Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.
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DOI：
10.1093/gigascience/giab077
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发表时间：
2021-12-06
期刊：
影响因子：
9.2
通讯作者：
Rendeiro AF
中科院分区：
文献类型：
--
作者：
Sheffield NC;Stolarczyk M;Reuter VP;Rendeiro AF
组织和注释生物样本数据在数据密集型生物信息学中至关重要。不幸的是，来自数据提供者的元数据格式通常与处理工具的要求不兼容。没有广泛接受的标准来组织跨生物项目和生物信息学工具的元数据，限制了注释数据集和分析软件的可移植性和可重用性。为了解决这个问题，我们提出了便携式封装项目（PEP）规范，生物样本元数据结构的正式规范。PEP规范适应具有许多生物样本的数据密集型生物信息学项目的典型特征。除了标准化之外，PEP规范还为项目级和样本级元数据提供了描述符和修饰符，这提高了跨计算环境和数据处理工具的可移植性。PEP包括一个模式验证器框架，允许对广泛的数据分析所需的元数据属性进行正式定义。我们已经实现了Python和R中阅读PEP的包，以提供一个与语言无关的接口来组织项目元数据。PEP规范是在数据密集型生物研究项目中统一数据注释和处理工具的重要一步。有关工具和文档的链接，请访问http://pep.databio.org/。
Organizing and annotating biological sample data is critical in data-intensive bioinformatics. Unfortunately, metadata formats from a data provider are often incompatible with requirements of a processing tool. There is no broadly accepted standard to organize metadata across biological projects and bioinformatics tools, restricting the portability and reusability of both annotated datasets and analysis software. To address this, we present the Portable Encapsulated Project (PEP) specification, a formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. In addition to standardization, the PEP specification provides descriptors and modifiers for project-level and sample-level metadata, which improve portability across both computing environments and data processing tools. PEPs include a schema validator framework, allowing formal definition of required metadata attributes for data analysis broadly. We have implemented packages for reading PEPs in both Python and R to provide a language-agnostic interface for organizing project metadata. The PEP specification is an important step toward unifying data annotation and processing tools in data-intensive biological research projects. Links to tools and documentation are available at http://pep.databio.org/.
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DOI：
10.1093/bioinformatics/btt765
发表时间：
2014-05-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Jupp S;Malone J;Bolleman J;Brandizi M;Davies M;Garcia L;Gaulton A;Gehant S;Laibe C;Redaschi N;Wimalaratne SM;Martin M;Le Novère N;Parkinson H;Birney E;Jenkinson AM
通讯作者：
Jenkinson AM
影响因子：
12.3
作者：
Smith JP;Dutta AB;Sathyan KM;Guertin MJ;Sheffield NC
通讯作者：
Sheffield NC
DOI：
10.14694/edbk_175029
发表时间：
2017-01-01
期刊：
American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting
影响因子：
--
作者：
Volchenboum, Samuel L;Cox, Suzanne M;Grossman, Robert
通讯作者：
Grossman, Robert
DOI：
10.1093/bioinformatics/btq415
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Rocca-Serra P;Brandizi M;Maguire E;Sklyar N;Taylor C;Begley K;Field D;Harris S;Hide W;Hofmann O;Neumann S;Sterk P;Tong W;Sansone SA
通讯作者：
Sansone SA
影响因子：
82.9
作者：
Sheffield NC;Pierron G;Klughammer J;Datlinger P;Schönegger A;Schuster M;Hadler J;Surdez D;Guillemot D;Lapouble E;Freneaux P;Champigneulle J;Bouvier R;Walder D;Ambros IM;Hutter C;Sorz E;Amaral AT;de Álava E;Schallmoser K;Strunk D;Rinner B;Liegl-Atzwanger B;Huppertz B;Leithner A;de Pinieux G;Terrier P;Laurence V;Michon J;Ladenstein R;Holter W;Windhager R;Dirksen U;Ambros PF;Delattre O;Kovar H;Bock C;Tomazou EM
通讯作者：
Tomazou EM