Orpheus Python API Docs | dltHub

Orpheus API is a biomedical research tool offering Semantic AI for drug discovery, with advanced ADMET models for pharmacokinetics and pharmacodynamics insights. It integrates seamlessly into research workflows. Orpheus API uses a trained graph embedding model for enhanced drug discovery accuracy. The REST API base URL is https://api.wisecube.ai and Requests require an API Key sent in request headers (x-api-key)..

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 Orpheus data in under 10 minutes.

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What data can I load from Orpheus?

Here are some of the endpoints you can load from Orpheus:

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How do I authenticate with the Orpheus API?

Obtain an API Key from Wisecube and include it in requests as header 'x-api-key: <your_key>' (docs also show using Authorization header with the API Key).

1. Get your credentials

1. Open the Orpheus API documentation page.
2. Click the link to request an API Key (a Google Form).
3. Fill in the required information and submit the form.
4. After review, Wisecube will email you the API Key.
5. Use the received key in the 'x-api-key' request header.

2. Add them to .dlt/secrets.toml

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[sources.orpheus_api_source]
api_key = "your_api_key_here"

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 Orpheus 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 orpheus_api_pipeline.py

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

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Pipeline orpheus_api_pipeline load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset orpheus_api_data
The duckdb destination used duckdb:/orpheus_api.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 orpheus_api_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 search_as_you_type and search_insights from the Orpheus 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 orpheus_api_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://api.wisecube.ai",
            "auth": {
                "type": "api_key",
                "api_key": api_key,
            },
        },
        "resources": [
            {"name": "search_as_you_type", "endpoint": {"path": "orpheus/graphql (searchAsYouType GraphQL query)", "data_selector": "searchAsYouType.data[0].searchLabels"}},
            {"name": "search_insights", "endpoint": {"path": "orpheus/graphql (searchInsights GraphQL query)", "data_selector": "searchInsights.data[0].documents"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="orpheus_api_pipeline",
        destination="duckdb",
        dataset_name="orpheus_api_data",
    )
    load_info = pipeline.run(orpheus_api_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("orpheus_api_pipeline").dataset()
sessions_df = data.search_insights.df()
print(sessions_df.head())

SQL (DuckDB example):

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SELECT * FROM orpheus_api_data.search_insights LIMIT 10;

In a marimo or Jupyter notebook:

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import dlt

data = dlt.pipeline("orpheus_api_pipeline").dataset()
data.search_insights.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 Orpheus 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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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