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polars-dovmedlisted

Search the PMC Open Access literature with polars-dovmed. Author structured JSON queries directly, then use the hosted API when an API key is available or fall back to local dovmed scan over PMC, bioRxiv, or both parquet corpora.
fmschulz/omics-skills · ★ 3 · AI & Automation · score 70
Install: claude install-skill fmschulz/omics-skills
# polars-dovmed Search PubMed Central Open Access and bioRxiv parquet corpora with `polars-dovmed`. Use the bundled helper, `skills/polars-dovmed/scripts/query_literature.py`, for hosted API or local parquet-backed searches. The helper auto-loads `~/.config/polars-dovmed/.env`. Current hosted API defaults: - Treat API keys as secrets in artifacts. Do not save keys in run directories, memory records, summaries, or final answers. - Save generated run artifacts under `tasks/polars-dovmed-runs/<slug>/` by default, not under `skills/polars-dovmed/`. - Prefer structured async search through `/api/jobs` targeting `scan_literature_advanced(mode="discovery")`. - Do not use the flat `/api/search_literature` endpoint for smoke tests or normal skill work. It is opt-in only with `--allow-flat-query` and may hang behind the edge proxy. - Do not start with `--corpus both`. Run `--corpus biorxiv` and `--corpus pmc` as separate calls, then merge results. - For OpenPMC/PMC, do not run a broad unbanded scan. Use the materialized clean year bands in parallel with direct FTS-backed calls: `--sync --year-bands clean_split --year-band-workers 4`. - If the user names a specific publication year or narrow range, map it to the matching clean band(s) and search only those bands. Use all clean bands only when no year constraint is given. - For recent or emerging taxa, run bioRxiv anchor-only discovery and OpenPMC clean-band discovery as separate searches. bioRxiv is small and often returns first; Ope