RO-Profiles

This section describes the RO-Crate profiles used in EMO-BON.

old text, relocated from data-products/crates/md

RO-Crate Profiles¶

EMO-BON defines specific profiles that describe the expected structure and content of different crate types:

• Observatory Profile: https://github.com/emo-bon/observatory-profile

• Analysis Results Profile: (in development)

• Sequencing Profile: (planned)

Profiles are themselves RO-Crates that formally describe the layout/structure of crates that declare conformance to them.

What are RO-Profiles?¶

An RO-Profile is itself an RO-Crate that formally describes the layout and structure of other RO-Crates that declare conformance to it. Profiles ensure consistency and interoperability across EMO-BON data products.

EMO-BON Profiles¶

Observatory Profile¶

Repository: https://github.com/emo-bon/observatory-profile

URI: https://data.emobon.embrc.eu/observatory-profile/latest/

Purpose: Defines the structure and required metadata for observatory crates.

Key Components:

• Logsheet structure and field definitions

• Sample metadata requirements

• Sampling event information

• Environmental measurement specifications

• Semantic templates for RDF generation

Conforming Crates: All observatory-{obsid}-crate repositories conform to this profile.

Analysis Results Profile¶

Status: In development

Purpose: Will define the structure for analysis results crates.

Planned Components:

• Taxonomic annotation requirements

• Functional annotation specifications

• OTU/ASV data structure

• Links to source samples

• Large file handling guidelines

Conforming Crates: analysis-results-{cluster}-crate repositories will conform to this profile.

Sequencing Profile¶

Status: Planned

Purpose: Will define the structure for sequencing metadata.

Planned Components:

• Batch information requirements

• Sequence run metadata

• Links to ENA accessions

• Sample-to-sequence mappings

Conforming Crates: The sequencing-logistics-crate repository will conform to this profile.

Profile Structure¶

Each profile contains:

1. Profile Metadata: Information about the profile itself (version, description, etc.)

2. Schema Definitions: Formal specifications of required and optional fields

3. Semantic Templates: Templates for generating RDF triples from data

4. Validation Rules: SHACL shapes or other validation specifications

5. Documentation: Human-readable descriptions and examples

Using Profiles¶

Profiles are used in the EMO-BON workflow to:

• Initialize new crates with the correct structure

• Validate crate contents against the profile requirements

• Generate RDF triples using the semantic templates

• Document the expected structure for manual crate creation

Profile Versioning¶

Profiles follow semantic versioning (vM.m.p):

• Major version changes indicate breaking changes

• Minor version changes add new features backward-compatibly

• Patch version changes fix bugs or clarify documentation

The latest version always points to the most recent stable release.