PGS Catalog Python API Docs | dltHub

PGS Catalog REST API is programmatic access to the PGS Catalog metadata (polygenic score metadata, traits, publications, performance metrics, cohorts, samples, releases and related information). The REST API base URL is https://www.pgscatalog.org/rest and No authentication required (public REST API)..

dlt is an open-source Python library that handles authentication, pagination, and schema evolution automatically. dlthub provides AI context files that enable code assistants to generate production-ready pipelines. Install with uv pip install "dlt[workspace]" and start loading PGS Catalog data in under 10 minutes.

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What data can I load from PGS Catalog?

Here are some of the endpoints you can load from PGS Catalog:

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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 API keys or tokens; requests can be made directly to endpoints under the base URL.

1. Get your credentials

No credentials required; skip credential setup.

2. Add them to .dlt/secrets.toml

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[sources.pgs_catalog_source]

dlt reads this automatically at runtime — never hardcode tokens in your pipeline script. For production environments, see setting up credentials with dlt for environment variable and vault-based options.

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How do I set up and run the pipeline?

Set up a virtual environment and install dlt:

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uv venv && source .venv/bin/activate
uv pip install "dlt[workspace]"

1. Install the dlt AI Workbench:

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dlt ai init --agent <your-agent> # <agent>: claude | cursor | codex

This installs project rules, a secrets management skill, appropriate ignore files, and configures the dlt MCP server for your agent. Learn more →

2. Install the rest-api-pipeline toolkit:

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dlt ai toolkit rest-api-pipeline install

This loads the skills and context about dlt the agent uses to build the pipeline iteratively, efficiently, and safely. The agent uses MCP tools to inspect credentials — it never needs to read your secrets.toml directly. Learn more →

3. Start LLM-assisted coding:

Use /find-source to load data from the PGS Catalog API into DuckDB.

The rest-api-pipeline toolkit takes over from here — it reads relevant API documentation, presents you with options for which endpoints to load, and follows a structured workflow to scaffold, debug, and validate the pipeline step by step.

4. Run the pipeline:

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python pgs_catalog_pipeline.py

If everything is configured correctly, you'll see output like this:

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Pipeline pgs_catalog_pipeline load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset pgs_catalog_data
The duckdb destination used duckdb:/pgs_catalog.duckdb location to store data
Load package 1749667187.541553 is LOADED and contains no failed jobs

Inspect your pipeline and data:

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dlt pipeline pgs_catalog_pipeline show

This opens the Pipeline Dashboard where you can verify pipeline state, load metrics, schema (tables, columns, types), and query the loaded data directly.

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Python pipeline example

This example loads score and publication from the PGS Catalog API into DuckDB. It mirrors the endpoint and data selector configuration from the table above:

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

@dlt.source
def pgs_catalog_source(=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.pgscatalog.org/rest",
            "auth": {
                "type": "none",
                "": ,
            },
        },
        "resources": [
            {"name": "score", "endpoint": {"path": "score/all", "data_selector": "results"}},
            {"name": "publication", "endpoint": {"path": "publication/all", "data_selector": "results"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> 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)

To add more endpoints, append entries from the resource table to the "resources" list using the same name, path, and data_selector pattern.

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How do I query the loaded data?

Once the pipeline runs, dlt creates one table per resource. You can query with Python or SQL.

Python (pandas DataFrame):

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import dlt

data = dlt.pipeline("pgs_catalog_pipeline").dataset()
sessions_df = data.score.df()
print(sessions_df.head())

SQL (DuckDB example):

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SELECT * FROM pgs_catalog_data.score LIMIT 10;

In a marimo or Jupyter notebook:

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import dlt

data = dlt.pipeline("pgs_catalog_pipeline").dataset()
data.score.df().head()

See how to explore your data in marimo Notebooks and how to query your data in Python with dataset.

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What destinations can I load PGS Catalog data to?

dlt supports loading into any of these destinations — only the destination parameter changes:

Change the destination in dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. See the full destinations list.

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Troubleshooting

Authentication failures

The PGS Catalog REST API is public; authentication errors should not occur. If you receive 401/403, verify you are using the correct base URL (https://www.pgscatalog.org/rest) and not a private/internal endpoint.

Rate limiting

The API enforces a rate limit of 100 requests per minute. When exceeded the API returns HTTP 429 or 200 with body: { "message": "request limit exceeded", "availableIn": "33 seconds" } Wait the indicated seconds before retrying.

Pagination

Endpoints that return multiple records are paginated (default limit 50, max 250). Paginated responses use the structure: { "size": <page_size>, "count": <total_count>, "next": <next_url_or_null>, "previous": <prev_url_or_null>, "results": [ ... ] }. Use limit and offset query params (limit max 250) to iterate pages. Exceeding limit >250 returns HTTP 400.

Ensure that the API key is valid to avoid 401 Unauthorized errors. Also, verify endpoint paths and parameters to avoid 404 Not Found errors.

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Next steps

Continue your data engineering journey with the other toolkits of the dltHub AI Workbench:

• data-exploration — Build custom notebooks, charts, and dashboards for deeper analysis with marimo notebooks.
• dlthub-runtime — Deploy, schedule, and monitor your pipeline in production.

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dlt ai toolkit data-exploration install
dlt ai toolkit dlthub-runtime install

• How to deploy a pipeline
• How to explore your data in marimo Notebooks
• How to query your data in Python with dataset
• Join the dlt community on Slack