Extracting Biological Pathway Models From NLP Event Representations

TL;DR

This paper introduces an open-source system that converts NLP event representations into standard biological pathway formats, facilitating integration of NLP data into systems biology modeling.

Contribution

It presents a novel software tool that automates the translation of NLP event data into SBML and BioPAX formats, bridging NLP and systems biology.

Findings

Enables automatic conversion of NLP event data to biological pathway formats.

Supports integration of NLP-derived information into pathway models.

Open-source implementation available for community use.

Abstract

This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX. It is part of a larger effort to make results of the NLP community available for system biology pathway modelers.