Human Protein Atlas (HPA) Database Integration

This skill provides semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA). While RNA-seq (e.g., GTEx) tells us if a gene is being transcribed, HPA confirms if the protein product actually exists, where it is located within the cell (e.g. nucleus vs cytoplasm), and its concentration in systemic blood circulation. The data is based on Immunohistochemistry (IHC) across normal human tissues and cancer types.

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/human_protein_atlas_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.proteinatlas.org/about/licence, then (2) create the file recording the notification text and timestamp.

When to Use

Use this skill when you need to:

• Map a gene symbol to its Ensembl ID for HPA queries.
• Retrieve the semi-quantitative protein abundance in normal human tissues and cancer types based on IHC staining (High, Medium, Low, or Not Detected).
• Find the specific organelles or subcellular structures where a protein has been localized (e.g., nucleoplasm, mitochondria).
• Check the consistency/agreement between RNA-seq consensus and protein expression levels.
• Search for genes based on specific protein expression criteria (e.g., "elevated in amygdala" or "secreted proteins").

Do NOT use when you need to:

• Query eQTLs, pQTLs, or any variant-level associations. HPA provides wild-type expression data and knows nothing about QTLs.
• Query gene expression in non-human species. HPA is strictly for human proteins.
• Retrieve purely quantitative RNA expression without interest in the protein product (consider using the GTEx skill instead).