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Get Started Free →Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis.
SkillScore68/100
Test results 68
3/3 safety checks passed
55%68%of test cases passed +14 pts
Passed 15 of 22 test cases with the skill, and 12 of 22 without it.
5 fixed10 passed either way5 still failing2 broke
This benchmark measured an earlier version of the skill.
One test taskWhen retrieving variant details from ClinVar for entry record 13921, naive tool calls often pass variant_id. What is the exact parameter name required by ClinVar_get_variant_details? Provide the parameter string.
Adds every file the skill has, pinned so you can update it. No account needed.
pip install "decimalai>=0.15"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosis
claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"The same install from Python, for a notebook or a setup script.
pip install "decimalai>=0.15"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
print("Added. Start Claude Code with the command below.")claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"Type these in a Claude Code session. No account or API key. It writes the skill and any files it bundles, and asks first when its safety rating isn't Passed.
/plugin marketplace add decimal-labs/decimalai-claude-plugins
/plugin install decimalai@decimalai/decimalai:install mims-harvard-tooluniverse-rare-disease-diagnosisThe plugin needs python3 and curl on your machine.
No Python or account. Claude Code picks it up in its next session.
curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md.claude/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdThis gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[claude-agent-sdk]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport asyncio
from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
async def main():
question = "Hello!"
async with support.run(question) as run: # one user message, one run
async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[claude-agent-sdk]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import asyncio
from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
async def main():
question = "Hello!"
async with support.run(question) as run: # one user message, one run
async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdimport asyncio
from pathlib import Path
from claude_agent_sdk import ClaudeAgentOptions, query
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
options = ClaudeAgentOptions(system_prompt=f"You are a helpful agent.\n\n{skill}", max_turns=6)
async def main():
async for message in query(prompt="Hello!", options=options):
print(message)
# In a notebook or async code: await main()
asyncio.run(main())This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai-agents]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom agents import Agent, Runner
from decimalai.openai_agents import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
name=support.name,
instructions=support.instructions, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai-agents]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from agents import Agent, Runner
from decimalai.openai_agents import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
name=support.name,
instructions=support.instructions, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from agents import Agent, Runner
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = Agent(name="support", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport json
from openai import OpenAI
from decimalai.openai import agent_config
client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
# run.system is your prompt, then the skill list.
messages = [{"role": "system", "content": run.system}, run.message]
while True:
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=messages,
tools=[*TOOLS, *run.tools], # your tools, then load_skill
).choices[0].message
messages.append(reply)
if not reply.tool_calls:
break
for call in reply.tool_calls:
# load_skill is answered by the run; your own tools by FUNCTIONS.
function = FUNCTIONS.get(call.function.name)
messages.append(run.tool_result(call) or {
"role": "tool", "tool_call_id": call.id,
"content": function(**json.loads(call.function.arguments)) if function
else f"There is no tool named {call.function.name!r}.",
})
print(reply.content)
# The Responses API takes run.response_tools instead of run.tools.The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[openai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import json
from openai import OpenAI
from decimalai.openai import agent_config
client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
# run.system is your prompt, then the skill list.
messages = [{"role": "system", "content": run.system}, run.message]
while True:
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=messages,
tools=[*TOOLS, *run.tools], # your tools, then load_skill
).choices[0].message
messages.append(reply)
if not reply.tool_calls:
break
for call in reply.tool_calls:
# load_skill is answered by the run; your own tools by FUNCTIONS.
function = FUNCTIONS.get(call.function.name)
messages.append(run.tool_result(call) or {
"role": "tool", "tool_call_id": call.id,
"content": function(**json.loads(call.function.arguments)) if function
else f"There is no tool named {call.function.name!r}.",
})
print(reply.content)
# The Responses API takes run.response_tools instead of run.tools.No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from openai import OpenAI
client = OpenAI()
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
reply = client.chat.completions.create(
model="gpt-5.4-mini",
messages=[
{"role": "system", "content": f"You are a helpful agent.\n\n{skill}"},
{"role": "user", "content": "Hello!"},
],
).choices[0].messageThis gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[anthropic]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport anthropic
from decimalai.anthropic import agent_config
client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
question = "Hello!"
