GeneNetMiner: accurately mining gene regulatory networks from literature

TL;DR

GeneNetMiner is a software tool that extracts gene regulatory and biological process relations from literature, providing confidence scores and sentence context to facilitate the construction of gene regulatory networks.

Contribution

It introduces a novel feature of capturing gene biological process relations and provides a confidence scoring system for regulatory relationships.

Findings

Accurately captures gene regulatory relationships from literature

Includes unique extraction of gene biological process relations

Provides confidence scores and sentence context for relations

Abstract

GeneNetMiner is standalone software which parses the sentences of iHOP and captures regulatory relations. The regulatory relations are either gene gene regulations or gene biological processes relations. Capturing of gene biological process relations is a unique feature for the tools of this kind. These relations can be used to build up gene regulatory networks for specific biological processes, diseases, or phenotypes. Users are able to search genes and biological processes to find the regulatory relationships between them. Each regulatory relationship has been assigned a confidence score, which indicates the probability of the true relation. Furthermore, it reports the sentence containing the queried terms, which allows users to manually checking whether the relation is true if they wish. GeneNetMiner is able to accurately capture the regulatory relationships between genes from literature.