polars-dovmed

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Search 2.4M+ full-text PubMed Central Open Access papers for literature reviews, trends, and data extraction.

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Sourcefmschulz/omics-skills
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NPX Install

npx skill4agent add fmschulz/omics-skills polars-dovmed

Tags

Translated version includes tags in frontmatter
pubmed-centralliterature-searchdata-extractionpolars-dovmedapi-integration

SKILL.md Content

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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

TaskAction
API key
POLARS_DOVMED_API_KEY
in env or 
~/.config/polars-dovmed/.env
Base URL
https://api.newlineages.com
Rate limit100 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)

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.