Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill pride-project-searchgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pride-project-search)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pride-project-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/pride-project-search/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pride-project-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/pride-project-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00044 | $0.00572 |
| Opus 5 | $0.00022 | $0.00286 |
| Sonnet 5 | $0.00009 | $0.00114 |
| Haiku 4.5 | $0.00004 | $0.00057 |
Grade A, and why
pride-project-search scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 58 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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, andproject_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
projectsforaccession,title,project_description,submission_type,publication_date,submission_date,organisms,keywords, andreferences. - 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
What ships with it
8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 6d ago First seen · 58 lines · 44 tokens per session scan A 4b87fe522f40
pride-project-search is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 44 tokens to every session and 572 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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