ENA v1.0

ENA (European Nucleotide Archive) is one of the primary repositories for nucleotide sequence data, operated by EMBL-EBI. The ENA metadata model defines the structure for submitting sequencing projects, samples, experiments, and data files to the archive.

The model is hierarchical: Studies contain Samples and Experiments, Experiments contain Runs with sequence data files, and Analyses contain derived data products. All entities receive ENA accession numbers upon submission.

flowchart TB
    subgraph core["Core Objects"]
        STU[Study]
        SAM[Sample]
        EXP[Experiment]
        RUN[Run]
        ANA[Analysis]
    end

    subgraph files["Data Files"]
        FILE[File]
    end

    subgraph attributes["Attributes"]
        SA[SampleAttribute]
        EA[ExperimentAttribute]
        RA[RunAttribute]
        AA[AnalysisAttribute]
        PL[ProjectLink]
    end

    %% Core relationships
    STU --> SAM
    STU --> EXP
    STU --> ANA
    EXP --> RUN

    %% References
    EXP -.->|study_ref| STU
    EXP -.->|sample_ref| SAM
    RUN -.->|experiment_ref| EXP
    ANA -.->|study_ref| STU

    %% File relationships
    RUN --> FILE
    ANA --> FILE

    %% Attribute relationships
    STU --> PL
    SAM --> SA
    EXP --> EA
    RUN --> RA
    ANA --> AA

    classDef core fill:#e8f5e9,stroke:#4caf50,stroke-width:2px
    classDef file fill:#fff3e0,stroke:#ff9800,stroke-width:2px
    classDef attr fill:#e3f2fd,stroke:#2196f3,stroke-width:2px

    class STU,SAM,EXP,RUN,ANA core
    class FILE file
    class SA,EA,RA,AA,PL attr

Entities

Category	Entities
Core Objects	Study, Sample, Experiment, Run, Analysis
Data Files	File
Attributes	SampleAttribute, ExperimentAttribute, RunAttribute, AnalysisAttribute, ProjectLink

Key Concepts

Study (Project): The top-level container that groups related submissions and controls release dates. Studies receive a BioProject accession (PRJEB) or legacy study accession (ERP). All data under a study is released together.

Sample: Describes the biological source material being sequenced. Samples are linked to NCBI taxonomy and annotated using ENA checklists (standardized attribute sets). Samples receive BioSample (SAMEA) or sample (ERS) accessions.

Attributes such as collection_date and geographic_location_country are checklist-level requirements (e.g. checklist ERC000011), not properties of the base Sample. They are therefore optional on the Sample entity, so valid public ENA/DDBJ records that omit them can be imported. Apply checklist-conditional requirements via the checklist field rather than expecting these attributes on every Sample.

Experiment: Describes the sequencing library and platform. Key fields include:

• library_strategy: Sequencing approach (WGS, RNA-Seq, ChIP-Seq, etc.)
• library_source: Material type (GENOMIC, TRANSCRIPTOMIC, METAGENOMIC)
• library_selection: Selection method (RANDOM, PCR, PolyA)
• platform: Sequencing platform (ILLUMINA, OXFORD_NANOPORE, PACBIO_SMRT)

Run: Contains the actual sequence data files (FASTQ, BAM, CRAM). Each run has associated checksums for data integrity verification.

Analysis: Contains secondary analysis results derived from runs, such as assemblies, variant calls, or annotations.

Accession Formats

Object	Accession Format	Example
Study	PRJEB or ERP	PRJEB12345, ERP123456
Sample	ERS or SAMEA	ERS123456, SAMEA123456
Experiment	ERX	ERX123456
Run	ERR	ERR123456
Analysis	ERZ	ERZ123456

Controlled Vocabularies

ENA uses controlled vocabularies for key fields:

Library Strategy (37 terms): WGS, WXS, RNA-Seq, ChIP-Seq, ATAC-seq, Hi-C, Bisulfite-Seq, etc.

Library Source (9 terms): GENOMIC, TRANSCRIPTOMIC, METAGENOMIC, SYNTHETIC, etc.

