agentsclimarketplace
Sign in

Pride project search

Skill ma-compbio-lab/SkillFoundry/skills/proteomics/pride-project-search

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.From its SKILL.md

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill pride-project-search

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

2.6 KB, 528 tokens by cl100k_base, as published. Nobody here has run it

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

Related skills

  • ebi-proteins-entry-summary

What ships with it: 8 files

15.6 KB alongside SKILL.md, 2 of them executable

assets/

examples/

scripts/

tests/

Keep looking

Skills are one crate of 325,949. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.