with support.run(question) as run: # one user message, one run
answer = client.beta.messages.tool_runner(
model="claude-haiku-5-5",
max_tokens=4096,
system=run.system, # your prompt, then the skill list
tools=[*run.tools], # your tools, then load_skill
messages=[{"role": "user", "content": question}],
).until_done()The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[anthropic]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import anthropic
from decimalai.anthropic import agent_config
client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
question = "Hello!"
with support.run(question) as run: # one user message, one run
answer = client.beta.messages.tool_runner(
model="claude-haiku-5-5",
max_tokens=4096,
system=run.system, # your prompt, then the skill list
tools=[*run.tools], # your tools, then load_skill
messages=[{"role": "user", "content": question}],
).until_done()No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
import anthropic
client = anthropic.Anthropic()
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
reply = client.messages.create(
model="claude-haiku-5-5",
max_tokens=4096,
system=f"You are a helpful agent.\n\n{skill}",
messages=[{"role": "user", "content": "Hello!"}],
)This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[google-genai]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom google import genai
from google.genai import types
from decimalai.google_genai import agent_config
client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
config = types.GenerateContentConfig(
system_instruction=run.system, # your prompt, then the skill list
tools=[*TOOLS, *run.tool_params], # your functions, then load_skill
)
contents = [{"role": "user", "parts": [{"text": run.message}]}]
while True:
response = client.models.generate_content(
model="gemini-3.5-flash", contents=contents, config=config,
)
if not response.function_calls:
break
contents.append(response.candidates[0].content)
parts = []
for call in response.function_calls:
# load_skill is answered by the run; your own functions by FUNCTIONS.
# A loop of your own rather than automatic function calling, which
# raises KeyError when the model asks for a function you did not pass.
function = FUNCTIONS.get(call.name)
parts.append(run.tool_result(call) or {"function_response": {
"name": call.name, "id": call.id,
"response": {"result": function(**(call.args or {})) if function
else f"There is no function named {call.name!r}."},
}})
contents.append({"role": "user", "parts": parts})
print(response.text)The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[google-genai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from google import genai
from google.genai import types
from decimalai.google_genai import agent_config
client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
def lookup_order(order_id: str) -> str:
return f"Order {order_id} shipped yesterday."
# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
"name": "lookup_order",
"description": "Look up the status of an order.",
"parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
"required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}
question = "Where is order A1001?"
with support.run(question) as run: # one user message, one run
config = types.GenerateContentConfig(
system_instruction=run.system, # your prompt, then the skill list
tools=[*TOOLS, *run.tool_params], # your functions, then load_skill
)
contents = [{"role": "user", "parts": [{"text": run.message}]}]
while True:
response = client.models.generate_content(
model="gemini-3.5-flash", contents=contents, config=config,
)
if not response.function_calls:
break
contents.append(response.candidates[0].content)
parts = []
for call in response.function_calls:
# load_skill is answered by the run; your own functions by FUNCTIONS.
# A loop of your own rather than automatic function calling, which
# raises KeyError when the model asks for a function you did not pass.
function = FUNCTIONS.get(call.name)
parts.append(run.tool_result(call) or {"function_response": {
"name": call.name, "id": call.id,
"response": {"result": function(**(call.args or {})) if function
else f"There is no function named {call.name!r}."},
}})
contents.append({"role": "user", "parts": parts})
print(response.text)No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from google import genai
from google.genai import types
client = genai.Client()
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
response = client.models.generate_content(
model="gemini-3.5-flash",
contents="Hello!",
config=types.GenerateContentConfig(system_instruction=f"You are a helpful agent.\n\n{skill}"),
)This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[langchain]" langchain-openai
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom langchain.agents import create_agent
from decimalai.langchain import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = create_agent(
"openai:gpt-5.4-mini",
tools=[], # your tools; the middleware adds load_skill
middleware=[support.middleware], # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[langchain]" langchain-openaifrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from langchain.agents import create_agent
from decimalai.langchain import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = create_agent(
"openai:gpt-5.4-mini",
tools=[], # your tools; the middleware adds load_skill
middleware=[support.middleware], # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from langchain.agents import create_agent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = create_agent("openai:gpt-5.4-mini", tools=[], system_prompt=f"You are a helpful agent.\n\n{skill}")
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})This gets SKILL.md only. The skill's 1 other file is not included.
CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" "crewai>=1.15.27"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport decimalai.crewai
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=decimalai.crewai.skills(), # the installed folder
tools=decimalai.crewai.skill_tools(), # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()The same install from Python, for a notebook or a setup script. CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" "crewai>=1.15.27"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import decimalai.crewai
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=decimalai.crewai.skills(), # the installed folder
tools=decimalai.crewai.skill_tools(), # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()No DecimalAI package. CrewAI's own loader reads the folder, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from crewai import Agent, Crew, Task
agent = Agent(
role="Support", goal="Help the customer", backstory="A support agent.",
llm=llm, # your own CrewAI LLM
skills=[Path(".agents/skills")],
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[adk]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = LlmAgent(
name="support", # ADK needs a Python identifier
model="gemini-3.5-flash",
instruction=support.instruction, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[adk]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = LlmAgent(
name="support", # ADK needs a Python identifier
model="gemini-3.5-flash",
instruction=support.instruction, # your prompt, then the skill list
tools=[*support.tools], # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from google.adk.agents import LlmAgent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = LlmAgent(
name="support",
model="gemini-3.5-flash",
instruction=lambda context: f"You are a helpful agent.\n\n{skill}",
)This gets SKILL.md only. The skill's 1 other file is not included.
agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[pydantic-ai]"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
"openai:gpt-4o-mini",
name=support.name,
tools=[], # your tools; the capability adds load_skill
capabilities=[support], # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.
The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.
pip install "decimalai[pydantic-ai]"from decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")
agent = Agent(
"openai:gpt-4o-mini",
name=support.name,
tools=[], # your tools; the capability adds load_skill
capabilities=[support], # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from pydantic_ai import Agent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = Agent("openai:gpt-4o-mini", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")This gets SKILL.md only. The skill's 1 other file is not included.
Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" deepagents
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport decimalai.deepagents
from deepagents import create_deep_agent
agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).
The same install from Python, for a notebook or a setup script. Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" deepagentsfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import decimalai.deepagents
from deepagents import create_deep_agent
agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from deepagents import create_deep_agent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = create_deep_agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})This gets SKILL.md only. The skill's 1 other file is not included.
Its own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" agent-framework
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisimport asyncio
from agent_framework import Agent
from decimalai.agent_framework import skills
agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))It caches skills by default, so restart the process after decimalai skills update.
The same install from Python, for a notebook or a setup script. Its own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" agent-frameworkfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
import asyncio
from agent_framework import Agent
from decimalai.agent_framework import skills
agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))It caches skills by default, so restart the process after decimalai skills update.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdimport asyncio
from pathlib import Path
from agent_framework import Agent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = Agent(client=client, instructions=f"You are a helpful agent.\n\n{skill}")
asyncio.run(agent.run("Hello!"))This gets SKILL.md only. The skill's 1 other file is not included.
Strands' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" strands-agents
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisfrom decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell
agent = Agent(
model=model, # always pass one: the default is Amazon Bedrock
system_prompt="You are a helpful agent.",
tools=[file_editor, shell],
plugins=[skills()],
)
agent("Hello!")Strands loads an agent's skills once, so build the agent again after decimalai skills update.
The same install from Python, for a notebook or a setup script. Strands' own skill loader reads the installed folder. No DecimalAI account needed.
pip install "decimalai>=0.16" strands-agentsfrom decimalai import skillpkg
# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("mims-harvard-tooluniverse-rare-disease-diagnosis")
if result.exit_code:
raise SystemExit(result.problems)
from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell
agent = Agent(
model=model, # always pass one: the default is Amazon Bedrock
system_prompt="You are a helpful agent.",
tools=[file_editor, shell],
plugins=[skills()],
)
agent("Hello!")Strands loads an agent's skills once, so build the agent again after decimalai skills update.
No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.
.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdfrom pathlib import Path
from strands import Agent
skill = Path(".agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md").read_text()
agent = Agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent("Hello!")This gets SKILL.md only. The skill's 1 other file is not included.
