human-protein-atlas-database

Retrieve protein expression and subcellular localization data from the Human Protein Atlas.

2.7k|283|Updated May 13, 2026

Search Tags:#bioinformatics #protein expression #human protein atlas #subcellular localization #gene to ensembl mapping #immunohistochemistry #scientific data retrieval

Ready to run

npx skills add https://github.com/google-deepmind/science-skills --skill human-protein-atlas-database

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: human-protein-atlas-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/human_protein_atlas_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill human-protein-atlas-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scienceskillscommon, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps you retrieve Human Protein Atlas (HPA) protein expression and spatial localization evidence for a protein using its Ensembl identifier, enabling protein-level biological insight beyond RNA expression alone.

Core Features & Use Cases

Retrieve protein expression by tissue: Get semi-quantitative IHC-derived levels (High, Medium, Low, Not Detected) for normal tissues and cancer types.
Identify subcellular localization: Determine where the protein is localized within cells (e.g., nucleus vs cytoplasm; specific organelles/structures).
Support protein-level discovery workflows: Resolve gene symbols to Ensembl IDs, fetch full atlas metadata entries, and search for genes matching expression/localization criteria.

Quick Start

Use the skill to map ERBB2 to an Ensembl ID, then fetch its subcellular location for interpretation in a protein-focused research workflow.

Frequently Asked Questions about human-protein-atlas-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I retrieve protein expression and subcellular localization data from the Human Protein Atlas?▼

To retrieve Human Protein Atlas expression and subcellular localization data, you must resolve a gene symbol to its Ensembl ID, then execute the provided HPA CLI wrapper with uv using supported subcommands that output JSON files for safe querying.

How do I find semi-quantitative immunohistochemistry expression levels for a specific gene across normal and cancer tissues?▼

You can find semi-quantitative immunohistochemistry expression levels like High, Medium, Low, or Not Detected by querying tissue and cancer expression data for normal and cancer types using the gene's corresponding Ensembl identifier.

What is the best way to map gene symbols to Ensembl IDs for protein-level discovery workflows?▼

To map gene symbols to Ensembl IDs for protein-level discovery, use the dedicated gene resolution workflow within this Human Protein Atlas retrieval process to fetch full atlas metadata entries and enable accurate expression queries.

Can I search for genes matching specific protein expression or subcellular localization criteria?▼

Yes, you can search for genes matching specific attribute criteria such as tissue expression levels or subcellular localization by executing targeted search subcommands through the HPA CLI wrapper to filter and retrieve matching proteins.

Do I need an Ensembl ID to query subcellular localization data for proteins?▼

Yes, resolving your target gene symbol to an Ensembl identifier is a required prerequisite, as the Human Protein Atlas relies on these stable IDs to accurately fetch subcellular location data and full metadata entries.

Why should I use the provided CLI wrapper instead of directly querying the Human Protein Atlas API?▼

You must use the provided HPA CLI wrapper with uv to generate JSON file outputs because direct querying is unsafe and unsupported, ensuring semi-quantitative protein expression and localization data is retrieved securely.