based the reporting format on the suggested mzTAB (small molecule section) standard (https://code.google.com/p/mztab). 
Type Of Technology Software 
Year Produced 2011 
Open Source License? Yes  
Impact Simplified metabolite annotations due to PubChem search integration. 
URL https://github.com/EBI-Metabolights/ISAcreatorPlugins
 
Title NMR & MS spectral viewer (SpeckTackle) 
Description SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is freely available and targeted at life science communities that deal with spectroscopic data such as coming from mass spectroscopy, infrared spectroscopy, or NMR. It contains several default chart types, supports common functionality, e.g. for spectra overlays or tooltips, and is designed to be portable. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact MetaboLights is using this component. This has given MetaboLights a more feature rich NMR & MS special viewer, which runs on top of the existing reference spectra. Example: http://www.ebi.ac.uk/metabolights/MTBLC27570#nmrspectra 
URL https://bitbucket.org/sbeisken/specktackle/wiki/Home
 
Description 2nd Metabolomics Sardinian Scientific School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact 2nd Metabolomics Sardinian Scientific School was aimed at post-grad students new to the field of metabolomics. We gave seminars and workshops in various tools and techniques in metabolomics.
Year(s) Of Engagement Activity 2016
 
Description Cambridge Science Week 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact took part in Cambridge Science week and put on a display on personalised medicine and health using advanced biochemical techniques.
Year(s) Of Engagement Activity 2017
 
Description Danish-UK Metabolism meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Taught postgrads how to use metabolomics and lipidomics to study aspects of type 2 diabetes and related disorders.
Year(s) Of Engagement Activity 2017
 
Description EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This course provided an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It was delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification. During this course the delegates learned about:
- Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches
- Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN
- Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts, data clustering and regression methods
- Metabolomics downstream analyses: KEGG, BioCyc, and MetExplore for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis
- Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository; PHENOMenal, workflows4metabolomics
- Metabolomics Flux and Stable Isotope Resolved Metabolomics (SIRM)
Year(s) Of Engagement Activity 2018
URL https://www.ebi.ac.uk/training/events/2018/embo-practical-course-metabolomics-bioinformatics-life-sc...
 
Description EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This course provided an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It was delivered using a mixture of lectures, computer-based practical sessions and interactive discussions.
Year(s) Of Engagement Activity 2017
URL https://www.ebi.ac.uk/training/events/2017/embo-practical-course-metabolomics-bioinformatics-life-sc...
 
Description EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 3rd EMBO metabolomics course at EMBL-EBI. This cource provided an overview of key issues that affect metabolomics studies, handling dataset and procedures for the analysis of metabolomics data using bioinformatics tools. This is hugely oversubscribed every year.
Year(s) Of Engagement Activity 2015
URL http://www.ebi.ac.uk/training/events/2015/embo-practical-course-metabolomics-bioinformatics-life-sci...
 
Description EMBRIC, Definition of strain and chemical data requirements 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a workshop on how to use ELIXIR/EMBl-EBI data resources to manage and search strain data and derived chemical data (especially through MetaboLights) with the aim of defining practical requirements and the possibility to run a pilot with one/two of the EMBRIC participants.
Year(s) Of Engagement Activity 2017
URL http://www.embric.eu
 
Description First Brazilian Workshop On Bioinformatics/Chemometrics For Metabolomics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The workshop grouped expertise on metabolomics data analysis spread in different science fields in the Brazilian community. It was also an attempt to strength community collaboration, exchanging resources and knowledge through the community mapping. MetaboLights was presented in the "Data sharing and standards in metabolomics: What we can learn from other "omics" " session.
Year(s) Of Engagement Activity 2015
URL http://cosmos-fp7.eu/node/71
 
Description MetaboFlow and Cambridge Metabolomics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Held a Metabolomics Interest group for the East Anglia/London region to increase interest in this research area.
Year(s) Of Engagement Activity 2017
 
Description MetaboGaps poster at the ICBB 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster session at the ICBB for MetaboGaps
Year(s) Of Engagement Activity 2014
 
Description MetaboLights and ChEBI at the Nutrition Society (London) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We did a full day MetaboLights and ChEBI presentation (incl Rhea, Reactome and the Enzyme Portal) and hands-on workshop at the Nutrition Society (London). There were 12-15 participants
Year(s) Of Engagement Activity 2015
URL http://www.nutritionsociety.org/training-and-education/bioinformatics-nutritionists
 
Description MetaboLights at 2nd International Conference on Biotechnology a Bioinformatics, Pune, India 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited to present MetaboLights at 2nd International Conference on Biotechnology a Bioinformatics, Pune, India
Year(s) Of Engagement Activity 2015
URL http://icbb.in
 
Description MetaboLights presentation at "Biomarkers for Brain Disorders: Challenges and Opportunities" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented MetaboLights (and COSMOS) during the conference, with a focus on standardisation in metabolomics.
Year(s) Of Engagement Activity 2015
URL http://conf.hinxton.wellcome.ac.uk/advancedcourses/Biomarkers2015ProvisionalProgramme.pdf
 
Description Metabolomics 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This is the largest yearly International Metabolomics conference, the 13th International Conference of the Metabolomics Society
Year(s) Of Engagement Activity 2017
URL http://metabolomics2017.org
 
