Agent skill

String Database

by aipoch in aipoch/medical-research-skills

Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.

MITAuto-check passedResearch & Science

Install String Database

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .claude/skills/string-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .claude/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .agents/skills/string-database && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .agents/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .cursor/skills/string-database && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .cursor/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/string-database'

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .gemini/skills/string-database && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .gemini/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .github/skills/string-database && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .github/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill string-database -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills string-database --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/string-database' .opencode/skills/string-database && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "string-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/string-database into .opencode/skills/string-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "string-database", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: string-database
GitHub stars: 2k
Token cost: ~928 tokens
SKILL.md length: 300 words
Files: 5 (incl. scripts, references)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.

Research & Science work in your project
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
Runs Python scripts from its folder; calls pip

What it does

String Database is an agent skill from aipoch/medical-research-skills. Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.

Its SKILL.md is about 930 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `references/string_reference.md`, `scripts/__init__.py` and `scripts/string_api.py`).

It sits in Research & Science. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/string-database”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

String Database loads about 928 tokens when it runs, and up to ~1.3k if it reads all its reference files. Until then it costs about 50 tokens; SKILL.md has 300 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~50
When it runs · the whole SKILL.md, loaded when a task matches: ~928
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 300 words, ~928 tokens.

Download SKILL.mdSave it as .claude/skills/string-database/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.

name: string-database
description: Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.
license: MIT
author: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

You have gene symbols (e.g., TP53) and need to resolve them to STRING protein identifiers for downstream analysis.
You want to retrieve a protein–protein interaction (PPI) network (functional/physical) with confidence scores for one or more proteins.
You need to find interaction partners for a target protein to expand a candidate list (e.g., add top N neighbors).
You want to perform functional enrichment (GO/KEGG/Reactome, etc.) for a protein set to interpret biological themes.
You need a quick static visualization (PNG/SVG) of a STRING network for reports or notebooks.

Key Features

ID Mapping: Convert gene/protein names to STRING identifiers for a given organism.
Network Retrieval: Fetch interaction edges with confidence scores from STRING.
Interaction Partners: Expand a protein list by retrieving interaction partners.
Enrichment Analysis:
- Functional enrichment (e.g., GO, KEGG, Reactome)
- PPI enrichment statistics
- Functional annotations (e.g., PFAM/SMART where supported by STRING endpoints)
Visualization: Download static network images (PNG/SVG).

Dependencies

Python >=3.8
requests (tested with >=2.28)
pandas (tested with >=1.5)

Install:

bash

pip install requests pandas

Example Usage

python

from scripts.string_api import StringClient

def main():
    # STRING does not require a secret API key, but providing a caller identity is recommended.
    client = StringClient(caller_identity="my_analysis_tool")

    # 1) Map an identifier (e.g., TP53 in Homo sapiens; NCBI taxonomy ID 9606)
    protein_id = client.map_id(identifier="TP53", species=9606)
    print("Mapped ID:", protein_id)

    # 2) Download a network image and expand by adding interaction partners
    client.get_network_image(
        identifiers=[protein_id],
        output_file="tp53_network.png",
        add_color_nodes=10,  # add 10 partners
    )
    print("Saved network image to tp53_network.png")

    # 3) Run PPI enrichment for the set
    ppi_stats = client.get_ppi_enrichment(identifiers=[protein_id])
    print("PPI enrichment:", ppi_stats)

if __name__ == "__main__":
    main()

Implementation Details

Client entry point: scripts/string_api.py provides the main wrapper (e.g., StringClient) around the STRING REST API.
Caller identity:
- STRING endpoints do not require an API key.
- A caller_identity string is strongly recommended (project name/email/URL) to support rate/load management.
- Pass it at initialization (e.g., StringClient(caller_identity="my_email@example.com")) or inject via environment variables in your own wrapper.
Organism selection:
- Most operations require a species identifier (commonly NCBI taxonomy ID, e.g., 9606 for human).
Network retrieval and scoring:
- Network endpoints return interactions with confidence scores; downstream filtering is typically done by applying a score threshold in your analysis code (if exposed by the wrapper).
Visualization:
- Static images are retrieved directly from STRING image endpoints and written to disk (PNG/SVG depending on the method/parameters).
Reference documentation:
- See references/string_reference.md for original API notes and endpoint details included with this skill.

Files

SKILL.md and 4 other files (scripts, references) in scientific-skills/Evidence Insight/string-database of aipoch/medical-research-skills.

SKILL.md
references/string_reference.md
scripts/__init__.py
scripts/string_api.py
string-database_audit_result_v1.json

Open the folder on GitHubat commit 686e09d

Compare with similar skills

String Database next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

String Database compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
String Database this skillaipoch/medical-research-skills	2k	—	~928	Automated safety check: Pass	MIT	21 days ago
Hypothesis Generationspacering-net/codeg	3.8k	15 repos	~3.6k	Automated safety check: Notes	MIT	today
GitHub Deep Researchbytedance/deer-flow	83k	5 repos	~1.3k	Automated safety check: Pass	MIT	today
Nature Paper CardYuan1z0825/nature-skills	46k	2 repos	~2.1k	Automated safety check: Pass	Apache-2.0	yesterday
Read arXiv Paperkarpathy/nanochat	58k	2 repos	~494	Automated safety check: Pass	MIT	1 mo ago
Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today

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Questions about String Database

What does String Database do?

Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set. String Database is an agent skill from aipoch/medical-research-skills. Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.

When should I use String Database?

String Database fits situations like: research & Science work in your project.

How do I install String Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill string-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/string-database in aipoch/medical-research-skills) into .claude/skills/string-database in your project. Claude Code loads it when a task matches its description.

How do I install String Database in Codex?

Run `npx skills add aipoch/medical-research-skills --skill string-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/string-database in aipoch/medical-research-skills) into .agents/skills/string-database in your project. Codex loads it when a task matches its description.

Can I use String Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill string-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/string-database, .gemini/skills/string-database, .github/skills/string-database and .opencode/skills/string-database in your project.

What does String Database need to run?

Going by SKILL.md and its folder, String Database needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does String Database access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is String Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does String Database use?

String Database is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does String Database use?

About 928 tokens (SKILL.md is roughly 3.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 358 tokens, read only when the agent opens those files.

What are the alternatives to String Database?

Skills that share tags, products or a category with String Database: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains String Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

String Database

Install String Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

When to Use

Key Features

Dependencies

Example Usage

Implementation Details

Files

Compare with similar skills

Similar skills

Hypothesis Generation

GitHub Deep Research

Nature Paper Card

Read arXiv Paper

Content Research Writer

Peer Review

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Questions about String Database

Install String Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

When to Use

Key Features

Dependencies

Example Usage

Implementation Details

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about String Database