Adds every file the skill has, pinned so you can update it. Cursor, Copilot, Cline and Warp read this folder by themselves.
pip install "decimalai>=0.15"
decimalai skills add mims-harvard-tooluniverse-rare-disease-diagnosisNo Python or account. Cursor, Copilot, Cline and Warp read this folder by themselves.
curl -fsSL --create-dirs -o .agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md.agents/skills/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdThis gets SKILL.md only. The skill's 1 other file is not included.
Give its text to your model as instructions. No account or package needed.
This gets SKILL.md only. The skill's 1 other file is not included.
Raw files: /s/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.md · /s/mims-harvard-tooluniverse-rare-disease-diagnosis.json
Fetch the file and give its text to your model as instructions. No account or package needed.
curl -fsSL https://app.decimal.ai/s/mims-harvard-tooluniverse-rare-disease-diagnosis/SKILL.mdcurl -fsSL https://app.decimal.ai/s/mims-harvard-tooluniverse-rare-disease-diagnosis.jsonThis gets SKILL.md only. The skill's 1 other file is not included.
You don't need a DecimalAI account.
Saved prompts and skills, pinned versions, and traces of this skill in your runs. DecimalAI does not run your agent.
Claude Code reads files from your project, so DecimalAI config does not apply there.
On Claude Agent SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On OpenAI Agents: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On OpenAI SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Anthropic: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Gemini API: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On LangChain: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On CrewAI: set DECIMAL_API_KEY and add decimalai.init(crewai=True) to record runs and skill use. The skill version stays in your repo.
On Google ADK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Pydantic AI: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.
On Deep Agents: set DECIMAL_API_KEY and add decimalai.init(langchain=True) to record runs and skill use. The skill version stays in your repo.
On Microsoft Agent Framework: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.
On Strands: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.
Editors read files from your project, so DecimalAI config does not apply there.
Anywhere else: record a use with decimalai.log_skill_activation() inside a trace.
Systematic diagnosis support for rare diseases using phenotype matching, gene panel prioritization, and variant interpretation across Orphanet, OMIM, HPO, ClinVar, and structure-based analysis.
KEY PRINCIPLES:
When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory.
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
Apply these strategies to form a 3-5 candidate differential, then use tools to confirm/refute:
Common pitfalls: Felty's (RA+splenomegaly+neutropenia) mimics infection; SLE nephritis mimics PSGN (check ASO); occupational exposures trigger autoimmunity (silica→scleroderma/RA/SLE).
| Tool | WRONG | CORRECT |
|---|---|---|
OpenTargets_get_associated_drugs_by_target_ensemblID | ensemblID | ensemblId |
ClinVar_get_variant_details | variant_id | id |
MyGene_query_genes | gene | q |
gnomad_get_variant | variant | variant_id |
Phase 0: Clinical Reasoning → 3-5 candidate differential
Phase 1: Phenotype → HPO terms (HPO_search_terms), core vs variable, onset, family history
Phase 2: Disease Matching → Orphanet_search_diseases, OMIM_search, DisGeNET_search_gene
Phase 3: Gene Panel → MARRVEL_get_gene (aggregated IDs) + MARRVEL_get_omim_phenotypes (OMIM disease+inheritance), ClinGen validation, GTEx expression, prioritization scoring
Phase 3.5: Expression Context → CELLxGENE, ChIPAtlas for tissue/cell-type confirmation
Phase 3.6: Pathway Analysis → KEGG, IntAct for convergent pathways
Phase 4: Variant Interpretation → FAVOR_annotate_variant (one-call: freq + CADD/SIFT/PolyPhen/AlphaMissense + ClinVar + conservation), then ClinVar, gnomAD frequency, EVE/SpliceAI, ACMG criteria
Phase 5: Structure Analysis → AlphaFold2, InterPro domains (for VUS)
Phase 6: Literature → PubMed, BioRxiv/MedRxiv, OpenAlex
Phase 7: Report Synthesis → Prioritized differential with next steps
Phase 2 - Disease Matching: Orphanet_search_diseases(operation="search_diseases", query=keyword) then Orphanet_get_genes(operation="get_genes", orpha_code=code). Score overlap: Excellent >80%, Good 60-80%, Possible 40-60%.
