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Find-Cohort-Gap Skill · aperivue | DecimalAI

Researchby aperivue

Find-Cohort-Gap Skill

Research gap finder for longitudinal cohort databases. Profiles cohort strengths, matches PI expertise, scans literature saturation, and outputs ranked topic proposals with gap evidence. Works with any cohort: NHIS, UK Biobank, institutional EMR, health checkup registries, or disease-specific registries.

Never made a case worseMaintained

SkillScore

SkillScore100/100

Test results 100

Safety

3/3 safety checks passed

Code scan
Intent
Content

What it changes

37%100%of test cases passed +63 pts

Without skill7 of 19

With skill19 of 19

12 fixed7 passed either way0 still failing0 broke3 errored

Measured on gemini-3.6-flash10/10/2026v422 attempted

Track record

Agent runs: 0; All time

See one task, with and without the skill

One test taskIn Phase 1 author profiling, we need to gather publication history for our principal investigator, Dr. Robert Chen. We want to search PubMed for his publications over the past 5 years using the lit-search tool. What command syntax should be executed?

Without the skillMissed

With the skillPassed

Same model, same task. Answers are capped and redacted.

Use this skill

Your agent runs on

Adds every file the skill has, pinned so you can update it. No account needed.

pip install "decimalai>=0.15"
decimalai skills add aperivue-find-cohort-gap
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.

Install

pip install "decimalai>=0.15"

Add the skill

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
if result.exit_code:
    raise SystemExit(result.problems)

print("Added. Start Claude Code with the command below.")

Start Claude Code with it

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.

Add the DecimalAI plugin, once

/plugin marketplace add decimal-labs/decimalai-claude-plugins
/plugin install decimalai@decimalai

Install this skill

/decimalai:install aperivue-find-cohort-gap

The plugin needs python3 and curl on your machine.

No Python or account. Claude Code picks it up in its next session.

Save it into your project

curl -fsSL --create-dirs -o .claude/skills/aperivue-find-cohort-gap/SKILL.md https://app.decimal.ai/s/aperivue-find-cohort-gap/SKILL.md

Copy SKILL.md

Save it in your project, as

.claude/skills/aperivue-find-cohort-gap/SKILL.md

This gets SKILL.md only. The skill's 5 other files are not included.

Other ways to add it

Claude Code docs

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.

Install

pip install "decimalai[claude-agent-sdk]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

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.

Install

pip install "decimalai[claude-agent-sdk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from claude_agent_sdk import ClaudeAgentOptions, query

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Claude Agent SDK docs

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.

Install

pip install "decimalai[openai-agents]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

Install

pip install "decimalai[openai-agents]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from agents import Agent, Runner

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

OpenAI Agents docs

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.

Install

pip install "decimalai[openai]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

Install

pip install "decimalai[openai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from openai import OpenAI

client = OpenAI()
skill = Path(".agents/skills/aperivue-find-cohort-gap/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].message

This gets SKILL.md only. The skill's 5 other files are not included.

Other ways to add it

OpenAI SDK docs

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.

Install

pip install "decimalai[anthropic]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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()

Install

pip install "decimalai[anthropic]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
import anthropic

client = anthropic.Anthropic()
skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Anthropic docs

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.

Install

pip install "decimalai[google-genai]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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)

Install

pip install "decimalai[google-genai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from google import genai
from google.genai import types

client = genai.Client()
skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Gemini API docs

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.

Install

pip install "decimalai[langchain]" langchain-openai
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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!"}]})

Install

pip install "decimalai[langchain]" langchain-openai

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from langchain.agents import create_agent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

LangChain docs

CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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()

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.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from 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 5 other files are not included.

Other ways to add it

CrewAI docs

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.

Install

pip install "decimalai[adk]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

Install

pip install "decimalai[adk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from google.adk.agents import LlmAgent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Google ADK docs

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.

Install

pip install "decimalai[pydantic-ai]"
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

Install

pip install "decimalai[pydantic-ai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from pydantic_ai import Agent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Pydantic AI docs

Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" deepagents
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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(...)).

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.

