polars-dovmed

Full-text search across 2.4M+ PMC Open Access papers for literature discovery and extraction tasks.

Instructions

1. Load the API key from a secure location.
2. Run a full-text search or metadata query.
3. Extract required fields (titles, DOIs, accessions, snippets).
4. Summarize results and cite sources.

Quick Reference

Task	Action
API key	POLARS_DOVMED_API_KEY in env or ~/.config/polars-dovmed/.env
Base URL	https://api.newlineages.com
Rate limit	100 queries/hour

Input Requirements

• API key (POLARS_DOVMED_API_KEY)
• Search query and filters (year, journal, organism, etc.)

Output

• Paper lists with metadata (PMC ID, DOI, title, year)
• Matched text snippets
• Extracted entities (genes, accessions, terms)

Quality Gates

• API key loaded successfully
• Query results match expected scope
• Extracted fields validated for completeness

Examples

Example 1: Minimal search (Python)

import httpx

headers = {"X-API-Key": "YOUR_KEY"}
resp = httpx.post(
    "https://api.newlineages.com/search",
    headers=headers,
    json={"query": "CRISPR archaea", "limit": 10},
)
print(resp.json())

Troubleshooting

Issue: 401 Unauthorized
Solution: Verify POLARS_DOVMED_API_KEY and reload the environment.

Issue: 429 Rate limited
Solution: Wait for quota reset or reduce request frequency.