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Hands-on session II - MetaboLights Study Semantic Curation

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Noemi Tejera, PhD

Scientific Database Curator

ebi.ac.uk/metabolights

License CC-BY-4.0

Thomas Payne, PhD

Project Lead

2026 Groningen Semantic Metabolomics ELIXIR Workshop

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What is MetaboLights?

https://www.ebi.ac.uk/metabolights

Database for metabolomics / lipidomics experiments and derived information

  • Develop standards and improve reporting

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  • Open Source/Open Access
  • Study repository
  • Reference Library of curated knowledge about metabolites

(Compound Library) - Links to ChEBI (Chemical Entities of Biological Interest)

ISA data model

Investigation/Study/Assay (ISA)

3 types of files to capture the experimental metadata

https://www.ebi.ac.uk/chebi/

(2007) Metabolomics Standards Initiative (MSI) guidelines - Reporting standards for metabolomics analysis

(2012) Public metabolomics databases and repositories 🡪 Deposition of metabolomic datasets

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EMBL-EBI- The FAIR data management principles

https://www.ebi.ac.uk/metabolights

https://blog.orvium.io/fair-principles-in-scientific-data/

https://biosistemika.com/blog/data-integrity-and-fair-principles-faq/  

European Molecular Biology Laboratory (EMBL) Intergovernmental organization that performs fundamental research in molecular biology and the life sciences - Six sites: in Heidelberg, Barcelona, Grenoble, Hamburg, EMBL-EBI, Rome.

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MetaboLights ̶ Data

Sample Preparation

Sample Collection

Data Acquisition

Data Interpretation

  • Cross species
  • Comprehensive information collection
  • Cross technique

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https://www.ebi.ac.uk/metabolights

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Or use: https://www.ebi.ac.uk/metabolights/MTBLS3563

Type MTBLS3563 – Hit Search

Go to MetaboLights: https://www.ebi.ac.uk/metabolights

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MetaboLights ̶ Study Information

ABSTRACT

PUBLICATIONS- it can be more than one

UNIQUE ACCESSION NUMBER // TITLE // CONTACTS

https://www.ebi.ac.uk/metabolights

SEARCH: STUDIES // SPECIES // COMPOUNDS (links to ChEBI)

STATUS: PROVISIONAL // PRIVATE // PUBLIC

ASSOCIATED STUDIES // LINKED CROSS OMIC DATA SETS (EMBL-EBI ENA, etc.)

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

PI contact details required – ORCID, AFFILIATION ROR linked

UPDATES have been implemented and more are on the way

Funding, Omics type, and other relevant data will be linked

More guidance on the submission requirements for each section of a study also will be displayed in the Editor

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

CONTROLLED VOCABULARIES // ONTOLOGIES

DESIGN DESCRIPTORS and FACTORS

As in Publications

Describe samples and stratify groups of interest 

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

DESIGN DESCRIPTORS and FACTORS

HOW ARE THEY ENCODED IN THE INVESTIGATION FILE?

Download the i.Investigation.txt file from the FILES

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Open using Excel (or equivalent)

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

DESIGN DESCRIPTORS and FACTORS

HOW ARE THEY ENCODED IN THE INVESTIGATION FILE?

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MetaboLights ̶ Ontologies

https://www.ebi.ac.uk/metabolights

Area

Ontology

Species/Organism, Organism part

National Center for Biotechnology Information Organismal Classification (NCBITAXON), World Register of Marine Species (WoRMS), National Cancer Institute Thesaurus (NCIT), Environment Ontology (ENVO), Brenda Tissue and Enzyme Source Ontology (BTO)

Sample details/factors (e.g., disease state, treatment, timings)

National Cancer Institute Thesaurus (NCIT), Experimental Factor Ontology (EFO), Plant Ontology (PO), Unit of Measurement Ontology (UO), Human Phenotype Ontology (HP), Orphanet Rare Disease ontology (ORDO)

Instrumentation

Metabolomics Standards Initiative Ontology (MSIO), Chemical Methods Ontology (CHMO), Mass Spectrometry Ontology (MS), Unit of Measurement Ontology (UO), MetaboLights (MTBLS) …

