External Storage (ENA)

This section describes how EMO-BON sequences are stored and accessed at ENA (European Nucleotide Archive).

What is ENA?¶

The European Nucleotide Archive (ENA) is one of the world’s primary repositories for nucleotide sequence data.

Website: https://www.ebi.ac.uk/ena/

Operated By: European Bioinformatics Institute (EMBL-EBI)

EMO-BON and ENA¶

All EMO-BON sequences are archived at ENA for:

• Long-term preservation: Guaranteed storage

• Public access: Open data for research community

• Standardization: ENA metadata standards

• Citability: Stable accession numbers

• Compliance: Meeting data management requirements

EMO-BON Project Structure at ENA¶

Umbrella Project¶

All EMO-BON data is grouped under a single umbrella project:

Accession: PRJEB51688

URL: https://www.ebi.ac.uk/ena/browser/view/PRJEB51688

Observatory Projects¶

Each observatory has its own ENA project:

Pattern: Each observatory receives a unique project accession

Examples:

• Observatory BPNS: PRJEB[NUMBER]

• Observatory HCMR-1: PRJEB[NUMBER]

Managed In: governance-data/observatories.csv

Data Submission Process¶

Sequence Generation¶

1. Sample Collection: Observatory collects samples

2. Sample to Genoscope: Samples sent to sequencing facility

3. Sequencing: Genoscope performs sequencing

4. Raw Data: Sequences stored on Genoscope cloud

Submission to ENA¶

General Process:

1. Prepare sequence files

2. Prepare metadata (sample information)

3. Submit to ENA via their API or web interface

4. Receive accession numbers

5. Link accessions to EMO-BON crates

Metadata Requirements¶

ENA requires extensive metadata:

• Sample metadata: Collection location, date, depth, etc.

• Experiment metadata: Library preparation, sequencing method

• Run metadata: Instrument, read length, quality scores

• Study metadata: Project description, publications

EMO-BON logsheets provide much of this information.

Accessing ENA Data¶

By Accession Number¶

Each sequence or sample has a unique accession:

Formats:

• Study: PRJEB[NUMBER]

• Sample: SAMEA[NUMBER]

• Run: ERR[NUMBER]

• Analysis: ERZ[NUMBER]

URL Pattern: https://www.ebi.ac.uk/ena/browser/view/{ACCESSION}

Via ENA Portal¶

Search: https://www.ebi.ac.uk/ena/browser/advanced-search

Filters:

• By project (PRJEB51688)

• By taxonomy

• By location

• By date range

Programmatic Access¶

ENA API: REST API for querying and downloading

Example:

curl "https://www.ebi.ac.uk/ena/portal/api/search?query=study_accession%3DPRJEB51688"

ENA Browser API: Direct file downloads

Integration with EMO-BON¶

Linking Sequences to Samples¶

EMO-BON maintains links between:

• Observatory samples (in observatory crates)

• ENA accessions (in sequencing logistics crate)

• Analysis results (in analysis results crates)

Sequencing Crate¶

Repository: sequencing-logistics-crate (planned)

Purpose: Central registry linking samples to their sequences

Contents:

• Sample ID to ENA accession mappings

• Batch information

• Sequencing run metadata

• Links to raw data on ENA

Metadata Flow¶

Logsheets (Google Sheets)
    ↓
Observatory Crates (GitHub)
    ↓
Sample Metadata
    ↓
ENA Submission
    ↓
ENA Accessions
    ↓
Sequencing Logistics Crate (GitHub)

ENA Metadata Standards¶

MIxS (Minimum Information about any Sequence)¶

ENA requires MIxS-compliant metadata.

EMO-BON Uses:

• MIMARKS (environmental markers)

• MIxS environmental packages

Fields Include:

• Geographic location

• Collection date

• Environmental context

• Sample processing

Darwin Core¶

EMO-BON also aligns with Darwin Core for biodiversity data:

• Occurrence records

• Taxonomic information

• Event details

Data Updates and Corrections¶

Metadata Updates¶

If metadata needs correction:

1. Update in ENA via their interface

2. Update in EMO-BON crates

3. Maintain synchronization

Data Withdrawal¶

In rare cases, data may need withdrawal:

• Contact ENA support

• Follow their withdrawal process

• Update EMO-BON records

Benefits of ENA Storage¶

For Researchers¶

• Free access: No cost to download

• Stable URLs: Accessions never change

• Searchable: Integrated with other databases

• Standardized: Common metadata format

For EMO-BON¶

• Reliable: ENA ensures long-term preservation

• Trusted: Recognized by research community

• Compliant: Meets funder requirements

• Visible: Increases data discoverability

Future Plans¶

Automation¶

• Automated submission pipeline

• Regular synchronization

• Validation before submission

Enhanced Integration¶

• Richer links between EMO-BON and ENA

• Bidirectional metadata flow

• Integrated search across both systems