/ORCS-REST-EXAMPLES

Sample code for working with the BioGRID ORCS REST Service API in Python

Primary LanguagePythonMIT LicenseMIT

BioGRID ORCS Web Service Examples

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

Development Status

  • Status: Stable
  • Version: 1.0

Requirements

  • Python 3.5.2+
  • 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://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: python <script name> at the command prompt. Example: python get_screen_tab.py

Examples

  • 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

Third Party Tools (Real World Examples)

The following are third party, open source tools that make use of the BioGRID ORCS API in interesting and useful ways.

  • ScreenHCA - A python script to cluster CRISPR screens from the BioGRID ORCS database using hierarchical clustering.