vtoure/causal-extractor

Extraction of causal interaction from pathway databases

causal-extractor

Extraction of causal interaction from pathway databases

Introduction

causal-extractor is a JAVA framework developed to extract causal molecular interactions from the Reactome database. Based on defined biological templates, biological processes depicted in Reactome are translated into causal statements. The causal statements extracted follow the MI2CAST guidelines. The output format is a PSI-MITAB 2.8.

Documentation

For more information about the extraction process, please read the documentation available at https://github.com/vtoure/causal-extractor/wiki.

Installation

Data

The causal interactions are available in the results in the following formats:

• SIF
• PSI-MITAB2.8

Formats planned to be supported:

• BEL

Notes

• 18/07/2020: Current export files contain causal interactions exported for human reactions. Patterns considered: transcription, translation and catalysis.

Contact

[email protected]

causal-extractor's Issues

SIF file - handle duplications

Duplications are present due to the split of defined set and candidate set.
Fix