Load PGS Catalog data to DuckDB

The PGS Catalog REST API provides programmatic access to metadata regarding published polygenic scores, traits, publications, and associated performance metrics. Everything needed to build a working PGS Catalog → 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 PGS Catalog 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 PGS Catalog 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 PGS Catalog 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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PGS Catalog API at a glance

These values come from the PGS Catalog API reference — the authoritative source if anything here looks out of date.

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How do I authenticate with the PGS Catalog API?

The PGS Catalog REST API is publicly accessible and does not require any authentication or headers.

No credentials required. The PGS Catalog API is public, so there is nothing to obtain and nothing to add to .dlt/secrets.toml — the pipeline above runs as written.

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What PGS Catalog data can I load into DuckDB?

These are the PGS Catalog endpoints dlt can load into DuckDB:

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How do I load only new PGS Catalog records?

The PGS Catalog API reference does not document a timestamp or sequence field for these endpoints, so there is nothing to advertise here as verified. Pick a field from the endpoints table above that increases with every write, then set it as the cursor_path.

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{"name": "score_all", "endpoint": {
    "path": "score/all",
    # Replace with a field that increases on every write.
    "incremental": {"cursor_path": "REPLACE_ME", "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 PGS Catalog pipeline look like?

A standard dlt REST API pipeline — the same code you would write by hand, loading score and publication from the PGS Catalog API into DuckDB:

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

@dlt.source
def pgs_catalog_source():
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.pgscatalog.org/rest",
        },
        "resources": [
            {"name": "score_all", "endpoint": {"path": "score/all", "data_selector": "results"}},
            {"name": "publication_all", "endpoint": {"path": "publication/all", "data_selector": "results"}}
        ],
    }
    yield from rest_api_resources(config)


def load_pgs_catalog_to_duckdb() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="pgs_catalog_pipeline",
        destination="duckdb",
        dataset_name="pgs_catalog_data",
    )
    load_info = pipeline.run(pgs_catalog_source())
    print(load_info)


if __name__ == "__main__":
    load_pgs_catalog_to_duckdb()

Run it with python pgs_catalog_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 PGS Catalog 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("pgs_catalog_pipeline").dataset()
df = data.score_all.df()
print(df.head())

SQL:

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SELECT * FROM pgs_catalog_data.score_all LIMIT 10;

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

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How do I deploy the PGS Catalog 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 PGS Catalog 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 PGS Catalog 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