Agent skill

Phenotype By Hpo Id

Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.

MITAuto-check passed

Install Phenotype By Hpo Id

skills CLI

$ npx skills add InternScience/scp --skill phenotype-by-hpo-id -a claude-code

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

GitHub CLI

$ gh skill install InternScience/scp phenotype-by-hpo-id --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/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/phenotype-by-hpo-id .claude/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .claude/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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/InternScience/scp/tree/main/skills/phenotype-by-hpo-id

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 InternScience/scp --skill phenotype-by-hpo-id -a codex

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

GitHub CLI

$ gh skill install InternScience/scp phenotype-by-hpo-id --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/phenotype-by-hpo-id .agents/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .agents/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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 InternScience/scp --skill phenotype-by-hpo-id -a cursor

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

GitHub CLI

$ gh skill install InternScience/scp phenotype-by-hpo-id --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/phenotype-by-hpo-id .cursor/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .cursor/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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/InternScience/scp.git --path skills/phenotype-by-hpo-id

--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 InternScience/scp --skill phenotype-by-hpo-id -a gemini-cli

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

GitHub CLI

$ gh skill install InternScience/scp phenotype-by-hpo-id --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/InternScience/scp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/phenotype-by-hpo-id .gemini/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .gemini/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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 InternScience/scp phenotype-by-hpo-id

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 InternScience/scp --skill phenotype-by-hpo-id -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/phenotype-by-hpo-id .github/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .github/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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 InternScience/scp --skill phenotype-by-hpo-id -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 InternScience/scp phenotype-by-hpo-id --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/phenotype-by-hpo-id .opencode/skills/phenotype-by-hpo-id && 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 "phenotype-by-hpo-id" agent skill from https://github.com/InternScience/scp/tree/main/skills/phenotype-by-hpo-id into .opencode/skills/phenotype-by-hpo-id/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-by-hpo-id", 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: phenotype-by-hpo-id
GitHub stars: 170
Used in: 1 other repo
Token cost: ~766 tokens
SKILL.md length: 51 words
Files: 1
Skills in repo: 73
Repo updated: Jun 3, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.

Works in 2 steps: MCP Server Definition → Phenotype Retrieval Workflow
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Phenotype By Hpo Id is an agent skill from InternScience/scp. Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.

Its SKILL.md is about 770 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

The licence is MIT.

Example prompts

“/phenotype-by-hpo-id”

Requirements

Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

MCP Server Definition
Phenotype Retrieval Workflow

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. 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
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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

Phenotype By Hpo Id loads about 766 tokens when it runs. Until then it costs about 38 tokens; SKILL.md has 51 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~38
When it runs · the whole SKILL.md, loaded when a task matches: ~766

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 51 words, ~766 tokens.

Download SKILL.mdSave it as .claude/skills/phenotype-by-hpo-id/SKILL.md (or your agent's skills folder).

name: phenotype-by-hpo-id
description: Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.
license: MIT license
metadata.skill-author: PJLab

Phenotype Retrieval by HPO ID

Usage

1. MCP Server Definition

python

import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class OrigeneClient:
    """Origene-Monarch MCP Client"""

    def __init__(self, server_url: str, api_key: str):
        self.server_url = server_url
        self.api_key = api_key
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(
                url=self.server_url,
                headers={"SCP-HUB-API-KEY": self.api_key}
            )
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            print(f"✗ connect failure: {e}")
            return False

    async def disconnect(self):
        try:
            if self.session:
                await self.session_ctx.__aexit__(None, None, None)
            if hasattr(self, 'transport'):
                await self.transport.__aexit__(None, None, None)
        except Exception as e:
            print(f"✗ disconnect error: {e}")

    def parse_result(self, result):
        if isinstance(result, dict):
            content_list = result.get("content") or []
        else:
            content_list = getattr(result, "content", []) or []
        texts = []
        for item in content_list:
            if isinstance(item, dict):
                if item.get("type") == "text":
                    texts.append(item.get("text") or "")
            else:
                if getattr(item, "type", None) == "text":
                    texts.append(getattr(item, "text", "") or "")
        return "".join(texts)

