europepmc-method-triage

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

1. 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.
2. Review the hitCount and the first page of resultList.result.
3. 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