BioGRID ORCS Web Service Examples
Sample code for accessing the BioGRID ORCS Rest Service and working with the resulting datasets.
- Status: In Progress
- Python 3.6.5+
- Required Python libraries are listed in requirements.txt. To install them all simply run the following from within your development environment:
- pip3 install -r requirements.txt
- We also recommend installing virtualenv and virtualenvwrapper for a containerized python environment (Setup Instructions) but this is optional.
- 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://orcsws.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/orcs:webservice
How to Run
- After completing the configuration steps above. Simply run: python3 <script name> at the command prompt. Example: python3 get_screen_tab.py
- get_organisms.py - Obtain currently supported organism ids
- get_vocab_terms.py - Obtain controlled vocabulary terms to help you create requests for other endpoints of the API
- get_screen_tab.py - Obtain score information for a single screen in tab format
- get_screen_json.py - Obtain score information for a single screen in json format
- get_screen_pandas.py - Obtain score information for a single screen, and load it into a pandas dataframe
- get_screens.py - Obtain screens with various configurable search criteria
- get_screens_and_scores.py - Obtain screens with various configurable search criteria and then fetch the score values associated with those screens with additional search criteria
- get_gene.py - Obtain a set of scores for a single gene with various configurable search criteria
- get_genes.py - Obtain a set of gene scores with various configurable search criteria
- get_genes_and_screens.py - Obtain a set of scores for a specific gene, with configured criteria and then fetch the annotation about the screens it returned