2. Phenotype Retrieval Workflow

Implementation:

python

## Initialize client
client = OrigeneClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch",
    "<your-api-key>"
)

if not await client.connect():
    print("connection failed")
    exit()

## Retrieve phenotype by HPO ID
result = await client.session.call_tool(
    "get_phenotype_by_HPO_ID",
    arguments={
        "id": "HP:0001250"  # Seizure
    }
)

result_data = client.parse_result(result)
print(result_data)

await client.disconnect()

Tool Descriptions

Origene-Monarch Server:

get_phenotype_by_HPO_ID: Retrieve phenotype information
- Args:
  - id (str): HPO ID (e.g., "HP:0001250")
- Returns: Phenotype description, associated genes, and diseases

Use Cases

Clinical diagnosis support
Genetic disorder characterization
Phenotype-driven gene discovery
Rare disease research

Files

Just SKILL.md in skills/phenotype-by-hpo-id of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Phenotype By Hpo Id 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.

Phenotype By Hpo Id compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Phenotype By Hpo Id this skillInternScience/scp	170	1 repos	~766	Automated safety check: Pass	MIT	4 mo ago
Iterative Retrievalaffaan-m/ECC	277k	7 repos	~1.6k	Automated safety check: Pass	MIT	today
Iterative Retrievalaffaan-m/ECC	277k	2 repos	~1.1k	Automated safety check: Pass	MIT	today
Iterative Retrievalaffaan-m/ECC	277k	2 repos	~1.3k	Automated safety check: Pass	MIT	today
Iterative Retrievalaffaan-m/ECC	276k	1 repos	~1.1k	Automated safety check: Pass	MIT	yesterday
Initiate SetupNousResearch/hermes-agent	252k	—	~2.3k	Automated safety check: Pass	MIT	yesterday

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Questions about Phenotype By Hpo Id

What does Phenotype By Hpo Id do?

Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations. Phenotype By Hpo Id is an agent skill from InternScience/scp. Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.

How do I install Phenotype By Hpo Id in Claude Code?

Run `npx skills add InternScience/scp --skill phenotype-by-hpo-id -a claude-code`. Or copy the skill folder (skills/phenotype-by-hpo-id in InternScience/scp) into .claude/skills/phenotype-by-hpo-id in your project. Claude Code loads it when a task matches its description.

How do I install Phenotype By Hpo Id in Codex?

Run `npx skills add InternScience/scp --skill phenotype-by-hpo-id -a codex`. Or copy the skill folder (skills/phenotype-by-hpo-id in InternScience/scp) into .agents/skills/phenotype-by-hpo-id in your project. Codex loads it when a task matches its description.

Can I use Phenotype By Hpo Id 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 InternScience/scp --skill phenotype-by-hpo-id -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/phenotype-by-hpo-id, .gemini/skills/phenotype-by-hpo-id, .github/skills/phenotype-by-hpo-id and .opencode/skills/phenotype-by-hpo-id in your project.

What does Phenotype By Hpo Id need to run?

SKILL.md names no scripts, command-line tools or credentials: Phenotype By Hpo Id is instructions for the agent only. Our summary lists: Python 3.

Does Phenotype By Hpo Id access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Phenotype By Hpo Id 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. Review the folder before installing.

What licence does Phenotype By Hpo Id use?

Phenotype By Hpo Id 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 Phenotype By Hpo Id use?

About 766 tokens (SKILL.md is roughly 3.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Phenotype By Hpo Id?

Skills that share tags, products or a category with Phenotype By Hpo Id: Iterative Retrieval (affaan-m/ECC, 277k stars), Iterative Retrieval (affaan-m/ECC, 277k stars), Iterative Retrieval (affaan-m/ECC, 277k stars) and Iterative Retrieval (affaan-m/ECC, 276k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Phenotype By Hpo Id?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 170 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Phenotype By Hpo Id

Install Phenotype By Hpo Id

Facts

At a glance

What it does

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Phenotype Retrieval by HPO ID

Usage

1. MCP Server Definition

2. Phenotype Retrieval Workflow

Tool Descriptions

Use Cases

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

Iterative Retrieval

Iterative Retrieval

Iterative Retrieval

Iterative Retrieval

Initiate Setup

Retrieval Reflex

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Questions about Phenotype By Hpo Id