Openalex literature search

Purpose

Search OpenAlex works metadata and save a reproducible JSON result set for paper triage.

When to use

• You need a quick literature sweep for a topic or method.
• You want machine-readable metadata for downstream ranking or deduplication.

When not to use

• You need full-text content or article annotations.
• You are working without network access.

Inputs

• Search query string
• Optional --per-page, --mailto, and --out

Outputs

• JSON payload from the OpenAlex works search endpoint

Requirements

• Python 3.13+
• Network access to api.openalex.org

Procedure

1. Run python3 skills/scientific-knowledge/openalex-literature-search/scripts/search_openalex.py --query "single-cell RNA-seq" --per-page 5 --out skills/scientific-knowledge/openalex-literature-search/assets/openalex_single_cell.json.
2. Inspect the meta block for count and pagination.
3. Use the first-pass results to rank or expand follow-up searches.

Validation

• Command exits successfully.
• Output JSON contains meta and results.
• results is non-empty for a known topic.

Failure modes and fixes

• HTTP 403 or throttling: provide --mailto and reduce request rate.
• Empty results: broaden the query or remove over-specific phrasing.

Safety and limits

• This skill surfaces public metadata only.
• Respect API terms and do not turn literature discovery into unsafe experimental planning.

Examples

• python3 .../search_openalex.py --query "spatial transcriptomics benchmark" --per-page 3

Provenance

• OpenAlex API overview: https://docs.openalex.org/how-to-use-the-api/api-overview

Related skills

• europepmc-method-triage