Load openFDA data to DuckDB

openFDA is an Elasticsearch-based platform providing REST APIs for public FDA data including drugs, medical devices, foods, and other regulated products. Everything needed to build a working openFDA → DuckDB pipeline is on this page: the API's base URL, authentication, endpoints, pagination and incremental field — plus a prompt that hands the whole job to your coding agent.

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Build your openFDA to DuckDB pipeline

Paste this prompt into Claude, Codex, or Cursor. The agent does the rest.

PromptCopy prompt
Run uvx dlthub-init@latest to build a pipeline from openFDA to DuckDB and run it on dltHub

That scaffolds a dltHub workspace and installs the dltHub AI harness — the project rules, the secrets-management skill, and the dlt MCP server your agent needs to work safely. From there it reads the openFDA API, proposes the endpoints to load, then writes, runs and validates the pipeline while you review rather than type. Credentials are inspected through MCP tools, so your agent never reads secrets.toml itself. How the LLM-native workflow works →

Prefer to write it yourself? Every fact the agent uses is below.

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openFDA API at a glance

These values come from the openFDA API reference — the authoritative source if anything here looks out of date.

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How do I authenticate with the openFDA API?

The API supports passing the API key as an 'api_key' query parameter or as a username in Basic Auth (the password field can be left empty).

1. Get your credentials

Visit the official openFDA authentication page (https://open.fda.gov/apis/authentication/) to request a free API key. You will need to provide a valid email address. Upon registration, you will receive an API key that you can use to increase your rate limits (up to 120,000 requests per day).

2. Add them to .dlt/secrets.toml

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[sources.openfda_source]
api_key = "your_api_key_here"

dlt reads this file automatically at runtime. With the harness, the setup-secrets skill prompts you for the values and never handles the raw credential in chat. For production, see setting up credentials with dlt.

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What openFDA data can I load into DuckDB?

These are the openFDA endpoints dlt can load into DuckDB:

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How do I load only new openFDA records?

openFDA exposes search_after on drug/event.json, so dlt can request only the records that changed since the last run. Set it as the cursor_path and dlt tracks the high-water mark for you between runs.

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{"name": "drug_event", "endpoint": {
    "path": "drug/event.json",
    "data_selector": "results",
    "incremental": {"cursor_path": "search_after", "initial_value": "2024-01-01T00:00:00Z"},
}}

On the first run dlt loads everything from initial_value; on every run after that it requests only what changed and appends with write_disposition="merge" if you set a primary key. See incremental loading.

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What does the generated openFDA pipeline look like?

A standard dlt REST API pipeline — the same code you would write by hand, loading drug/event and drug/label from the openFDA API into DuckDB:

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import dlt
from dlt.sources.rest_api import RESTAPIConfig, rest_api_resources

@dlt.source
def openfda_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://api.fda.gov",
            "auth": {"type": "http_basic", "username": "REPLACE_ME", "password": api_key},
        },
        "resources": [
            {"name": "drug_event", "endpoint": {"path": "drug/event.json", "data_selector": "results"}},
            {"name": "drug_label", "endpoint": {"path": "drug/label.json", "data_selector": "results"}}
        ],
    }
    yield from rest_api_resources(config)


def load_openfda_to_duckdb() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="openfda_pipeline",
        destination="duckdb",
        dataset_name="openfda_data",
    )
    load_info = pipeline.run(openfda_source())
    print(load_info)


if __name__ == "__main__":
    load_openfda_to_duckdb()

Run it with python openfda_pipeline.py. The agent iterates on this until it loads cleanly — you review and approve, rather than write it from scratch.

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How do I query openFDA data in DuckDB?

dlt creates one table per resource. Query the loaded data with Python or SQL — or ask your agent to, through the MCP server's execute_sql_query tool.

Python (pandas DataFrame):

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import dlt

data = dlt.pipeline("openfda_pipeline").dataset()
df = data.drug_event.df()
print(df.head())

SQL:

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SELECT * FROM openfda_data.drug_event LIMIT 10;

See querying your data with dataset and exploring it in marimo notebooks.

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How do I deploy the openFDA to DuckDB pipeline in production?

The pipeline runs locally, which is ideal for prototyping and one-off analysis. When you need it on a schedule, monitored on every load, and shared with your team, deploy the same dlt code on the dltHub platform — no infrastructure to maintain. The prompt above already ends with "run it on dltHub", so your agent can take it there directly.

• Deploy & schedule — run the pipeline as a managed job with automatic retries.
• Monitor — observable job queues, alerting, and load metrics for every run.
• Transform — promote raw openFDA loads into governed, documented models.
• Visualize & share — explore data in notebooks and publish live dashboards instead of static screenshots.

Book a demo →

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What other destinations can I load openFDA data to?

dlt loads into any of these — only the destination argument changes:

Set dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. On the dltHub platform the same pipeline runs against a managed Iceberg lakehouse. See the full destinations list.

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Next steps

• Ready for production? Book a demo of the dltHub platform →
• dlt LLM-native workflow docs
• REST API source reference
• Join the dlt community on Slack