EMO-BON Crates

EMO-BON Crates are RO-crates that contain EMO-BON associated data, like logsheets from observatories, MetaGOflow runs, sequencing metadata, etc.

What is an RO-Crate?
An RO-Crate is a structured collection of data files, metadata, and contextual information designed to make research data easy to share, reuse, and understand - both by humans and machines. Also characterized by the pressence of an ro-crate-metadata.json file.

What is an ro-crate-metadata.json file?
The ro-crate-metadata.json file is the central metadata file in an RO-Crate. It:

• Describes the contents of the crate

• Defines relationships between files and their associated metadata

• Provides traceability, context, and purpose

• Adheres to the RO-Crate specification

• Is structured as JSON-LD, enabling integration with knowledge graphs

Types of EMO-BON Crates¶

In EMO-BON context, there are various types of emo-bon ro-crates identifiable. Usually, an EMO-BON Crate corresponds to a single (GitHub) repository, but in some cases, a (GitHub) repository can contain multiple EMO-BON Crates.

• Governance Crate¶

  • Purpose: Central coordination and configuration for the EMO-BON data system.

  • Contents:

    • List of observatories

    • Logsheet registry (logsheets.csv)

    • Overall project configuration

    • Cross-cutting metadata

  • URI: https://data.emobon.embrc.eu/governance-data
    (Maintained at: https://github.com/emo-bon/governance-data)

• Observatory Crate¶

  • Purpose: Store and publish data collected by individual observatories.

  • Contents:

    • Logsheet data (CSV files from Google Sheets)

    • Sample and sampling event metadata

    • Environmental measurements

    • Links to related sequences

    • RDF triples describing the data

  • URI pattern: {{base}}/observatory-{observatory_id}-crate
    Example: https://data.emobon.embrc.eu/observatory-bpns-crate/
    (Maintained at: https://github.com/emo-bon/observatory-bpns-crate)

• Analysis Results Crate¶

  • Purpose: Store and publish results from bioinformatics analysis of sequences.

  • Contents:

    • MetaGOflow analysis outputs

    • Processed sequences (OTUs/ASVs)

    • Taxonomic summaries

    • Functional annotations

    • Large files managed via DVC and S3

  • URI pattern: {{base}}/analysis-results-{cluster}-crate/{materialSampleId}
    Examples:

    • overview of batch?: https://data.emobon.embrc.eu/analysis-results-cluster-01-crate/
      (Maintained at https://github.com/emo-bon/analysis-results-cluster-01-crate)

    • analysis results of a sample: https://data.emobon.embrc.eu/analysis-results-cluster-01-crate/EMOBON_NRMCB_Wa_24-ro-crate/
      (Maintained at: https://github.com/emo-bon/analysis-results-cluster-01-crate)

• Sequencing Logistics Crate - TBD¶

  • Purpose: Track sequencing operations and link samples to their sequences.

  • Contents:

    • Sequencing metadata

    • Batch information

    • Links to sequences in ENA

    • Sequence run details

  • URI pattern: sequencing-logistics-crate Example: ... (Maintained at: ...)