name: polars-dovmed description: Search 2.4M+ full-text PubMed Central Open Access papers for literature reviews, trends, and data extraction. user-invocable: true

polars-dovmed

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

Input Requirements

• API key (POLARS_DOVMED_API_KEY)
• Search query and filters (year, journal, organism, etc.)
• Optional fast_mode:
  • false (default): full-text search (title, abstract_text, abstract, full_text)
  • true: abstract-only search (abstract_text, abstract)

Output

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

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/api/search_literature",
    headers=headers,
    json={
        "query": "CRISPR archaea",
        "max_results": 10,
        "extract_matches": False,
        "fast_mode": False,  # set True for abstract-only
    },
)
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.

Issue: Fast mode returns too few results Solution: Retry with fast_mode=false to include full text.