string-database

1# STRING Database Skill
2 
3This skill allows you to query the STRING database programmatically using a
4bundled Python CLI wrapper.
5 
6## Prerequisites
7 
81.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
9    `uv` is installed and on PATH.
102.  **User Notification**: If .licenses/string_database_LICENSE.txt does not
11    already exist in the workspace root directory then (1) prominently notify
12    the user to check the terms at https://string-db.org/cgi/access, then (2)
13    create the file recording the notification text and timestamp.
14 
15## Core Rules
16 
171.  **MANDATORY: Ask for Species First:** The STRING API requires NCBI Taxon
18    IDs. **You MUST NOT guess or assume a species.** If the user does not
19    explicitly state a species or Taxon ID, you MUST stop and ask: "Which
20    species are you interested in? I need the NCBI Taxon ID to proceed." Even
21    for well-known proteins like TP53, BRCA1, or MDM2 that are commonly
22    associated with human studies, you MUST still ask — do not default to Human.
232.  **Never print output to stdout:** The `--output <file.tsv>` is required.
24    Never read large outputs into context. Instead use jq, python or file
25    operations (`grep`, `head`) to process large output.
263.  **Map Identifiers first:** If you only have common gene names (e.g.,
27    'TP53'), map them to STRING IDs first as this guarantees much faster server
28    responses. Use the `map` command for this.
29…