Database Schema

Database Schema

Tables

study

One row per accession.

Column	Type	Description
accession	TEXT PRIMARY KEY	PRIDE accession (e.g. PXD000001)
title	TEXT	Dataset title
organism	TEXT	Organism name
organism_id	TEXT	Taxonomy accession (e.g. NEWT:9606)
instrument	TEXT	Instrument name
submission_year	INTEGER	Year of submission
submission_type	TEXT	COMPLETE or PARTIAL
keywords	TEXT	Comma-separated keywords
repository	TEXT	Source repository (always "PRIDE")
fetched_at	TEXT	ISO 8601 fetch timestamp

study_files

One row per file.

Column	Type	Description
accession	TEXT	FK to study.accession
file_name	TEXT NOT NULL	File name
file_category	TEXT	PRIDE fileCategory value
file_extension	TEXT	File extension
ftp_location	TEXT	FTP download URL
file_size	INTEGER	File size in bytes
checksum	TEXT	MD5 checksum when PRIDE provides one
checksum_type	TEXT	Always "MD5" when checksum is present

audit

One row per accession.

Column	Type	Description
accession	TEXT PRIMARY KEY	FK to study.accession
tier	TEXT	Computed FAIR tier (None through Diamond)
quant_tier	TEXT	Computed quant tier
has_title	INTEGER	Non-empty title present
has_organism	INTEGER	Organism name present
has_organism_id	INTEGER	Taxonomy ID present (recorded, not tier-gating)
has_instrument	INTEGER	Instrument name present
has_result_files	INTEGER	Processed result files found
has_psi_results	INTEGER	PSI-standard results (mzIdentML / mzTab)
has_open_spectra	INTEGER	Open-format spectra (mzML / MGF)
has_organism_part	INTEGER	Tissue or cell type annotated
has_publication	INTEGER	PubMed ID linked and non-zero
has_tabular_quant	INTEGER	Quant table present (QUANT_MATRIX or ID_LIST)
has_quant_metadata	INTEGER	Quantification methods described via CV terms
has_sdrf	INTEGER	SDRF experimental-design file present
has_mztab	INTEGER	mzTab summary present
files_fetch_failed	INTEGER	File endpoint returned an error
is_unverifiable	INTEGER	Non-PRIDE accession that could not be checked
tier_logic_version	TEXT	Version of tier logic used to score

Example queries

-- Tier distribution
SELECT tier, COUNT(*) AS n FROM audit GROUP BY tier ORDER BY n DESC;

-- All Diamond datasets
SELECT accession, quant_tier FROM audit WHERE tier = 'Diamond';

-- Datasets needing re-scoring after a logic update
SELECT accession FROM audit WHERE tier_logic_version != 'v2.0';

-- File breakdown for a single accession
SELECT file_category, COUNT(*) AS n
FROM study_files
WHERE accession = 'PXD004683'
GROUP BY file_category;

-- Studies with files but no SDRF (potential Silver tier)
SELECT s.accession, s.title
FROM study s
JOIN audit a ON s.accession = a.accession
WHERE a.has_sdrf = 0 AND a.has_result_files = 1;

Migrations

These functions upgrade databases from earlier schema versions. All are idempotent and safe to run multiple times:

• migrate_audit_v2(conn): adds v2 flag columns to audit and submission_type to study
• migrate_study_v2(conn): adds fetched_at to study
• migrate_study_files_v2(conn): adds checksum and checksum_type to study_files