Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Measures for interoperability of phenotypic data: minimum information requirements and formatting.
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DOI：
10.1186/s13007-016-0144-4
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发表时间：
2016
期刊：
影响因子：
5.1
通讯作者：
Krajewski P
中科院分区：
文献类型：
--
作者：
Ćwiek-Kupczyńska H;Altmann T;Arend D;Arnaud E;Chen D;Cornut G;Fiorani F;Frohmberg W;Junker A;Klukas C;Lange M;Mazurek C;Nafissi A;Neveu P;van Oeveren J;Pommier C;Poorter H;Rocca-Serra P;Sansone SA;Scholz U;van Schriek M;Seren Ü;Usadel B;Weise S;Kersey P;Krajewski P
植物表型数据包含丰富的信息，当这些信息被准确分析并与其他数据类型相关联时，可以揭示关于生命机制的知识。由于表型分析是一个研究领域，包括多种多样，多样化和耗时的实验，可以通过重用和组合现有数据集来促进研究结果。只要收集到的观测资料配有一套适当的元数据，就有可能对这些数据作出正确的解释，从而实现可复制性、可比性和互操作性。到目前为止，还没有一个共同的标准来管理表型数据的描述，这阻碍了数据的交换和重用。在本文中，我们提出了正确处理有关植物表型实验的信息的指导方针，在两个方面的描述和格式的建议内容。我们提供了一个名为“关于植物表型分析实验的最小信息”的文档，该文档指定了应该给出的关于每个实验的信息，以及ISA-Tab格式的表型分析配置，该文件允许在数据集中实际组织这些信息。我们提供了ISA-Tab格式的表型数据的例子，并对一些系统的建议已经实施的一般描述。接受本文所描述的规则，植物表型社区将有助于实现可查找，可访问，可互操作和可重用的数据。本文的在线版本（doi：10.1186/s13007-016-0144-4）包含补充材料，可供授权用户使用。
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data. The online version of this article (doi:10.1186/s13007-016-0144-4) contains supplementary material, which is available to authorized users.
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影响因子：
3.6
作者：
Fiehn, Oliver;Robertson, Don;Sansone, Susanna-Assunta
通讯作者：
Sansone, Susanna-Assunta
影响因子：
46.9
作者：
Taylor, Chris F.;Paton, Norman W.;Hermjakob, Henning
通讯作者：
Hermjakob, Henning
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：
3.6
作者：
Fiehn, Oliver;Sumner, Lloyd W.;Nikolau, Basil
通讯作者：
Nikolau, Basil
影响因子：
3.6
作者：
Morrison, Norman;Bearden, Dan;Viant, Mark R.
通讯作者：
Viant, Mark R.