Causaly Bio Graph API

The Causaly Bio Graph API provides data scientsts and bioinformaticians with computational
access to the Causaly Knowledge Graph, which contains over 400 million high-fidelity
triplets. This enables users to analyze cause-and-effect biological evidence.

Getting access to Bio Graph API

Step 0: Login 

Refer to https://med.causaly.com 

Step 1: Open the API Settings Page

Once logged into Causaly Bio Graph, click on "API Settings" in the User Menu or access the page directly at https://med.causaly.com/api-settings.

Figure 1: Access "API settings" from the User Menu

Step 2: Create a New API Token

On the API Settings page, click the "Generate your token" button to generate your API token.

Step 3: Copy the API Token

After clicking the "Generate your token" button, a pop-up window will appear containing the API token. Be sure to copy it.

Figure 2: Pop-up window containing the API token

You can use the API token for authentication with the Bio Graph API.

Lost or Expired API Token

If your API token is lost or expired, you can revoke it and issue a new one

Making the first API call

There are two ways to start calling the API for the first time, once you have the API token.

Option 1: "View API Request" functionality

Causaly Bio Graph can serve as a companion application to the API, offering a playground for API users to develop and validate their search strategies. Any Intelligent Search and Advanced Search query can be converted into an equivalent Bio Graph API request using the "View API Request" feature:

Figure 3: Click the"View API Request" to convert searches into an equivalent Bio Graph API request 

Clicking on the "View API Request" button opens a modal window with code snippets in Python and R. These snippets include the API request, the endpoint URL, and the payload for the specified search.

Figure 5: Modal window with code snippets in Python and R

Copy the API request code snippet in your preferred language and paste it into your notebook or IDE. Make sure to replace MY-API-KEY with a valid API token.

Option 2: API Documentation

The API Documentation contains comprehensive details about all the endpoints of the Causaly Bio Graph API and includes built-in Swagger functionality. You can use Swagger to build and test API requests directly from the documentation without needing to leave the page.

Figure 6: API Documentation containing details about all the endpoints of the Causaly Bio Graph API