The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
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DOI：
10.1186/2047-217x-1-7
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发表时间：
2012-07-12
期刊：
影响因子：
9.2
通讯作者：
Caporaso JG
中科院分区：
文献类型：
--
作者：
McDonald D;Clemente JC;Kuczynski J;Rideout JR;Stombaugh J;Wendel D;Wilke A;Huse S;Hufnagle J;Meyer F;Knight R;Caporaso JG
我们提出了生物观测矩阵（BIOM，发音为“biome”）格式：一个基于JSON的文件格式，用于表示任意观察的样本列联表与相关的样本和观察元数据。随着比较组学数据类型（统称为“ome-ome”）的类别数量迅速增长，表示和存档这些数据的通用格式将促进现有生物信息学工具和未来元分析的互操作性。BIOM文件格式由一个独立的开源软件项目（biom-format项目）支持，该项目最初包含支持在Python程序中使用和操作BIOM数据的Python对象，并且旨在成为一个开放的开发工作，开发人员可以在其他编程语言中提交这些对象的实现。BIOM文件格式和biom-format项目是朝着减少目前在生物科学的不同领域正在经历的“生物信息学瓶颈”迈出的一步，并将帮助我们走向比较组学的下一阶段，其中基础科学转化为临床和环境应用。BIOM文件格式目前被公认为地球微生物组计划标准，并被基因组标准联盟（Genomic Standards Consortium）视为候选标准。
We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the “ome-ome”) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.