Data Standards, Repositories & FAIR in Metabolomics — Hands-on

Learn how to make your metabolomics and lipidomics projects Findable, Accessible, Interoperable and Reusable (FAIR) . This module covers data standards, repository submissions, metadata models and documentation practices so that your LC–MS/GC–MS/NMR studies are reusable by collaborators, reviewers and the wider community.

Data Standards, Repositories & FAIR in Metabolomics

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Session Index

Session 1 — Data Standards, Formats & Metadata Models Session 2 — Repositories & Submission Workflows Session 3 — FAIR Principles & Reproducible Pipelines Session 4 — Mini Capstone: Submission Package & FAIR Checklist

Session 1

Fee: Rs 8800

Data Standards, Formats & Metadata Models

Why standards matter in metabolomics and lipidomics

reusability, comparability and longevity reviewer and journal expectations regulatory and consortium drivers

Core file formats and standards

raw vendor formats vs open formats (mzML) mzTab / mzTab-M, mzIdentML, nmrML (overview) feature tables and peak lists

Metadata models and ontologies

ISA-Tab / ISA-JSON concepts experimental factors, protocols and samples using ontologies for controlled vocabulary

Session 2

Fee: Rs 11800

Repositories & Submission Workflows

Major metabolomics and spectral repositories

MetaboLights and Metabolomics Workbench GNPS / MassIVE and related resources journal and funder deposition policies

Preparing a submission package

organising raw, processed and metadata files anonymisation and consent considerations checklists and pre submission QA

Repository portals and validation checks

step by step upload and metadata entry automated format and consistency checks public vs embargoed access modes

Session 3

Fee: Rs 14800

FAIR Principles & Reproducible Pipelines

Translating FAIR into practical metabolomics steps

persistent identifiers and versioning rich metadata and documentation licensing and reuse conditions

Workflow capture and reproducibility

capturing analysis steps and parameters notebooks, scripts and pipeline definitions containerisation ideas (Docker/Singularity)

Data management plans and lab practices

folder structures and naming conventions backup, archival and access control lab SOPs and training for FAIR workflows

Session 4

Fee: Rs 18800

Mini Capstone: Submission Package & FAIR Checklist

Building a mock submission from a teaching dataset

raw, processed and metadata bundle

FAIR and repository readiness checklist

coverage of required metadata fields validation of file formats and links clarity for external re users

Deliverables: template submission package & SOP text

folder structure and manifest files example ISA tables or metadata sheets ready to edit data management SOP

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Data Standards, Repositories & FAIR in Metabolomics Training | MetaboLights, GNPS & Reproducible Workflows

Data Standards, Repositories & FAIR in Metabolomics — Hands-on