embl-ebi-ols

1# EMBL-EBI Ontology Lookup Service (OLS)
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/embl_ebi_ols_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.ebi.ac.uk/ols4/api-docs, then (2)
10    create the file recording the notification text and timestamp.
11 
12## Core Rules
13 
14-   [!IMPORTANT] **Use the Utility Scripts**: You MUST ALWAYS use the provided
15    utility script under `scripts/` for all API interactions, including checking
16    status. NEVER use `curl` or custom Python requests to query API directly.
17 
18-   **Rate Limiting & Resilience**: You MUST respect EBI's Terms of Use with a
19    maximum 5 requests per second. The provided utility scripts automatically
20    enforce this.
21 
22-   **Notification**: If this skill is used, ensure this is mentioned in the
23    output.
24 
25## When to Use — Quick Recipes
26 
27Use this skill whenever a user query matches one of these patterns:
28 
29-   **Definition** of a disease, phenotype, or term → `get_term.py --obo_id <ID>
30    --summary`
31-   **Subtypes** or **children** of a term → `get_term.py --obo_id <ID>
32    --relations children`
33-   **Parent** of a term → `get_term.py --obo_id <ID> --relations parents`
34-   **Ancestors** / disease **categories** / **classified under** → `get_term.py
35    --obo_id <ID> --relations ancestors`
36…