polars-dovmedlisted
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