Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/google-deepmind/science-skills/string_databasenpx skills add google-deepmind/science-skills --skill string_databasegit clone --depth 1 https://github.com/google-deepmind/science-skillsWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00050 | $0.00687 |
| Opus 5 | $0.00025 | $0.00344 |
| Sonnet 5 | $0.00010 | $0.00137 |
| Haiku 4.5 | $0.00005 | $0.00069 |
Grade A, and why
string-database scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 67 lines — stays where its author put it; the contents beside it link to each section on GitHub.
STRING Database Skill
This skill allows you to query the STRING database programmatically using a bundled Python CLI wrapper.
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- 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
- 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.
- 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. - 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
mapcommand for this. - Notification: If this skill is used, ensure this is mentioned in the output.
Tool Execution
The CLI is at scripts/string_cli.py and should be run using uv run:
uv run scripts/string_cli.py <command> [options] --output /tmp/out.tsv
Feature Domains (Progressive Disclosure)
Read the following reference files based on the user's request:
- Mapping Identifiers - Map common protein names to STRING IDs.
- Interactions & Network - Find interacting proteins, network topologies, mediators, homology, and visual network images.
- Enrichment & Functional Annotations - Analyze pathway enrichment (GO, KEGG, Pfam), PPI significance, or find all proteins associated with a specific term (e.g. Melanoma).
- Values/Ranks Enrichment - Submit full experimental datasets (e.g., logFC, p-values) for rank-based enrichment analysis using the async background API.
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 67 lines · 50 tokens per session scan A 6de0f5994327
string-database is a skill published in the GitHub repository google-deepmind/science-skills (2,814 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 50 tokens to every session and 687 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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