Phase 3 - Gene Panel: For each candidate gene, MARRVEL_get_gene(symbol) resolves OMIM/HGNC/Ensembl/Entrez/UniProt IDs in one call, and MARRVEL_get_omim_phenotypes(symbol) lists the Mendelian diseases linked to the gene with mode of inheritance — use the inheritance pattern to filter candidates against the pedigree (e.g. drop AR genes for a clearly dominant pedigree). Then ClinGen classification drives inclusion (Definitive/Strong/Moderate = include; Limited = flag; Disputed/Refuted = exclude). Scoring: Tier 1 (top disease gene +5), Tier 2 (multi-disease +3), Tier 3 (ClinGen Definitive +3), Tier 4 (tissue expression +2), Tier 5 (pLI >0.9 +1).
Phase 3 - Clinical Testing Panels (PanelApp): Cross-check candidate genes against Genomics England PanelApp, the curated gene-panel source NHS and other genomic medicine services actually order testing from — a genuinely different signal from MARRVEL/ClinGen's disease-gene curation, since it reflects what a real diagnostic lab panel would include today.
PanelApp_search_panels(search=<phenotype/disease keyword>) — find the relevant clinical panel(s) for the working differential, e.g. search="intellectual disability" returns panel id 285 ("Intellectual disability", disease group "Developmental disorders", versioned — panels are actively curated and re-versioned).PanelApp_get_panel(panel_id=<id>) — full gene list for that panel with each gene's confidence level: 3=green (diagnostic-grade, strong evidence), 2=amber (borderline), 1=red (low evidence, do not use for diagnostic reporting) — only report green genes as actionable findings; amber/red are candidates for research follow-up, not a diagnosis.PanelApp_search_genes(gene_symbol=<symbol>) — reverse lookup: which clinical panels (and at what confidence) already include a specific candidate gene, e.g. PTEN appears on 54 panels (cancer predisposition, overgrowth, macrocephaly panels, etc.) — a gene appearing on many panels at green confidence is a stronger candidate than one appearing nowhere.
Use PanelApp as a real-world-testing-relevance check alongside (not instead of) the MARRVEL/ClinGen tier scoring above: a green-confidence PanelApp hit that also has ClinGen Definitive classification is the strongest possible signal that a lab would both classify AND actually test for the gene.Phase 4 - Variants: Start with FAVOR_annotate_variant("chr-pos-ref-alt") (GRCh38) for a single-call snapshot — population frequencies (gnomAD by ancestry, BRAVO), GENCODE consequence, CADD/SIFT/PolyPhen-2/AlphaMissense scores, conservation, and ClinVar significance — then drill into ClinVar/gnomAD/EVE/SpliceAI for detail. gnomAD frequency classes: ultra-rare <0.00001, rare <0.0001, low-freq <0.01. ACMG: PVS1 (null), PS1 (same AA), PM2 (absent pop), PP3 (computational), BA1 (>5% AF). 2+ concordant predictors strengthen PP3.
| Tier | Criteria |
|---|---|
| T1 (High) | Phenotype match >80% + gene match |
| T2 (Medium-High) | Phenotype match 60-80% OR likely pathogenic variant |
| T3 (Medium) | Phenotype match 40-60% OR VUS in candidate gene |
| T4 (Low) | Phenotype <40% OR uncertain gene |
| Primary | Fallback 1 | Fallback 2 |
|---|---|---|
get_joint_associated_diseases_by_HPO_ID_list | Orphanet_search_diseases | PubMed phenotype search |
MARRVEL_get_omim_phenotypes | OMIM_search | Orphanet gene-disease |
PanelApp_search_genes | PanelApp_search_panels (browse by phenotype instead) | ClinGen validation only |
FAVOR_annotate_variant | ClinVar_get_variant_details | gnomad_get_variant |
ClinVar_get_variant_details | gnomad_get_variant | VEP annotation |
GTEx_get_expression_summary | HPA_search_genes_by_query | Tissue-specific literature |
scripts/clinical_patterns.py - Clinical pattern lookup (syndromes, differentials, red flags, occupational exposures)Only when you call it by name. Your agent never loads it on its own. Use for diagnostic odyssey assistance, phenotype-to-disease ranking, and genetic-counseling differential generation.
Skills that do similar work, with their headline benchmark lift.
From the same source and nearby in the catalogue.