BioPAX-Parser：解析和富集分析 BioPAX 通路。
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways.
机构信息
Department of Legal, Economic and Social Sciences.
Data Analytics Research Center, Magna Graecia University of Catanzaro, Catanzaro, Italy.
出版信息
Bioinformatics. 2020 Aug 1;36(15):4377-4378. doi: 10.1093/bioinformatics/btaa529.
SUMMARY
Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, e.g. BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or stand-alone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform pathway enrichment analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap, we introduce BiP (BioPAX-Parser), an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with PEA by using information coming from pathways encoded in BioPAX.
AVAILABILITY AND IMPLEMENTATION
BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
生物途径对于了解健康和疾病状态至关重要。许多现有的格式都支持对生物途径进行自动软件分析，例如 BioPAX（生物途径交换）。虽然有一些算法可作为 Web 应用程序或独立工具使用，但没有用于解析 BioPAX 途径数据的通用图形应用程序。此外，很少有工具可以使用 BioPAX 格式编码的途径进行途径富集分析（PEA）。为了填补这一空白，我们引入了 BiP（BioPAX-Parser），这是一个自动的图形软件工具，旨在执行解析和访问 BioPAX 途径数据，以及使用来自 BioPAX 编码途径的信息进行 PEA。
可用性和实现
BiP 可在 https://gitlab.com/giuseppeagapito/bip 上免费供学术和非营利组织使用，遵循 LGPL 2.1，即 GNU Lesser General Public License。
补充信息
补充数据可在 Bioinformatics 在线获得。
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