Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data management and sharing

MESSES

MESSES extracts tagged experimental metadata from spreadsheets or CSV into JSON, validates structured metadata against schemas and converts supported records to mwTab for Metabolomics Workbench deposition.

Platform-independentPython packageCommand lineSource available with restrictions
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Overview

MESSES extracts tagged experimental metadata from spreadsheets or CSV into JSON, validates structured metadata against schemas and converts supported records to mwTab for Metabolomics Workbench deposition. Its command-line and Python interfaces separate extraction, validation and conversion.

What can this tool do?

Metadata-based contextualizationProvenance tracking

Common uses

  • MESSES extracts tagged experimental metadata from spreadsheets or CSV into JSON, validates structured metadata against schemas and converts supported records to mwTab for Metabolomics Workbench deposition.

Scientific fit

Primary function

Data management and sharing

Other functions

Data conversion and import, Workflow management and reproducibility

Data compatibility

Inputs

Sample metadata

Outputs

Sample metadata

Input formats

Tagged Excel/CSV metadata and extraction/schema directives

Output formats

Structured JSON metadata, validation messages and mwTab exports

Scope and considerations

Designed for

  • MESSES extracts tagged experimental metadata from spreadsheets or CSV into JSON, validates structured metadata against schemas and converts supported records to mwTab for Metabolomics Workbench deposition.

Not designed for

  • Raw spectral processing or confirmation that scientifically incorrect metadata becomes correct merely because it passes a schema.

Important requirements

  • Python dependencies, tagged source tables and the extraction directives and validation schemas appropriate to the experiment and destination repository.

Considerations

  • Tagging and schema setup require knowledge of the study. Review identifiers, units and repository-specific fields after extraction and conversion.

Access and documentation

Primary accessDocumentation

Repository LICENSE adds a publication-citation condition to Clear BSD and grants no patent rights. The custom text is identified explicitly rather than labelled standard BSD-3-Clause.

License: Modified Clear BSD with citation requirement

Evidence and review

Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. MESSES: Software for Transforming Messy Research Datasets into Clean Submissions to Metabolomics Workbench for Public Sharing. Metabolites (2023). doi:10.3390/metabo13070842

Related tools

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Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 45 source-reviewed Enveda tool entries in third expansion batch

    View change · Entry at this revision

Full GitHub history