kth_hpalisted

Programmatically fetch data from the Human Protein Atlas (proteinatlas.org, the KTH/SciLifeLab resource) — per-gene records (tissue & single-cell RNA expression, subcellular localization, pathology/cancer prognostics, antibody reliability, protein class) and multi-gene search/download queries with chosen columns, as JSON/TSV/XML. Use whenever the user wants to get, download, query, scrape, or batch-pull Human Protein Atlas / HPA / proteinatlas.org data for one or many genes, asks "does proteinatlas have an API", wants HPA tissue or subcellular or single-cell expression for a gene list, needs the HPA record for an Ensembl ID or gene symbol, or wants to know which HPA bulk file to download. Trigger even when they just paste a proteinatlas.org URL or a list of genes and say "get their HPA data".
Agents365-ai/kth_hpa · ★ 0 · Data & Documents · score 63

Install: claude install-skill Agents365-ai/kth_hpa

# KTH HPA — Human Protein Atlas programmatic access The Human Protein Atlas (HPA, proteinatlas.org — the KTH / SciLifeLab resource led by Mathias Uhlén) has no REST-with-docs API, but exposes three reliable programmatic paths. This skill wraps the two per-request ones in one stdlib script and points to the third (bulk download) for large jobs. ## Pick the access path - **A few genes, want the full record** → `entry` subcommand (per-gene `.json`). - **Many genes, only specific fields** → `search` subcommand (one call, chosen columns) — or a bulk file if you want the whole atlas. - **Whole-atlas / hundreds+ of genes** → download a bulk TSV, don't loop the API. See `references/columns.md` → "Bulk downloads". ## Usage The script is `scripts/hpa.py` (Python 3, stdlib only — no installs). ```bash # Per-gene record by symbol or Ensembl ID. --fields summary (default) gives a # compact subset; --fields all gives the full ~100-field record. python3 scripts/hpa.py entry EGFR TP53 ENSG00000141510 --fields summary # Full record as TSV or XML (returned verbatim): python3 scripts/hpa.py entry EGFR --format tsv --out egfr.tsv # Multi-gene query with chosen columns (codes in references/columns.md): python3 scripts/hpa.py search --query "EGFR" --columns "g,eg,scl,rnats,rnascs" --format tsv # Write JSON to a file: python3 scripts/hpa.py entry EGFR TP53 --fields all --out out.json ``` `entry` accepts gene symbols and/or `ENSG…` IDs mixed freely; symbols are resolved to Ensembl IDs