生物途径交换格式验证器。
The BioPAX Validator.
机构信息
The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
出版信息
Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5.
SUMMARY
BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation-detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs >100 classes of consistency checks.
AVAILABILITY AND IMPLEMENTATION
The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at sf.net/p/biopax, and the latest stable version of the web application is available at biopax.org/validator.
摘要
BioPAX 是一种用于生物途径数据的社区开发的标准语言。高效的 BioPAX 数据交换所需的关键功能是验证-检测 BioPAX 文档中的错误和不一致。BioPAX Validator 是一个命令行工具、Java 库和在线 Web 服务，用于执行 >100 类一致性检查。
可用性和实现
验证器识别常见的语法错误和语义不一致，并以可定制的人类可读格式报告它们。它还可以自动修复一些错误并规范化 BioPAX 数据。自发布以来，验证器已成为途径信息学社区的重要工具，检测了数千个错误，并帮助大大提高了 BioPAX 格式数据的一致性和统一性。BioPAX Validator 是开源的，并根据 LGPL v3 许可证发布。所有源代码、二进制文件和文档都可以在 sf.net/p/biopax 上找到，最新的稳定版 Web 应用程序可在 biopax.org/validator 上获得。
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