Tutorial: Acquiring and Setting an Entrez API Key

1. What is the Entrez API key?

The Entrez API key is a personal access token issued by the NCBI that allows applications to make authenticated requests to their E-utilities web services. These services power many bioinformatics tools and are widely used for retrieving literature, gene annotations, and other biological data directly from NCBI databases such as PubMed and Gene.

While the API can be used without a key, setting one unlocks significant advantages for research workflows that require frequent or large-scale data retrieval.

2. Why using an API key is beneficial

There are several reasons why obtaining and configuring an Entrez API key is recommended:

• Increased request rate: Without a key, the default rate limit is 3 requests per second. With a key, this increases to 10 requests per second per IP address.
• Improved reliability: Authenticated requests are less likely to be throttled or blocked during large-scale queries.
• Faster article retrieval: Queries to PubMed, PubTator, or other NCBI resources complete faster, particularly in workflows that retrieve many abstracts or annotations.
• Better reproducibility: Using a key ensures consistent performance across sessions and is useful when running automated pipelines.
• Access tracking: Requests made with a key are logged in your NCBI account, helping you monitor usage and troubleshoot if needed.

3. How to obtain an Entrez API key

Follow these steps to create your personal API key:

1. Go to the NCBI website and sign in or create a free account.
2. Once logged in, click on your username at the top right and choose “Dashboard” or “Account Settings.”
3. Scroll down to the section labeled “API Key Management”.
4. Click “Create API Key” and give it a descriptive name (e.g., “pathXcite”).
5. Copy the generated key: it will be a long alphanumeric string. Store it securely.

4. Setting the API key in pathXcite

After obtaining your key, you need to tell pathXcite (or any tool using NCBI E-utilities) to use it. There are typically two ways to do this:

Option A: Set via the application settings

• Open the Settings panel in pathXcite.
• Locate the field labeled “Entrez API Key”.
• Paste your API key into the input box and save the settings.
• Restart the application or refresh the retrieval module if prompted.

Option B: Set as an environment variable

If you prefer configuring it system-wide (e.g., on a server or in a pipeline), you can set the key as an environment variable:

export NCBI_API_KEY="your_api_key_here"

Tools that support this variable will automatically use the key without additional configuration.

5. Confirming the key is active

Once configured, you can verify that the key is being used by running a retrieval task and observing the speed and stability of queries. You should notice:

• Faster response times for article retrieval and annotation downloads.
• Fewer rate-limit errors or delays when running large queries.
• More consistent throughput during repeated runs or automated workflows.

6. Best practices

• Keep your key private. Do not share it in public repositories or logs.
• Use separate keys for different tools or environments if you want to track usage individually.
• Rotate keys periodically if your workflows run in shared or automated environments.
• Monitor usage in your NCBI account dashboard to ensure you stay within rate limits.

7. Summary

Using an Entrez API key is an easy but powerful way to improve the performance and reliability of any workflow that relies on NCBI data. It enables higher request rates, smoother large-scale retrieval, and more robust automation, all of which are especially valuable in literature mining and enrichment pipelines.