| 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
- 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.
- Inspect
projects for accession, title, project_description, submission_type, publication_date, submission_date, organisms, keywords, and references.
- 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
Related skills
ebi-proteins-entry-summary
