BIOGRID-REST-EXAMPLES

Sample code for accessing the BioGRID Rest Service and working with the resulting datasets.

Development Status

• Status: Stable
• Version: 1.0

Requirements

• Python 3.6.9+
• Pipenv
• Requirements are located in the Pipfile, simply execute pipenv shell inside this directory to activate the virtual environment and install required dependencies.
• If dependencies are not installed, run pipenv install when inside your virtual environment

Configuration

• All configuration options are located in the config/config.sample.yml file in YAML format. Simply rename the file to config.yml and update the options contained within to reflect your own environment.
• All access to the BioGRID ORCS Webservice requires an individual access key. It's free to signup to use it. You will need to register at https://webservice.thebiogrid.org/ to obtain one, and enter it in your config file for it to be accessible from all example code in this repository.
• For a listing of all configurable search parameters when making requests, visit our wiki: https://wiki.thebiogrid.org/doku.php/biogridrest

How to Run

• After completing the configuration steps above. Simply run: python <script name> at the command prompt. Example: python get_organisms.py

Examples

• get_experimental_evidence_types.py - Obtain a list of the supported experimental evidence types in BioGRID
• get_identifier_types.py - Obtain a list of the supported identifier types in BioGRID
• get_interaction.py - Obtain a single interaction record by interaction id
• get_interactions_by_gene.py - Obtain a list of interactions by one or more gene identifiers
• get_interactions_by_pubmed.py - Obtain a list of interactions by one or more pubmed ids
• get_interactions_for_pandas.py - Obtain a list of interactions and add them to a pandas dataframe
• get_organisms.py - Obtain currently supported organism names and ids