TCT 0.2.0

Translator Component Toolkit

Introduction

What is TCT?

Translator Component Toolkit is a python library that allowing users to explore and use KGs in the Translator ecosystem. Users can check out the key function documentations here: https://ncatstranslator.github.io/Translator_component_toolkit/

Key features for TCT

Allowing users to select APIs, predicates according to the user's intention.
Parallel and fast querying of the selected APIs.
Providing reproducible results by setting constraints.
Allowing testing whether a user defined API follows a TRAPI standard or not.
Faciliting to explore knowledge graphs from both Translator ecosystem and user defined APIs.
Connecting large language models to convert user's questions into TRAPI queries.

How to use TCT

Install Requirements

To install TCT as a python library:

pip install TCT

This the recommended approach for installation.

Development Installation

The TCT is continuously updated, if you would like to use the latest functions, you can clone this repository and install it in development mode:

Using UV (recommended for development):

git clone https://github.com/NCATSTranslator/Translator_component_toolkit.git
cd Translator_component_toolkit
uv sync

Using pip:

git clone https://github.com/NCATSTranslator/Translator_component_toolkit.git
cd Translator_component_toolkit
pip install -e .

Building and Deployment

Using UV:

• Build: uv build
• Install dependencies: uv sync
• Run in UV environment: uv run python your_script.py

Using pip:

• Build: python -m build
• Install dependencies: pip install -e .

Please follow the example notebooks (four utilities) below to explore the Translator APIs.

KG overview

Explore different KGs KG overview

Name Resolver and Node Normalizer

Example notebook for Name Resolver and Node Normalizer

Neighborhood finder

Example notebook for NeighborhoodFinder

Path finder

Example notebook for PathFinder

Network finder

Example notebook for NetworkFinder

Translate users' questions into TRAPI queries

Example notebook for translating users' questions into TRAPI queries can be found here.

Connecting to a user's API

API should be developed following the standard from TRAPI.
An example notebook for add a user's API can be found here.
Warning: It does not work if no user' API is established

Key Translator components

Connecting to key Translator components can be found here

Contributing

TCT is a tool that helps to explore knowledge graphs developed in the Biomedical Data Translator Consortium. Consortium members and external contributors are encouraged to submit issues and pull requests.

Contact info

Guangrong Qin, [e-mail]