cmi-pb-terminology

CMI-PB Controlled Terminology

This repository contains:

1. code and data for building the terminology into an OWL file
2. a Python library for browsing, searching, and updating the terminology
3. a basic Flask server for testing

1. Building the Terminology

Requirements: GNU Make, Java 8+.

We use ROBOT to build the ontology, following common OBO development patterns. Just run make to rebuild the cmi-pb.owl file.

2. Using the Terminology

You can install the Python library via pip:

pip install git+https://github.com/jamesaoverton/cmi-pb-terminology.git

The package, called terminology, has two functions:

• search: accepts text and returns the JSON search results (based on labels)
• term: accepts a term ID and returns the HTML tree browser for build/cmi-pb.db at that term

3. Test Server

We provide a simple Flask server that will serve terminology pages without the need to build the ontology.