Install

pip install "decimalai>=0.16" deepagents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from deepagents import create_deep_agent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Deep Agents docs

Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

The same install from Python, for a notebook or a setup script. Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from agent_framework import Agent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Microsoft Agent Framework docs

Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents
decimalai skills add aperivue-find-cohort-gap

Add it to your agent

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.

The same install from Python, for a notebook or a setup script. Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("aperivue-find-cohort-gap")
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.

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

Give it to your agent

from pathlib import Path
from strands import Agent

skill = Path(".agents/skills/aperivue-find-cohort-gap/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 5 other files are not included.

Other ways to add it

Strands docs

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 aperivue-find-cohort-gap

No Python or account. Cursor, Copilot, Cline and Warp read this folder by themselves.

Save it into your project

curl -fsSL --create-dirs -o .agents/skills/aperivue-find-cohort-gap/SKILL.md https://app.decimal.ai/s/aperivue-find-cohort-gap/SKILL.md

Copy SKILL.md

Save it in your project, as

.agents/skills/aperivue-find-cohort-gap/SKILL.md

This gets SKILL.md only. The skill's 5 other files are not included.

Other ways to add it

Cursor and other editors docs

Fetch the file and give its text to your model as instructions. No account or package needed.

Get the file

curl -fsSL https://app.decimal.ai/s/aperivue-find-cohort-gap/SKILL.md

Read the summary as JSON

curl -fsSL https://app.decimal.ai/s/aperivue-find-cohort-gap.json

This gets SKILL.md only. The skill's 5 other files are not included.

Other ways to add it

Other setups docs

You don't need a DecimalAI account.

Version: v4, tested 10/10/2026
Source: aperivue/medsci-skills ↗
License: MIT

Manage it in DecimalAI

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.

Use this skill

SKILL.md

Find-Cohort-Gap Skill

Output directory: user-specified (default: current working directory).

Phase 0: Cohort Intake

The cohort does not have to be one this skill has heard of. Route on what the user actually has.

The user has…	Do this
A named public cohort (NHIS, UK Biobank, KNHANES, …)	Fill the profile from published documentation. Cite the source for every field.
A codebook / data dictionary / CSV export of their own registry or EMR extract	Run the input adapter below. This is the common case — an institutional registry or single-centre export that no public documentation describes.
A review, guideline, or preprint defining the clinical domain	Attach it as domain context (`--context`), as a file or a URL.

Input adapter (local codebook / documents)

python3 "${CLAUDE_SKILL_DIR}/scripts/build_cohort_profile.py" \
  --codebook data_dictionary.csv \
  --context narrative_review.pdf --context https://example.org/guideline \
  --cohort-name "Institutional CT registry" --out-dir .

Formats: .csv / .tsv / .json / .md / .txt (stdlib), .xlsx (needs openpyxl), .pdf (needs pdftotext). A .csv is auto-detected as a codebook (rows are variables) or a data export (the header row is the variable list). Writes cohort_profile.md + cohort_profile.json (+ context_extract.md).

Do not read the codebook yourself and summarise it. A paraphrased, merged, or invented variable poisons every downstream claim — the intersection matrix, the feasibility gate, and eventually the manuscript's Methods. The adapter enumerates variables verbatim with provenance (file:row). Read cohort_profile.md; do not re-derive it.

The adapter infers, and shows its work for, the variable cluster map, serial / repeated-measure groups (evidence for P1 Longitudinal Advantage), and endpoint candidates (evidence for P2 Endpoint Upgrade). A variable matching no cluster keyword is left unclassified — review those, since the lexicon is not exhaustive.

What the adapter cannot know — ASK, never guess

A codebook does not state any of the following; each is emitted as [UNKNOWN - ask the user]:

Sample size (N at baseline, N with follow-up)
Time span (enrollment period, follow-up duration, measurement intervals)
Known limitations (healthy volunteer bias, attrition, missing-data patterns)
Existing publications from this cohort (to avoid duplicating them)
IRB status and data-access route

Collect these from the user before Phase 2, because a guessed N flows into the Phase 5 feasibility gate and makes it pass or fail for a reason unrelated to the cohort. Also confirm the setting (institution type, country, population type) and any special strengths the variable names cannot reveal — registry linkage, biobank availability, a distinctive population.

Gate: Present the cohort profile summary, including the [UNKNOWN] list and the unclassified variables. Confirm before proceeding.

