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BMC Research Notes

, 2:122

First Online: 07 July 2009Received: 13 January 2009Accepted: 07 July 2009DOI: 10.1186-1756-0500-2-122

Cite this article as: Muller, B., Richards, A.J., Jin, B. et al. BMC Res Notes 2009 2: 122. doi:10.1186-1756-0500-2-122

Abstract

BackgroundThe Gene Ontology is the most commonly used controlled vocabulary for annotating proteins. The concepts in the ontology are organized as a directed acyclic graph, in which a node corresponds to a biological concept and a directed edge denotes the parent-child semantic relationship between a pair of terms. A large number of protein annotations further create links between proteins and their functional annotations, reflecting the contemporary knowledge about proteins and their functional relationships. This leads to a complex graph consisting of interleaved biological concepts and their associated proteins. What is needed is a simple, open source library that provides tools to not only create and view the Gene Ontology graph, but to analyze and manipulate it as well. Here we describe the development and use of GOGrapher, a Python library that can be used for the creation, analysis, manipulation, and visualization of Gene Ontology related graphs.

FindingsAn object-oriented approach was adopted to organize the hierarchy of the graphs types and associated classes. An Application Programming Interface is provided through which different types of graphs can be pragmatically created, manipulated, and visualized. GOGrapher has been successfully utilized in multiple research projects, e.g., a graph-based multi-label text classifier for protein annotation.

ConclusionThe GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-2-122 contains supplementary material, which is available to authorized users.

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Autor: Brian Muller - Adam J Richards - Bo Jin - Xinghua Lu

Fuente: https://link.springer.com/







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