88 lines
2.6 KiB
Markdown
88 lines
2.6 KiB
Markdown
---
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title: "PRIDE Archive REST API Reference"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/pride.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# PRIDE Archive REST API Reference
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## Overview
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PRIDE (PRoteomics IDEntifications Database) at EMBL-EBI provides a full public REST API for querying proteomics datasets, proteins, peptides, and spectra.
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## Base URL
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```
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https://www.ebi.ac.uk/pride/ws/archive/v2
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```
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(Legacy v1 also exists but v2 is current)
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## Authentication
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- **No authentication required** for read access
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- Open and free to use
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## Key Endpoints
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| Endpoint | Description |
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|---|---|
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| `GET /projects` | Search/list proteomics projects |
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| `GET /projects/{accession}` | Get a specific project by PXD accession |
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| `GET /projects/{accession}/files` | List files for a project |
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| `GET /spectra` | Search spectra |
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| `GET /peptideevidences` | Search peptide evidences |
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| `GET /proteinevidences` | Search protein evidences |
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| `GET /stats` | Database statistics |
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## Query Parameters
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- `keyword` — free-text search
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- `filter` — field-specific filters (e.g., species, instrument, modification)
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- `pageSize` — results per page (default 10, max 100)
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- `page` — page number (0-indexed)
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- `sortDirection` — ASC or DESC
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- `sortFields` — field to sort by
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## Example Calls
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```bash
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# Search projects by keyword
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curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=alzheimer&pageSize=5"
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# Get a specific project
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curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000"
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# List files for a project
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curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD010000/files?pageSize=10"
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# Search by species (human = 9606)
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curl "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?filter=organisms_facet==9606&pageSize=5"
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# Get database statistics
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curl "https://www.ebi.ac.uk/pride/ws/archive/v2/stats"
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```
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## Response Format
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JSON. Example (project):
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```json
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{
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"accession": "PXD010000",
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"title": "Project title here",
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"projectDescription": "...",
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"organisms": [{"accession": "9606", "name": "Homo sapiens"}],
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"instruments": [{"name": "Q Exactive"}],
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"submissionDate": "2018-05-01",
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"publicationDate": "2018-09-01",
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"numAssays": 12,
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"references": [{"pubmedId": 12345678}]
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}
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```
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## Rate Limits
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- No strict published rate limits, but standard EBI fair-use policies apply
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- Recommended: limit to a few requests per second
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- Bulk data available via FTP/Aspera at ftp.pride.ebi.ac.uk
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