Library Selection (31 terms): RANDOM, PCR, PolyA, ChIP, MNase, Hybrid Selection, etc.

Platform (14 terms): ILLUMINA, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, etc.

Validation Rules

The ENA profile includes validation rules for:

• Accession format patterns (PRJEB, ERS, ERX, ERR, ERZ)
• Taxon ID must be positive integer
• MD5 checksum format (32 hexadecimal characters)
• Library vocabulary constraints
• Coordinate ranges for geographic metadata
• Reference integrity between objects

Use Cases

• Genome sequencing: Whole genome sequencing projects
• Transcriptomics: RNA-Seq and single-cell RNA-Seq studies
• Metagenomics: Environmental and microbiome sequencing
• Epigenomics: ChIP-Seq, ATAC-seq, bisulfite sequencing
• Assemblies: Genome and transcriptome assembly submission
• Variant data: SNP and structural variant submissions

Entity-Relationship Diagram

erDiagram
    Study {
        string alias PK
        string accession
        string title
        string description
        string study_type
        string center_name
    }

    Sample {
        string alias PK
        string accession
        string title
        integer taxon_id
        string scientific_name
        string collection_date
        string geographic_location_country
    }

    Experiment {
        string alias PK
        string accession
        string study_ref FK
        string sample_ref FK
        string library_strategy
        string library_source
        string library_selection
        string platform
        string instrument_model
    }

    Run {
        string alias PK
        string accession
        string experiment_ref FK
        date run_date
    }

    Analysis {
        string alias PK
        string accession
        string study_ref FK
        string title
        string analysis_type
    }

    File {
        string filename PK
        string filetype
        string checksum_method
        string checksum
    }

    SampleAttribute {
        string tag
        string value
        string units
    }

    ProjectLink {
        string db
        string id
        string label
    }

    Study ||--o{ Sample : samples
    Study ||--o{ Experiment : experiments
    Study ||--o{ Analysis : analyses
    Study ||--o{ ProjectLink : project_links
    Experiment ||--o{ Run : runs
    Experiment }o--|| Study : study_ref
    Experiment }o--|| Sample : sample_ref
    Run }o--|| Experiment : experiment_ref
    Run ||--|{ File : files
    Analysis }o--|| Study : study_ref
    Analysis ||--|{ File : files
    Sample ||--o{ SampleAttribute : sample_attributes

References

Resource	URL
ENA Homepage	https://www.ebi.ac.uk/ena/browser/home
ENA Submission Guide	https://ena-docs.readthedocs.io/
ENA Metadata Model	https://ena-docs.readthedocs.io/en/latest/submit/general-guide/metadata.html
Webin XML Schemas	https://github.com/enasequence/webin-xml
ENA Checklists	https://www.ebi.ac.uk/ena/browser/checklists

Usage

from metaseed import ena

e = ena()

# Create Study
study = e.Study(
    alias="my-study-001",
    title="Whole genome sequencing of Arabidopsis thaliana ecotypes",
    description="Genomic variation across 100 A. thaliana ecotypes"
)

# Create Sample
sample = e.Sample(
    alias="sample-001",
    title="Arabidopsis thaliana Col-0 leaf tissue",
    taxon_id=3702,
    scientific_name="Arabidopsis thaliana",
    collection_date="2024-06-15",
    geographic_location_country="Germany"
)

# Create Experiment
experiment = e.Experiment(
    alias="experiment-001",
    study_ref="my-study-001",
    sample_ref="sample-001",
    library_strategy="WGS",
    library_source="GENOMIC",
    library_selection="RANDOM",
    library_layout="PAIRED",
    platform="ILLUMINA",
    instrument_model="Illumina NovaSeq 6000"
)

# Create Run with files
run = e.Run(
    alias="run-001",
    experiment_ref="experiment-001",
    run_date="2024-06-20"
)

# Create File
file = e.File(
    filename="sample1_R1.fastq.gz",
    filetype="fastq",
    checksum_method="MD5",
    checksum="d41d8cd98f00b204e9800998ecf8427e"
)