Phenopacket-tools: Building and validating GA4GH Phenopackets.
Phenopacket-tools: Building and validating GA4GH Phenopackets.
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Phenopacket-tools：建筑和验证GA4GH现场。
DOI：
10.1371/journal.pone.0285433
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发表时间：
2023
期刊：
影响因子：
3.7
通讯作者：
Robinson, Peter N.
中科院分区：
文献类型：
--
作者：
Danis, Daniel;Jacobsen, Julius O. B.;Wagner, Alex H.;Groza, Tudor;Beckwith, Martha A.;Rekerle, Lauren;Carmody, Leigh C.;Reese, Justin;Hegde, Harshad;Ladewig, Markus S.;Seitz, Berthold;Munoz-Torres, Monica;Harris, Nomi L.;Rambla, Jordi;Baudis, Michael;Mungall, Christopher J.;Haendel, Melissa A.;Robinson, Peter N.
全球基因组学与健康联盟（GA 4GH）是一个标准制定组织，正在为基因组学制定一套协调标准。GA 4GH Phenopacket模式是用于共享表征个体或生物样本的疾病和表型信息的标准。Phenopacket模式是灵活的，可以代表任何类型的人类疾病的临床数据，包括罕见疾病，复杂疾病和癌症。它还允许联盟或数据库应用额外的限制，以确保为特定目标收集统一的数据。我们提出了phenopacket-tools，一个开源的Java库和命令行应用程序的建设，转换和验证的phenopackets。Phenopacket-tools通过提供简洁的构建器、编程快捷方式和预定义的构建块（本体类）来简化Phenopackets的构建，这些构建块用于诸如解剖器官、发病年龄、生物标本类型和临床修饰符等概念。Phenopacket-tools可用于验证Phenopackets的语法和语义，以及评估是否符合其他用户定义的要求。该文档包括一些示例，展示了如何使用Java库和命令行工具来创建和验证phenopackets。我们将演示如何使用库或命令行应用程序创建、转换和验证phenopackets。源代码、API文档、全面的用户指南和教程可以在https://github.com/phenopackets/phenopacket-tools上找到。该库可以从公共的Maven Central工件存储库安装，应用程序可以作为独立的存档。phenopacket-tools库帮助开发人员实现和标准化表型和其他临床数据的收集和交换，用于表型驱动的基因组诊断，转化研究和精准医学应用。
The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.
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影响因子：
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