eQTL Catalogue Python API Docs | dltHub

The eQTL Catalogue REST API provides access to molecular QTL summary statistics and study metadata from the eQTL Catalogue project. The REST API base URL is https://www.ebi.ac.uk/eqtl/api/ and The API is open and does not require authentication or tokens..

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 add "dlt[hub]" and start loading eQTL Catalogue data in under 10 minutes.

---

What data can I load from eQTL Catalogue?

Here are some of the endpoints you can load from eQTL Catalogue:

---

How do I authenticate with the eQTL Catalogue API?

The eQTL Catalogue API is a public service and does not require authentication for data access.

1. Get your credentials

The eQTL Catalogue REST API is a public service provided by EMBL-EBI. It does not require any API keys, tokens, or registration to access. You can send GET requests directly to the API endpoints without providing any authentication headers.

2. Add them to .dlt/secrets.toml

Copy
[sources.eqtl_catalogue_source]
# Note: The eQTL Catalogue API is public and does not require authentication. # The following is a placeholder structure if your dlt pipeline expects a # configuration block for consistency with other connectors. [sources.eqtl_catalogue]
api_key = ""

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.

---

How do I set up and run the pipeline?

Set up a virtual environment and install dlt:

Copy
uv init
uv add "dlt[hub]"

1. Install the dlt AI harness:

Copy
uv run dlthub 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:

Copy
uv run dlthub ai toolkit install rest-api-pipeline

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 eQTL Catalogue 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:

Copy
uv run python eqtl_catalogue_pipeline.py

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

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

Inspect your pipeline and data:

Copy
uv run dlthub show

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

---

Python pipeline example

This example loads /eqtl/api/v3/studies and /eqtl/api/v3/datasets from the eQTL Catalogue API into DuckDB. It mirrors the endpoint and data selector configuration from the table above:

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

@dlt.source
def eqtl_catalogue_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.ebi.ac.uk/eqtl/api/",
            "auth": {"type": "api_key", "api_key": api_key, "name": "token"},
        },
        "resources": [
            {"name": "studies", "endpoint": {"path": "eqtl/api/v3/studies"}},
            {"name": "datasets", "endpoint": {"path": "eqtl/api/v3/datasets"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="eqtl_catalogue_pipeline",
        destination="duckdb",
        dataset_name="eqtl_catalogue_data",
    )
    load_info = pipeline.run(eqtl_catalogue_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.

---

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):

Copy
import dlt

data = dlt.pipeline("eqtl_catalogue_pipeline").dataset()
sessions_df = data.studies.df()
print(sessions_df.head())

SQL (DuckDB example):

Copy
SELECT * FROM eqtl_catalogue_data.studies LIMIT 10;

In a marimo or Jupyter notebook:

Copy
import dlt

data = dlt.pipeline("eqtl_catalogue_pipeline").dataset()
data.studies.df().head()

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

---

What destinations can I load eQTL Catalogue 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.

---

Next steps

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

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

Copy
uv run dlthub ai toolkit install data-exploration
uv run dlthub ai toolkit install dlthub-platform

• 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