string-databaselisted

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