pride-project-search

name	pride-project-search
description	Use this skill to search PRIDE Archive v2 proteomics projects by keyword and return compact dataset-discovery summaries. Do not use it for raw file download orchestration or unsupported PRIDE endpoints.

Purpose

Search PRIDE Archive v2 project metadata and summarize matching proteomics studies in a small stable JSON payload.

When to use

• You need a quick proteomics dataset discovery entry point by keyword.
• You want PRIDE accessions, project titles, organisms, dates, and references before deeper analysis.

When not to use

• You need raw file download planning or file-by-file manifest handling.
• You need peptide- or protein-level quantification results.
• You need large bulk exports.

Inputs

• Keyword query
• Optional page and page size
• Optional output path

Outputs

• JSON payload containing compact PRIDE project summaries with accession, title, project_description, submission_type, publication_date, submission_date, updated_date, organisms, keywords, references, experiment_types, and project_url.

Requirements

• Python 3.10+
• Network access to www.ebi.ac.uk

Procedure

1. Run python3 skills/proteomics/pride-project-search/scripts/search_pride_projects.py --keyword phosphoproteomics --page-size 2 --out skills/proteomics/pride-project-search/assets/phosphoproteomics_projects.json.
2. Inspect projects for accession, title, project_description, submission_type, publication_date, submission_date, organisms, keywords, and references.
3. Use the returned PRIDE accession in downstream dataset or literature workflows.

Validation

• Command exits successfully.
• Output contains at least one PXD... accession for a known keyword.
• Each project summary includes a non-empty title.

Failure modes and fixes

• No hits: broaden the keyword or try a better-known assay term.
• Unexpected payload shape: confirm the PRIDE Archive v2 search endpoint is still returning project lists.
• Need file manifests: build a separate PRIDE file-level skill instead of overloading this one.

Safety and limits

• Metadata discovery only.
• This skill does not download raw data or interpret proteomics results.

Example

• python3 skills/proteomics/pride-project-search/scripts/search_pride_projects.py --keyword phosphoproteomics --page-size 2

Provenance

• PRIDE Archive API docs: https://www.ebi.ac.uk/pride/ws/archive/
• Search endpoint used by this skill: https://www.ebi.ac.uk/pride/ws/archive/v2/search/projects

Related skills

• ebi-proteins-entry-summary