Europepmc method triage

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

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.From its SKILL.md

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.

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

What ships with it: 7 files

6.6 KB alongside SKILL.md, 1 of them executable