drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/pride.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
PRIDE Archive REST API Reference		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/pride.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

PRIDE Archive REST API Reference

Overview

PRIDE (PRoteomics IDEntifications Database) at EMBL-EBI provides a full public REST API for querying proteomics datasets, proteins, peptides, and spectra.

Base URL

https://www.ebi.ac.uk/pride/ws/archive/v2

(Legacy v1 also exists but v2 is current)

Authentication

• No authentication required for read access
• Open and free to use

Key Endpoints

Endpoint	Description
GET /projects	Search/list proteomics projects
GET /projects/{accession}	Get a specific project by PXD accession
GET /projects/{accession}/files	List files for a project
GET /spectra	Search spectra
GET /peptideevidences	Search peptide evidences
GET /proteinevidences	Search protein evidences
GET /stats	Database statistics

Query Parameters

• keyword — free-text search
• filter — field-specific filters (e.g., species, instrument, modification)
• pageSize — results per page (default 10, max 100)
• page — page number (0-indexed)
• sortDirection — ASC or DESC
• sortFields — field to sort by

Example Calls

# Search projects by keyword
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=alzheimer&pageSize=5"

# Get a specific project
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000"

# List files for a project
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000/files?pageSize=10"

# Search by species (human = 9606)
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?filter=organisms_facet==9606&pageSize=5"

# Get database statistics
curl "https://www.ebi.ac.uk/pride/ws/archive/v2/stats"

Response Format

JSON. Example (project):

{
  "accession": "PXD010000",
  "title": "Project title here",
  "projectDescription": "...",
  "organisms": [{"accession": "9606", "name": "Homo sapiens"}],
  "instruments": [{"name": "Q Exactive"}],
  "submissionDate": "2018-05-01",
  "publicationDate": "2018-09-01",
  "numAssays": 12,
  "references": [{"pubmedId": 12345678}]
}

Rate Limits

• No strict published rate limits, but standard EBI fair-use policies apply
• Recommended: limit to a few requests per second
• Bulk data available via FTP/Aspera at ftp.pride.ebi.ac.uk