Metabolites

Chemical Entities of Biological Interest (ChEBI ) … cross ref to other databases

  • Metadata capture using controlled vocabularies / ontologies

OLS, BioPortal- ontologies repositories

Zooma- tool for mapping free text annotations to ontology term

  • Give semantics to the data- Query in a meaningful way, easier visualization and integration

MetaboLights prioritised-control-lists

LINK HERE

OLS

EMBL-EBI

Ontology Lookup Service

https://www.ebi.ac.uk/ols4/

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Minimum reporting standards for the chemical analysis aspects of metabolomics and lipidomics experiments

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LC-MS // GC-MS PRE-DEFINED SECTIONS:

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  • Sample Collection
  • Extraction
  • Chromatography
  • Mass Spectrometry
  • Data Transformation
  • Metabolite Identification

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DI-MS: Chromatography – Direct Infusion

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ASSAY SPECIFIC SECTIONS:

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MS-Imaging: Preparation, Histology

NMR: NMR sample, NMR Spectroscopy, NMR Assay

PROTOCOLS

Future plans Link to Protocols.io

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MetaboLights ̶ Study Information

HOW ARE THEY ENCODED IN THE INVESTIGATION FILE?

PROTOCOLS

https://www.ebi.ac.uk/metabolights

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

  • One Sample Sheet per Study
  • Each row - a distinct sample: QCs, Experimental Samples, Blanks, etc
  • Organism, Organism part, Information re-Cultivar, Breed, etc., Type of Sample and Factors

Samples

Mandatory Fields

Organism – NCBITaxon, ENVO (Other Sources: wikidata, ILX)

Organism Part – UBERON, BTO, NCIT, MSIO

Sample Name – min 3 characters (alphanumeric, space, - and _ )

Factor (min 1) –OBI, EFO, CHMO, NCIT, NCBITaxon, MS, BTO, etc.

MetaboLights

prioritised-control-lists- SAMPLE

LINK HERE

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Samples – GUIDES: https://ebi-metabolights.github.io/guides/Sample/

HOW ARE THEY ENCODED IN THE INVESTIGATION FILE?

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Assays

Specific instrument information provided in detail and using controlled vocabulary - FAIR - Studies using the same approach are easily findable

Scroll right on the Editor →

MetaboLights

prioritised-control-lists- LC-MS ASSAY

LINK HERE

HOW ARE THEY ENCODED IN THE INVESTIGATION FILE?

– GUIDES: HERE

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Metabolite Annotation Files (MAF)

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  • They are linked to Assays
  • Each row is reserved to a Metabolite/feature/peak/unknown
  • If Metabolites identified- Provided Compound Name associated to a specific ID using ChEBI ontology

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  • Mandatory: Metabolite/Feature identification, Mass to charge (m/z), RT
  • SMILES, InChi, Fragmentation, Modifications, MSI levels (Reliability), Quantification values, etc. are recommended

Metabolites - Metabolite Annotation File (m_MTBLSxxx.tsv)

– GUIDES: HERE

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MetaboLights ̶ Study Information

https://www.ebi.ac.uk/metabolights

Metadata Files

Samples, Assays, MAF - ISA metadata

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Data Files

RAW and DERIVED files

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Download

  • Folders
  • Individual Files
  • FTP and Aspera Download

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FILES

raw

.d

.raw

.ser

.ibd

.wiff

.wiff.scan

.dat

.cmp

.lcd

.fid

.jpf

.smp

.peg

derived

.mzML

.nmrml

.mzxml

.mzdata

.cef

.cnx

.peakml

.xy

.imzml

.scan

.mgf

.cdf

– GUIDES: HERE

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MetaboLights ̶ HANDS ON exercise

https://www.ebi.ac.uk/metabolights

Use the Publication and terms identified in

Hands-on session I

Use the following Publication

https://www.medrxiv.org/content/10.1101/2025.10.16.25338140v1

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Dietary Bioactives and Microbiome Diversity – DIME Study

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USE

Hands On II-Part_01-Groningen Semantic Metabolomics ELIXIR Workshop to complete exercise

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