Data Model

The SeqDB data model mirrors the ENA submission hierarchy: Project → Sample → Experiment → Run.

Entity Relationship Diagram

erDiagram
    PROJECT ||--o{ SAMPLE : contains
    SAMPLE ||--o{ EXPERIMENT : has
    EXPERIMENT ||--o{ RUN : produces
    RUN ||--o{ QC_REPORT : generates
    USER ||--o{ PROJECT : owns
    USER ||--o{ STAGED_FILE : uploads

    PROJECT {
        int id PK
        string internal_accession UK
        string ena_accession
        string title
        string description
        string project_type
        date release_date
        string license
        int user_id FK
        datetime created_at
    }

    SAMPLE {
        int id PK
        string internal_accession UK
        string ena_accession
        string organism
        int tax_id
        string breed
        date collection_date
        string geographic_location
        string host
        string tissue
        string sex
        string checklist_id
        json custom_fields
        int project_id FK
    }

    EXPERIMENT {
        int id PK
        string internal_accession UK
        string platform
        string instrument_model
        string library_strategy
        string library_source
        string library_layout
        int insert_size
        int sample_id FK
    }

    RUN {
        int id PK
        string internal_accession UK
        string file_type
        string file_path
        bigint file_size
        string checksum_md5
        string checksum_sha256
        int experiment_id FK
    }

    QC_REPORT {
        int id PK
        string tool
        string status
        json summary
        string report_path
        int run_id FK
    }

    STAGED_FILE {
        int id PK
        string filename
        bigint file_size
        string checksum_md5
        string status
        string upload_method
        int user_id FK
    }

Accession format

Every entity receives a persistent internal accession:

Entity	Format	Example
Project	NFDP-PRJ-NNNNNN	NFDP-PRJ-000001
Sample	NFDP-SAM-NNNNNN	NFDP-SAM-000042
Experiment	NFDP-EXP-NNNNNN	NFDP-EXP-000007
Run	NFDP-RUN-NNNNNN	NFDP-RUN-000015

Accessions are sequential and never reused. After ENA submission, an ena_accession is added alongside the internal one.

ENA mapping

SeqDB	ENA Equivalent	ENA Accession
Project	Study	ERP* / PRJ*
Sample	Sample	ERS* / SAM*
Experiment	Experiment	ERX*
Run	Run	ERR*

Enums

FileType

FASTQ, BAM, CRAM, VCF, OTHER

Platform

ILLUMINA, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, BGISEQ

LibraryStrategy

WGS, WXS, RNA_SEQ, AMPLICON, TARGETED_CAPTURE, OTHER

LibrarySource

GENOMIC, TRANSCRIPTOMIC, METAGENOMIC, METATRANSCRIPTOMIC, VIRAL_RNA, OTHER

LibraryLayout

PAIRED, SINGLE

Storage paths

Files in MinIO follow this path structure:

{bucket}/{project_accession}/{sample_accession}/{run_accession}/{filename}

Example:

nfdp-raw/NFDP-PRJ-000001/NFDP-SAM-000001/NFDP-RUN-000001/SAMPLE_001_R1.fastq.gz

Buckets

Bucket	Purpose
nfdp-raw	Original uploaded sequence files
nfdp-staging	Temporary staging area before linking
nfdp-qc	QC reports (FastQC, MultiQC)
nfdp-processed	Pipeline output files
nfdp-snpchip	SNP chip genotyping data