Openalex Database

Prerequisites

pip install requests pandas

• No API key required; add [email protected] to join the polite pool
• Rate limits: 10 req/s; cursor pagination supports up to 10,000 results per query

Quick Start

import requests

BASE = "https://api.openalex.org"
r = requests.get(f"{BASE}/works",
                 params={"search": "CRISPR gene editing",
                         "filter": "publication_year:2023",
                         "per_page": 5,
                         "mailto": "[email protected]"})
r.raise_for_status()
data = r.json()
print(f"Total: {data['meta']['count']}")
for work in data["results"][:3]:
    print(f"  {work['title'][:80]} ({work['publication_year']}) cites={work['cited_by_count']}")

Core API Summary

For complete runnable code (6 query types, systematic search, collaboration network, batch DOI lookup, country analysis), see references/api_queries.md.

Key Concepts

Inverted Index Abstracts

OpenAlex stores abstracts as inverted indexes (word → positions) due to copyright restrictions. Reconstruct with:

inv = work.get("abstract_inverted_index")
if inv:
    words = {pos: w for w, ps in inv.items() for pos in ps}
    text = " ".join(words[i] for i in sorted(words))

Cursor-Based Pagination

Use cursor="*" to start, then read next_cursor from each response. Max 200 per page, up to 10,000 results via cursor pagination.

Key Parameters

Best Practices

1. Always include mailto: Joins polite pool for priority processing without extra rate throttling.
2. Use select for large paginations: e.g., select=id,doi,title,cited_by_count to reduce response size.
3. Use cursor pagination, not offset: OpenAlex does not support offset beyond 10,000 results.
4. Check abstract_inverted_index is not None before reconstructing — not all works have abstracts.
5. Cache by work ID: OpenAlex Work IDs (W…) are stable; cache to avoid re-fetching.

Troubleshooting

Related Skills

• pubmed-database — Biomedical literature with MeSH controlled vocabulary
• literature-review — Systematic review methodology and PRISMA framework
• scientific-brainstorming — Hypothesis generation using literature as input

References

• OpenAlex documentation
• OpenAlex API endpoint
• OpenAlex paper (Priem et al. 2022)
• Entity types reference