Load NCBI Datasets data in Python using dltHub

Build a NCBI Datasets-to-database or-dataframe pipeline in Python using dlt with automatic Cursor support.

In this guide, we'll set up a complete NCBI data pipeline from API credentials to your first data load in just 10 minutes. You'll end up with a fully declarative Python pipeline based on dlt's REST API connector, like in the partial example code below:

Example code
@dlt.source
def ncbi_datasets_migrations_source(access_token=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.ncbi.nlm.nih.gov/",
            "auth": {
                "type": "bearer",
                "token": access_token,
            },
        },
        "resources": [
            cdd,,snp,,gene
            ],
    }
    [...]
    yield from rest_api_resources(config)


def get_data() -> None:
    # Connect to destination
    pipeline = dlt.pipeline(
        pipeline_name='ncbi_datasets_migrations_pipeline',
        destination='duckdb',
        dataset_name='ncbi_datasets_migrations_data', 
    )
    # Load the data
    load_info = pipeline.run(ncbi_datasets_migrations_source())
    print(load_info)

Why use dltHub Workspace with LLM Context to generate Python pipelines?

  • Accelerate pipeline development with AI-native context
  • Debug pipelines, validate schemas and data with the integrated Pipeline Dashboard
  • Build Python notebooks for end users of your data
  • Low maintenance thanks to Schema evolution with type inference, resilience and self documenting REST API connectors. A shallow learning curve makes the pipeline easy to extend by any team member
  • dlt is the tool of choice for Pythonic Iceberg Lakehouses, bringing mature data loading to pythonic Iceberg with or without catalogs

What you’ll do

We’ll show you how to generate a readable and easily maintainable Python script that fetches data from ncbi_datasets_migrations’s API and loads it into Iceberg, DataFrames, files, or a database of your choice. Here are some of the endpoints you can load:

  • Gene Information: Access genetic information including details on specific genes
  • SNP Information: Retrieve information on single nucleotide polymorphisms
  • Genome Assemblies: Access various genome assembly data
  • Data Retrieval: General endpoint for fetching NCBI datasets
  • Books and Publications: Access books and research publications from NCBI

You will then debug the NCBI pipeline using our Pipeline Dashboard tool to ensure it is copying the data correctly, before building a Notebook to explore your data and build reports.

Setup & steps to follow

💡
Before getting started, let's make sure Cursor is set up correctly:

Now you're ready to get started!

  1. ⚙️ Set up dlt Workspace

    Install dlt with duckdb support:

    pip install "dlt[workspace]"

    Initialize a dlt pipeline with NCBI support.

    dlt init dlthub:ncbi_datasets_migrations duckdb

    The init command will setup the necessary files and folders for the next step.

  2. 🤠 Start LLM-assisted coding

    Here’s a prompt to get you started:

    Prompt
    Please generate a REST API Source for NCBI API, as specified in @ncbi_datasets_migrations-docs.yaml 
Start with endpoints cdd and  and skip incremental loading for now. 
Place the code in ncbi_datasets_migrations_pipeline.py and name the pipeline ncbi_datasets_migrations_pipeline. 
If the file exists, use it as a starting point. 
Do not add or modify any other files. 
Use @dlt rest api as a tutorial. 
After adding the endpoints, allow the user to run the pipeline with python ncbi_datasets_migrations_pipeline.py and await further instructions.

  3. 🔒 Set up credentials

    Authentication is required to access the NCBI API, utilizing OAuth2 with a refresh token. Users must set up a connected app in the NCBI system to manage authentication.

    To get the appropriate API keys, please visit the original source at https://www.ncbi.nlm.nih.gov/. If you want to protect your environment secrets in a production environment, look into setting up credentials with dlt.

  4. 🏃‍♀️ Run the pipeline in the Python terminal in Cursor

    python ncbi_datasets_migrations_pipeline.py

    If your pipeline runs correctly, you’ll see something like the following:

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

  5. 📈 Debug your pipeline and data with the Pipeline Dashboard

    Now that you have a running pipeline, you need to make sure it’s correct, so you do not introduce silent failures like misconfigured pagination or incremental loading errors. By launching the dlt Workspace Pipeline Dashboard, you can see various information about the pipeline to enable you to test it. Here you can see:

    • Pipeline overview: State, load metrics
    • Data’s schema: tables, columns, types, hints
    • You can query the data itself
    dlt pipeline ncbi_datasets_migrations_pipeline show dashboard

  6. 🐍 Build a Notebook with data explorations and reports

    With the pipeline and data partially validated, you can continue with custom data explorations and reports. To get started, paste the snippet below into a new marimo Notebook and ask your LLM to go from there. Jupyter Notebooks and regular Python scripts are supported as well.

    import dlt

data = dlt.pipeline("ncbi_datasets_migrations_pipeline").dataset()
# get d table as Pandas frame
data.d.df().head()

Running into errors?

The NCBI API requires an OAuth2 setup which involves creating a connected app. Users may encounter null values in deeply nested fields, and authentication issues may lead to error messages. It's essential to handle token management properly and be aware that the API may return errors if authentication is not correctly configured.

Extra resources:

Next steps