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STRING Database Skill · mkurman | DecimalAI

scienceby mkurman

STRING Database Skill

mkurman/string-database

Source mkurman/zorai ↗License MIT

Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology.

SkillScore25Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 2 of 8 test cases with the skill, and 1 of 8 without it.

Without skill17%

With skill25%

Checks it passed that the model alone missed

Refrains from assuming Homo sapiens or NCBI Taxon ID 9606.
Asks for the species or NCBI Taxon ID before executing queries.
Stops to ask the user for the species or NCBI Taxon ID before querying.

and 2 more in the full report

4 fixed2 passed either way16 still failing2 broke

Pass-rate lift: +8 pp
Tokens: -34%
Agent turns: 0%
Response time: -54%

Model gemini-3.6-flashMeasured 8/21/2026v16 of 24 cases passed with skill · 8 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-string-database/SKILL.md https://app.decimal.ai/s/mkurman-string-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-string-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-string-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-string-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-string-database/SKILL.md https://app.decimal.ai/s/mkurman-string-database/SKILL.md

Raw file: /s/mkurman-string-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-string-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 4

Prompt

I need to get PPI network data for OCT4, SOX2, and NANOG from the STRING database and put the network table in a TSV file.

What was checked, without and with the skill
Checked	Without skill	With skill
Asks for the species or NCBI Taxon ID before executing queries.	Missed	Passed

case-08 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md57 lines6 filesincludes scripts

STRING Database Skill

This skill allows you to query the STRING database programmatically using a bundled Python CLI wrapper.

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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 map command 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)

Track record

Benchmark

2 / 8

test cases passed, vs 1 / 8 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/string_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 5 files · scripts

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See it in action

What's inside

STRING Database Skill

Prerequisites

Core Rules

Tool Execution

Feature Domains (Progressive Disclosure)

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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