Phase 1: PI/CA Profiling

Profile the intended PI or corresponding author to find topic-expertise alignment. If no PI is specified, skip this phase and use variable clusters alone in Phase 2.

Search PubMed for the PI's recent publications (last 5 years) with /search-lit's E-utilities script: bash "${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh" search "AuthorLastName AuthorFirstInitial[Author]" 30 Extract top keyword clusters from titles/abstracts.
Identify specialty signals: academic society positions (president, board member, editor), subspecialty focus areas, preferred journal tiers.
Build a PI keyword map: 5-10 keyword clusters ranked by publication frequency.

Output: PI profile card (name, affiliation, top keywords, society roles, preferred journals).

Phase 2: Intersection Matrix

Cross cohort variable clusters with PI expertise to generate candidate topics.

Method

Create a matrix: rows = DB variable clusters, columns = PI keyword clusters. Score each cell 0-3:

3: PI has published in this exact intersection (direct match)
2: PI's subspecialty covers this area (strong relevance)
1: Tangential connection (possible but needs framing)
0: No connection

Candidate Generation

Extract all cells scoring 2-3 as primary candidates.
For cells scoring 1, apply the A-B substitution test: "Has someone published [this analysis] with [a different exposure/outcome] in a similar cohort?" If yes, substituting the PI's specialty variable creates a viable candidate.
Generate 20-40 candidate topic statements in PICO format — P population from the cohort, E exposure/predictor variable(s), C comparison group, O outcome (preferably hard endpoint).

Discipline Alignment Filter

Before saturation scanning, identify the intended first author's department/specialty. The primary exposure variable must belong to that discipline (e.g., radiology first author → imaging variable as the primary exposure). Kill candidates where the primary exposure is outside the first author's discipline — a strong PI match alone is insufficient if the first author cannot claim ownership of the core variable.

Gate: Present the intersection matrix and top 20 candidates (post-discipline filter). User selects 8-12 for saturation scanning.

Phase 3: Literature Saturation Scan

For each selected candidate, determine how saturated the literature is.

Search Strategy

For each candidate:

Build a PubMed query: (exposure terms) AND (outcome terms) AND (cohort OR longitudinal OR prospective)
Execute search via /search-lit E-utilities.
Count total results, then ask the Critical Filter question — "Has anyone published this with serial/repeated measurements?" — and check whether a meta-analysis exists. Grade:

Papers	Longitudinal papers	MA exists?	Grade	Interpretation
0-2	0	No	Blue Ocean	First report possible. Verify the topic has audience interest.
3-10	0	No	Green Field	Optimal zone — established interest, longitudinal gap wide open.
11-30	0	No	Green Field (upgraded from Yellow)	As above.
1-30	1+	No	Yellow	Viable only with very specific angle (unique population, novel endpoint).
>30	Any	No	Yellow (borderline Red)	As above.
Any	Any	Yes, outdated (>5 yr) or limited scope	Yellow	As above.
Any	Any	Yes, recent	Red	Avoid unless doing NMA or using truly unique data.

"So What" Test

For each candidate, articulate 2-3 potential clinical implications of the findings. If you cannot state why a clinician or policymaker would care about the result, the topic fails regardless of gap score.

Output: Saturation table with grade, paper count, longitudinal gap status, and "So What" statement for each candidate.

Gate: Present saturation results. User selects 3-5 finalists for deep scoring.

Phase 4: 6-Pattern Scoring + Comparison Table

Apply the 6-Pattern framework to each finalist. Score each pattern 0 or 1.

6 Patterns (Universal)

Read the detailed rubric at ${CLAUDE_SKILL_DIR}/references/pattern_scoring_rubric.md and score each finalist on P1 Longitudinal Advantage, P2 Endpoint Upgrade, P3 Cohort Uniqueness, P4 PI-Topic Alignment (skip if no PI specified), P5 Comparison Table Gaps (3+ features unique to THIS STUDY in the table below), and P6 Complementary Design.

Comparison Table Construction

For each finalist, build a table comparing the top 3-5 existing papers against THIS STUDY, one row per feature (design, N, serial data, hard endpoint, population, ethnicity, subgroup analysis, …) — the rubric's P5 lists the construction steps and differentiator categories. Cite existing papers only with a /search-lit-confirmed DOI or PMID; otherwise mark the reference [UNVERIFIED - NEEDS MANUAL CHECK].

