Ontology Lookup with OLS

This is a simple Ruby wrapper for the Ontology Lookup Service.

It allows you to query the OLS for ontology id and retrieve meta information about the ontology.

The project is tested under Linux and windows, and should work on Mac OS.

Set up

This project requires Ruby 3.14 or higher.

$ git clone https://github.com/yah-yuan/ols-ontology-query.git ols
$ cd ols
$ bundle install

This script will install required gems.

Usage

To query the OLS for an ontology id, run the following command:

$ ruby main.rb <ontology id>

If the ontology id is valid, the script will return the following information in JSON format:

• The full ontology title
• The ontology description
• The number of terms
• The current status

Example

$ ruby main.rb agro
{
  "title": "Agronomy Ontology",
  "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities",
  "numberOfTerms": 3736,
  "status": "LOADED"
}

Docker Usage

To build docker image, you need to have Docker installed.

The following assumes you have already granted correct privileges to current user to access docker.

To build the docker image, run the following command:

# with the repository cloned, run the following command:
$ docker build -t ols .
# OR, without cloning the repository, run the following command:
$ docker build -t ols github.com/yah-yuan/ols-ontology-query

Then we have an image named ols built.

To run the docker image to query ontology, run the following command:

$ docker run --rm ols <ontology id>