MetaboLights features
How to submit data
There are two possible ways to submit data into MetaboLights:
- Online Study Submission. This is the recommended submission method. Data submission is done online through a web-interface. A good starting point is the video for step by step guide to create a MetaboLights study online.
- ISAcreator tool. Step by step guide for this submission method can be found in the Quick tour section of EMBL-EBI train online. This method requires the download and installation of the ISAcreator tool.
Non-Personal vs Personal data
Non-personal data (non-identifiable).
Access to data
Open access.
Embargo
Possible. A minimum of 28 days from submission to allow for manual curation of the study. A longer period may be selected.
Data licence
All data is governed by the EMBL-EBI’s Terms of use.
Data/Experiments types
- Mass Spectrometry (MS)
- NMR spectroscopy
Metadata
- Study: title, summary/description, keywords
- Assay: technique and assay type, both defined by controlled vocabulary. For each assay type a set of specific metadata will be required. Find here the specific metadata for each assay type.
- Protocol description: sample collection, extraction, chromatography, MS, data transformation, metabolite identification.
- Experimental control names
- Sample names
- Sample details: organism, organism part, variant, custom factors/variable. Controlled vocabulary is provided for each metadata field.
- Metabolite annotation: database_identifier, chemical_formula, smiles, inchi, metabolite_identification, mass_to_charge, fragmentation, modifications, charge, retention_time, taxid, species, database, database_version, reliability, uri, search_engine search_engine_score, smallmolecule_abundance_sub, smallmolecule_abundance_stdev_sub, smallmolecule_abundance_std_error_sub. Controlled vocabulary is provided for most of the metadata field.
Ontology
Many ontologies are embedded in the submission form. One of the used ontology is EFO. Additionally, MetaboLights recommends the use of Bioportal to find or resolve any ontologies.
Data documentation
MetaboLights doesn’t allow upload of README file. All relevant information about the data need to be provided in the designated metadata fields.
File format(s)
- Accepted raw file formats: eg. .raw, .d, .cdf, open source formats (.mzML, .nmrML).
- Study description (i_MTBLSxxx.txt).
- Sample information (s_MTBLSxxx.txt).
- Assay information (a_MTBLSxxx.txt).
- Metabolite information (m_MTBLSxxx.tsv).
Data volume and costs
No limit for data volume. No costs.
Data quality
MetaboLights submission process includes a validation and a manual curation steps. See here for more details.
Identifiers
Unique accession numbers are minted for every study submitted.
Guide and manual
Quick Start Overview. MetaboLights https://www.ebi.ac.uk/metabolights/guides/study/overview.
Online Study Submission. MetaboLights https://www.ebi.ac.uk/metabolights/help.