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DeepGO - Predicting Gene Ontology Functions

DeepGO is a novel method for predicting protein functions using protein sequences and protein-protein interaction (PPI) networks. It uses deep neural networks to learn sequence and PPI network features and hierarchically classifies it with GO classes. PPI network features are learned using a neuro-symbolic approach for learning knowledge graph representations by Alshahrani, et al.

This repository contains script which were used to build and train the DeepGO model together with the scripts for evaluating the model's performance.

Dependencies

To install python dependencies run: pip install -r requirements.txt

Scripts

The scripts require GeneOntology in OBO Format.

Running

Data

Citation

If you use DeepGO for your research, or incorporate our learning algorithms in your work, please cite:

Maxat Kulmanov, Mohammed Asif Khan, Robert Hoehndorf; DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier, Bioinformatics, 2017. https://doi.org/10.1093/bioinformatics/btx624