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Documentation Overview

SolveBio is a cloud-based operating system for molecular information that enables cross-disciplinary R&D groups to use complex multi-omics data from disparate sources to find biomarkers, stratify populations, and design clinical trials. SolveBio’s mapping technology transforms structured data into biomedical entities such as variants, genes, patients, samples, compounds, and phenotypes. Harmonized datasets are indexed and maintained on SolveBio and can be easily delivered to end-users via APIs and applications built upon them.

SolveBio provides many options for developers looking to enhance existing applications or build new ones quickly. Bioinformatics skills are not required but can be very helpful.


Getting Started

To get started, choose one of the available client libraries and work through the Dataset Quickstart. There are also a few example scripts available.

Authentication

There are two ways clients can authenticate with SolveBio: using an API key, or an OAuth2 access token. Some endpoints will return 404 Not Found instead of 403 Forbidden to prevent leakage of private information to unauthorized users. Other requests will return a 401 Not Authorized response when provided with invalid credentials.

Where is my API key?

You can find your API key in your Security Settings.

Using stored credentials

The Python, and R client libraries look for the $SOLVEBIO_API_KEY environment variable upon initialization. You can find your API key in your Security Settings. To store your credentials locally, use one of the following methods:

Python:

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# Log in and store your credentials with the following command:
solvebio login

# Alternatively, if you use Single Sign-On (SSO) and have your API key ready:
solvebio login --api-key "Your API key"

R:

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# Add the following to the .Rprofile file in your home directory
Sys.setenv(SOLVEBIO_API_KEY="Your API key")

Running the interactive SolveBio Python shell will automatically load your saved credentials. To load them in a custom script, use the login() method or set them manually:

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import solvebio

# Set your API key automatically
solvebio.login()

# Set your API key manually
solvebio.api_key = "YOUR API KEY"
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# By default it will look for a key in the $SOLVEBIO_API_KEY environment variable.
library(solvebio)

# You may also supply an API key in your code
login(api_key="<Your API key>")
# RStudio users can put the following line in ~/.Rprofile
# Sys.setenv(SOLVEBIO_API_KEY="<Your API key>")

Testing your credentials

There are a few ways to test your credentials. If you are using the Python client, you can run solvebio whoami from the command line:

solvebio whoami
# You are logged-in to the "***" domain as ****@****.com with role member.

Within a block of python code

# Login
solvebio.login()

# See currently set API key
print solvebio.api_key

# Get current User
solvebio.User.retrieve()

Within a block of R code

# Login
solvebio::login()

# See currently set API key
Sys.getenv(x='SOLVEBIO_API_KEY')

# Get current User
User.retrieve()$email

You can also test a key with Curl by specifying the API key in the Authorization: Token header:

curl --header "Authorization: Token <API KEY>" https://api.solvebio.com
# {"detail": "Your API key is valid. Welcome to the SolveBio API!"}

You can test an access token using the Authorization: Bearer header:

curl --header "Authorization: Bearer <ACCESS TOKEN>" https://api.solvebio.com
# {"detail": "Your API key is valid. Welcome to the SolveBio API!"}

You may also specifying it in the access_token query parameter:

curl "https://api.solvebio.com?access_token=<ACCESS TOKEN>"
# {"detail": "Your API key is valid. Welcome to the SolveBio API!"}

Can't find what you're looking for? Contact SolveBio Support and we'll do our best to assist you.


Not a developer?

Building applications using SolveBio requires some development skills. You can always use SolveBio through its intuitive and friendly web interface: sign in here.


We're here to help!

We're always happy to help out with code or any questions you may have. Feel free to submit a ticket at any time or email support@solvebio.com to get in touch.