Using Biological Pathway Data with Paxtools

被引：35

作者：

Demir, Emek ^{[1
]}

Babur, Oezguen ^{[1
]}

Rodchenkov, Igor ^{[2
]}

Aksoy, Buelent Arman ^{[1
,3
]}

Fukuda, Ken I. ^{[4
]}

Gross, Benjamin ^{[1
]}

Suemer, Onur Selcuk ^{[1
]}

Bader, Gary D. ^{[2
]}

Sander, Chris ^{[1
]}

机构：

[1] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10021 USA

[2] Univ Toronto, Donnelly Ctr, Toronto, ON, Canada

[3] Computat Biol & Med New York, Triinst Training Program, New York, NY USA

[4] Natl Inst Adv Ind Sci & Technol, Intelligent Informat Infrastruct Div, Tsukuba, Ibaraki, Japan

来源：

PLOS COMPUTATIONAL BIOLOGY | 2013年 / 9卷 / 09期

基金：

美国国家卫生研究院;

关键词：

CANCER GENOMICS DATA; GENE PRIORITIZATION; ENRICHMENT ANALYSIS; SBGN MAPS; VISUALIZATION; EXPRESSION; NETWORKS; RESOURCE; INTEGRATION; DATABASES;

D O I：

10.1371/journal.pcbi.1003194

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax. org/paxtools.

引用

页数：5

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