Data Repositories & Metadata

Fields, Standards & Minimal Requirements

Maja Magel

Charlie Pauvert

2024-07-18

Learning objectives

• recall at least two mandatory metadata fields
• name at least one metadata standards used in the life sciences
• identify relevant data repository

Metadata fields

Metadata fields

• A column header expects one or more cell values
• A metadata field expects one or more values

Metadata field	Type of constraint
description	free-text
geolocation	coordinates
biome	ontology term

Metadata standards

Metadata standards

• Fields are organized into coherent metadata standard for a given type of data

  • e.g., genomes, soil samples

• They are built and maintained by a combination of stakeholders

  • e.g., users community, data repositories

Standards expectations

Metadata standards (should) indicate for each field:

• the description of the metadata field

• the level of requirements (mandatory, recommended, optional)

• the cardinality, that is the range of expected values for the metadata field

• a persistent identifier for the field

Exercise: Metadata standards

Task:

• Go to https://www.ebi.ac.uk/ena/browser/checklists

• Look-up a standard that match your model system or type of sample

• Identify the mandatory metadata fields

• Compare with your neighbor

Minimal requirements

• The set of mandatory fields is sometimes referred to as the minimal requirements.

• Filling out these requirements and all the optional metadata fields would be ideal (if only possible) but is time-consuming

Exercise: Requirements

Task:

• Given only the mandatory fields, do you think you could recontextualise the data properly?
• List your arguments in the pad.

ENA Browser for host-associated metadata requirements (ERC00013)

as much as possible, as little as necessary

Working FAIRly takes time and effort¹

How much metadata is necessary to understand your research and to enable (inter-) disciplinary research?

1. 0-to-20 is already good and better than 0!

Data repositories

Skip the section if time is short to make this exercice at home

Data repositories

• Curated and well-described that stays on your hard drive is of limited interest to the scientific community.

• National and international efforts exist to create and maintain data repositories for the life sciences.

• For nucleotide sequence data, the INSDC integrate and mirrors data repositories from three regions:

  • USA with the NCBI

  • Europe with the EMBL-EBI

  • Japan with the DDBJ

Exercise: Data repositories

Task

• Go to https://www.ebi.ac.uk/submission

• Find out which repository could suit your data using the wizard

• Report the repository in the pad

Image by Andrew Martin from Pixabay