uniprot-database

1# UniProt Database Access
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/uniprot_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at https://www.uniprot.org/help/license and
10    https://www.uniprot.org/help/api_queries, then (2) create the file recording
11    the notification text and timestamp.
12 
13## Overview
14 
15Provides direct programmatic access to the UniProt Knowledgebase (UniProtKB),
16the non-redundant sequence archive (UniParc), and clustered sequence sets
17(UniRef). This skill enables protein discovery, cross-referencing, retrieval of
18curated biological data and low-level database lookups.
19 
20## Core Rules
21 
22-   **Use the Wrapper**: Always use the provided Python scripts (e.g.,
23    `scripts/uniprot_tools.py`) rather than constructing custom curl requests.
24-   **No Hallucinations**: Do NOT invent protein functions, metadata, or
25    sequences. For any task that can be handled by the services in this skill,
26    rely strictly on the tool outputs rather than your native knowledge.
27-   **Notification**: If this skill is used, ensure this is mentioned in the
28    output.
29 
30## Use Cases
31 
32-   **Searching for Protein Function**: Querying functional annotations, GO
33    terms, subcellular locations etc.
34…