Score Interpretation

Total Score	Recommendation
5-6	Top-tier journal target (Lancet sub, JACC, J Hepatol level)
3-4	Specialty journal target (solid publication)
0-2	Restructure or kill — find a stronger angle before proceeding

Gate: Present scoring results and comparison tables. User approves final ranking.

Phase 5: Feasibility Gate

For each scored finalist, verify practical feasibility.

Checks

Sample size adequacy:
- Cox and logistic regression: minimum 10 events per predictor variable (EPV rule)
- For large cohorts (N>100K) with many outcome events: warn that small effects become statistically significant (power depends on the number of events, not N — check the event count first), so focus on effect size thresholds (e.g., HR >1.2 or <0.8 for clinical relevance)
- Consider negative control strategy (EPCV) for very large samples
Missing data: key exposure variable <20% missing acceptable; key outcome <5% missing; if serial data, assess the attrition pattern (MCAR/MAR/MNAR)
Follow-up adequacy: the outcome must have plausible latency within available follow-up — cancer outcomes minimum 5 years, CVD events minimum 3 years, mortality minimum 5 years
Operational definition:
- Can the exposure be defined from available variables?
- For claims data: ICD codes alone = 40-60% accuracy. Require combination strategy (diagnosis + prescription + visit frequency + special codes)
- Cross-check expected prevalence against known epidemiological data
- Flag any clinical definition, diagnostic criterion, or guideline claim you cannot source with [VERIFY] and ask the user.
IRB/ethics: is the data already IRB-approved for this type of analysis? Any additional approvals needed for data linkage?
Disease Novelty Bonus (informational, not Go/No-Go): idiopathic etiology or debated mechanism → higher journal interest; established mechanism → needs stronger methodological novelty

Decision

Go: All checks pass.
Conditional Go: Minor issues solvable (e.g., missing data manageable with imputation).
No-Go: Fatal flaw (insufficient events, no valid endpoint, key variable unavailable).

Output: Feasibility report for each finalist with Go/Conditional/No-Go status.

Phase 6: Output — Ranked Proposals + One-Pagers

Ranked Summary Table

| Rank | Topic (PICO) | Saturation | 6-Pattern Score | Feasibility | Target Journal | Timeline |
|------|--------------|------------|-----------------|-------------|----------------|----------|
| 1 | ... | Green (0 longitudinal) | 5/6 | Go | JACC | 6 months |
| 2 | ... | Blue (0 papers) | 3/6 | Conditional | Radiology | 8 months |

One-Pager for Each Finalist

Fill every section of the template at ${CLAUDE_SKILL_DIR}/references/onepager_template.md; give the target journal with its rationale (PI alignment, scope match, gap fit). Save one-pagers as markdown files: {output_dir}/gap_proposal_{rank}_{short_topic}.md

Downstream: output feeds into /design-study → /write-paper.

About this skill

Automatic

Research pack

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 10/10/2026

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IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

aperivue / medsci-skills

skills/find-cohort-gap/SKILL.md

View on GitHub ↗

License MITImported 10/10/2026Version v4Bundled 5 files · scripts

Illustrative Want to see what aperivue/find-cohort-gap would put in front of your model? Preview the rendered body and check its trigger phrases — no LLM call, no signup.

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Use this skill

Find-Cohort-Gap Skill

Phase 0: Cohort Intake

Input adapter (local codebook / documents)

What the adapter cannot know — ASK, never guess

Phase 1: PI/CA Profiling

Phase 2: Intersection Matrix

Method

Candidate Generation

Discipline Alignment Filter

Phase 3: Literature Saturation Scan

Search Strategy

"So What" Test

Phase 4: 6-Pattern Scoring + Comparison Table

6 Patterns (Universal)

Comparison Table Construction

Score Interpretation

Phase 5: Feasibility Gate

Checks

Decision

Phase 6: Output — Ranked Proposals + One-Pagers

Ranked Summary Table

One-Pager for Each Finalist

SkillSafety

Source

Related skills

More in the registry