Description Metabolomics Workflows 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This course will provide an introduction to metabolomics data analysis using publicly available software and tools. Participants will become familiar with the current state of data sharing and data standards in metabolomics, particularly through using the EMBL-EBI's MetaboLights repository. In addition, participants will have a hands-on session using the PhenoMeNal Compute infrastructure. There will be a large practical component, where participants will learn throughhands-on tutorials on data submission, and using a workflow-based approach and compute infrastructure for data analysis, under the guidance of the lecturers and teaching assistants. Syllabus, tools and resources
- OpenMS workflows
- Knime workflows
- PhenoMeNal
- MetaboLights
Outcomes:
After this course you should be able to:
- Use open source software and web-based tools to construct metabolomics analysis workflows
- Access metabolomics databases
- Discuss the issues of data sharing and data standards in metabolomics
Year(s) Of Engagement Activity 2017
URL https://www.ebi.ac.uk/training/events/2017/metabolomics-workflows
 
Description NIH Common Fund Metabolomics Program 2015 Annual Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We presented recent updates in MetaboLights to the metabolomics core centres in USA. We generally participate in these meetings as we were advising the NIH before they set up Metabolomics Workbench
Year(s) Of Engagement Activity 2015
URL http://www.metabolomicsworkbench.org/meetings/201509/agenda.php
 
Description NIH Common Fund Metabolomics Program 2017 Annual Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact EMBL-EBI MetaboLights team partake as advisors in the NHI common funds annual meetings. We also share data with the Metabolomics Workbench, which is the NIH funded Metabolomics repository.
Year(s) Of Engagement Activity 2017
 
Description Pint of science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talked about the research behind the debate about whether it is increased carbohydrate or saturated fat intake that is driving the obesity and type 2 diabetes epidemics.
Year(s) Of Engagement Activity 2017
 
Description Poster and presentation at the MetaboMeeting on Cambridge 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact At the MetaboMeeting we presented posters for ChEBI and MetaboLights. We also had a presentation on metabolomics that covered both these resources.
We get quite a lot of interest as a result of these activities, and study submission frequency normally increase as a result
Year(s) Of Engagement Activity 2015
URL http://thempf.org/mpf_cms3/conferences/forthcoming-meetings/metabomeeting-2015
 
Description Posters 11th Annual International Metabolomics Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We presented 3 separate posters on the 11th Annual International Metabolomics Conference in San Fransisco summer 2015.
We presented:
- New developments in MetaboLights
- R-Cloud based MetaboAnalyst integration into MetaboLights LABS
- MetaboLights LABS
Year(s) Of Engagement Activity 2015
 
Description Posters at the 12th Annual International Metabolomics Conference in Dublin, Ireland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We presented 3 posters on "Metabolic Pathways and Networks Integration", "MetaboLights - New features", "MetaboLights a reference repository for METASPACE" and "The Lipidome in Weight Loss". This is the larger (about 900 people) yearly International Metabolomics conference. In 2016 it was in Dublin, and attracts researchers from all over the world.
Year(s) Of Engagement Activity 2016
URL http://metabolomics2016.org
 
Description Presentation of MetaboLights to the BD2K consortium 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The MetaboLights team is part of one of the awarded NIH BD2K grants. We are supplying metabolomics data to the Omics Data Discovery Index. (http://www.ebi.ac.uk/Tools/omicsdi/#/). We presented MetaboLights to the rest of the consortia.
Year(s) Of Engagement Activity 2015
URL http://newsroom.ucla.edu/releases/ucla-receives-11-million-grant-to-lead-nih-center-of-excellence-fo...
 
Description Presentations on 8th international biocuration conference in China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We presented MetaboLights and ChEBI at the 8th international biocuration conference in China. We presentation MetaboLights in Mandarin, and we saw more submissions coming in from China as a result of this.
Year(s) Of Engagement Activity 2015
URL http://biocuration2015.big.ac.cn
 
Description Sardinian summer school: Metabolomics and more. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Sardinian summer school to spread the use of tools in metabolomics and lipidomics.
Year(s) Of Engagement Activity 2017
 
Description Science Week cambridge 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact : volunteering on 13th March 2016 Cambridge science festival HNR stand: Blood, Fat & the Future
Year(s) Of Engagement Activity 2016
 
Description UK-China research partnership (Cuddel) workshop 2016, EBI, November 23-25 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In total 15 participants attended this 3 days workshop, from GigaScience (China), EMBL-EBI, University of Birmingham and the University of Oxford based at EMBL-EBI 23-25 November 2016.
This meeting was both discussion and hands-on coding related to metabolomics data sharing and standards, details:
Updates on the ISA Model specification 2.0, Updates on ML activities and PhenoMeNal
Main objectives: development of mzML2 ISA tool: Integration with ML, Galaxy and PhenoMeNal, Working on examples - generated for submission

Integration with ISA API and to apply ISA 2.0 to metabolomics data sets:
GSK longitudinal dataset examined and used.
BGI lipidomics dataset from GigaScience paper in review: "Lipidomic profiling reveals progressive changes of plasma lipids from normal to type 2 diabetes" was examined and used.
Generation and visualisation of ISA files in GigaDB:
Other activities: New configuration files that are missing identified, Updates on the capturing imaging dataset, Link and collaboration with MetaSpace, Capturing SIRM data, Capturing chromatography dataset
Year(s) Of Engagement Activity 2016
 
Description West African Centre for cell Biology of Infectious Pathogens College of Basic and Applied Sciences, Ghana Research Conference 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Took part in a 3 day conference/workshop to discuss advances in Biology that could be applied within Western Africa to treat human disease.
Year(s) Of Engagement Activity 2017
 
Description Workshops at the 11th Annual International Metabolomics Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We participated and presented MetaboLights in two workshops, "Coordination of standards in Metabolomics (COSMOS) Hackathon" and "Metabolomics Data standards"

We decided to collaborate and contribute to new developments in other areas, like SPLASH (The Spectral Hash Identifier, http://splash.fiehnlab.ucdavis.edu), which is now implemented in the MetaboLights reference layer
Year(s) Of Engagement Activity 2015
URL http://splash.fiehnlab.ucdavis.edu