human-protein-atlas-database

1# Human Protein Atlas (HPA) Database Integration
2 
3This skill provides semi-quantitative protein expression and spatial
4localisation data from the Human Protein Atlas (HPA). While RNA-seq (e.g., GTEx)
5tells us if a gene is being transcribed, HPA confirms if the protein product
6actually exists, where it is located within the cell (e.g. nucleus vs
7cytoplasm), and its concentration in systemic blood circulation. The data is
8based on Immunohistochemistry (IHC) across normal human tissues and cancer
9types.
10 
11## Prerequisites
12 
131.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
14    `uv` is installed and on PATH.
152.  **User Notification**: If .licenses/human_protein_atlas_database_LICENSE.txt
16    does not already exist in the workspace root directory then (1) prominently
17    notify the user to check the terms at
18    https://www.proteinatlas.org/about/licence, then (2) create the file
19    recording the notification text and timestamp.
20 
21## When to Use
22 
23**Use this skill when you need to:**
24 
25-   Map a gene symbol to its Ensembl ID for HPA queries.
26-   Retrieve the semi-quantitative protein abundance in normal human tissues and
27    cancer types based on IHC staining (High, Medium, Low, or Not Detected).
28-   Find the specific organelles or subcellular structures where a protein has
29    been localized (e.g., nucleoplasm, mitochondria).
30-   Check the consistency/agreement between RNA-seq consensus and protein
31    expression levels.
32…