Europepmc method triage

Skill ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/europepmc-method-triage

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill europepmc-method-triage

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

What its author says it does

Copied from the file, not written here

Use this skill to search life-science literature through Europe PMC when you need publication metadata oriented toward biomedical method triage. Do not use it when you need offline execution or cluster-scale batch processing.

SKILL.md

1.9 KB, 397 tokens by cl100k_base, as published. Nobody here has run it

Purpose

Search Europe PMC and capture structured records for biomedical literature triage and method discovery.

When to use

You need PubMed-adjacent life-science coverage.
You want a method-search corpus with stable JSON output.

When not to use

You need complete full-text retrieval.
You are working without network access.

Inputs

Query string
Optional --page-size, --sort, and --out

Outputs

Europe PMC JSON search payload

Requirements

Python 3.13+
Network access to www.ebi.ac.uk

Procedure

Run python3 skills/scientific-knowledge/europepmc-method-triage/scripts/search_europepmc.py --query "single-cell RNA-seq" --page-size 5 --out skills/scientific-knowledge/europepmc-method-triage/assets/europepmc_single_cell.json.
Review the hitCount and the first page of resultList.result.
Refine the query for organism, assay, benchmark, or package terms.

Validation

Command exits successfully.
Output JSON contains hitCount.
At least one result is returned for a common biomedical topic.

Failure modes and fixes

Empty result set: switch to broader biomedical wording.
API timeout: reduce --page-size and retry.

Safety and limits

Use for literature discovery, not for unsafe operational biological guidance.
Respect service limits and article-specific rights.

Examples

python3 .../search_europepmc.py --query "spatial transcriptomics benchmark" --page-size 3

Provenance

Europe PMC RESTful Web Service: https://europepmc.org/RestfulWebService
Europe PMC Annotations API: https://europepmc.org/annotations_api

Related skills

openalex-literature-search

Gives 0 of the 12 instructions most debug triage skills give in 397 tokens

Counted across 839 of the 1,149 authors here whose files we hold, read 2026-08-06

investigate root cause before proposing any fixin 102 of 839, across 65 files
read error messages completelyin 90 of 839, across 48 files
create a failing test case before fixingin 84 of 839, across 44 files
reproduce the issue consistentlyin 82 of 839, across 40 files
change one variable at a timein 82 of 839, across 42 files
check recent changesin 74 of 839, across 35 files
write the regression test before fixingin 74 of 839, across 36 files
fix the root cause not the symptomin 60 of 839, across 43 files
implement a single fix at a timein 59 of 839, across 20 files
trace data flow backward to the sourcein 50 of 839, across 20 files
remove all debug instrumentationin 49 of 839, across 13 files
form a single hypothesisin 48 of 839, across 18 files

Said here and by no other author read

run the search script with a query string
review the hit count and first page of results
refine the query for organism, assay, benchmark, or package terms
switch to broader biomedical wording on empty results
reduce page size and retry on api timeout
verify the output json contains a hit count

Grouped from the skills themselves: near-identical wordings counted once, and counted by distinct author, so one author publishing three of these counts once. Length counted with cl100k_base; the agent that loads this file may tokenize it differently.