Overview

Time estimation:

Version: main

Last update: 2026-09-21

Questions:

Objectives:

RDM Microbial Training Course - in preparation

Learning goals:

• Describe the term Data Management (DM)
• Describe a Data Management Plan (DMP)

  Understand:

• Data Life Cycle & FAIR
• Documentation

  Apply:

• ELIXIR RDMkit (https://rdmkit.elixir-europe.org/)
• DSW (https://ds-wizard.org)

Chapters

1. The Basics

1. What are scientific data?

Scientific data?

All digital data used or generated in the research process.

• Raw and processed data
• Simulation data
• Observational data
• Code, algorithms, scripts
• Audiovisual data

Meta data?

Structured data containing information about characteristics of other data.

• Who, When, Why, How
• Resources used
• Abbreviations, units, names used
• Licenses

2. Common data types in microbiology

• Microbiome data
• Crystallographic data for small molecules
• Protein sequences
• Nucleic acid sequences
• Linked genotype and phenotype data
• Macromolecular structures
• Clinical data
• Functional genomics and gene expression data
• Standardised bacterial information

3. Centralised repository for (meta)data standards

• Audience: the international microbiological community
• Content: easily accessible compilation of established standards
• Aim: to facilitate efficient navigation and use for researchers involved in the collection and submission of (meta)data to public repositories
• Technical (e.g., sequencing method, sample volume or weight for DNA extraction, nucleic acid extraction, library size, etc.)
  • Automatically generated by software associated to research instruments (see table)
  • Metadata acquisition can be partly configured in the software settings
  • Metadata export must sometimes be initiated deliberately
  • Biological and environmental metadata (e.g., broad-scale environmental context, local environmental context, environmental medium, geographic location (latitude) and geographic location (longitude), host metadata, sample collection metadata, etc.)

4. Overview of Minimal Technical Metadata for FASTA Files

Table

5. Minimal Information Standards in the life sciences

• Bio-Formats for microscopy image data (OME-XML)
• Crystallographic Information Framework (CIF)
• Minimal Information about a Flow Cytometry Experiment (MIFLowCyt)
• Minimum Information about a Marker Gene Sequence (MIMARKS)
• Minimum Information about a Microarray Experiment (MIAME)
• Minimum Information about a Next-generation Sequencing Experiment (MINSEQE)
• Minimal Information about a Proteomics Experiment (MIAPE)
• Minimum Information about a Single Amplified Genome (MISAG)
• Minimum Information about any (x) Sequence (MIxS)
• Minimum Information for Biological and Biomedical Investigations (MIBBI)
• NeXuS Data Format for neutron, x-ray and muon science

6. Metadata standards directories, registries and repositories

• Basel Register of Thesauri, Ontologies & Classifications (BARTOC)
• DCC Disciplinary Metadata guide
• RDA Metadata Standards Directory
• BioPortal - Repository of biomedical ontologies
• Cancer Data Standards Registry and Repository (caDSR)
• FAIRsharing.org (search results for microbiology)

Key Points