Qualitative translation of relations from BioPAX to SBML qual.
Qualitative translation of relations from BioPAX to SBML qual.
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DOI：
10.1093/bioinformatics/bts508
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发表时间：
2012-10-15
期刊：
影响因子：
--
通讯作者：
Zell A
中科院分区：
文献类型：
--
作者：
Büchel F;Wrzodek C;Mittag F;Dräger A;Eichner J;Rodriguez N;Le Novère N;Zell A
动机：生物路径交换语言(BioPAX)和系统生物学标记语言(SBML)属于系统生物学中最流行的建模和数据交换语言。SBML的重点是模型的定量建模和动态模拟，而BioPAX规范主要集中在路径图的可视化和定性分析。BioPAX描述反应和关系。相比之下，SBML核心只描述定量过程，如反应。随着SBML定性模型扩展(QUAL)的出现，用SBML描述关系也成为可能。在开发SBML Qual之前，关系无法正确转换为SBML。到目前为止，还没有完全能够翻译反应和关系的BioPAX到SBML的转换器。结果：通过使用新的QUAL扩展包，整个自然途径相互作用数据库已从BioPAX(2级和3级)转换为SBML(3级版本1)，包括反应和关系。此外，我们还提供了新的Web工具BioPAX2SBML，用于进一步将BioPAX转换为SBML。与以往的转换工具相比，BioPAX2SBML更全面、更健壮、更准确。供货情况：BioPAX2SBML可在http://webservices.cs.uni-tuebingen.de/上免费获得，完整的PID模型集合可在http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/.上获得联系方式：finja.buechel@uni-tuebingen.de补充信息：补充数据可从BioInformation Online获得。
Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. With the SBML qualitative models extension (qual), it has recently also become possible to describe relations in SBML. Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations. Results: The entire nature pathway interaction database has been converted from BioPAX (Level 2 and Level 3) into SBML (Level 3 Version 1) including both reactions and relations by using the new qual extension package. Additionally, we present the new webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared with previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact. Availability: BioPAX2SBML is freely available at http://webservices.cs.uni-tuebingen.de/ and the complete collection of the PID models is available at http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/. Contact: finja.buechel@uni-tuebingen.de Supplementary Information: Supplementary data are available at Bioinformatics online.
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