Sample code for accessing the BioGRID Rest Service and working with the resulting datasets.
- Status: Stable
- Version: 1.0
- Python 3.6.9+
- Requirements are located in the Pipfile, simply execute
pipenv shellinside this directory to activate the virtual environment and install required dependencies.
- If dependencies are not installed, run
pipenv installwhen inside your virtual environment
- 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
- 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