Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.
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DOI：
10.3389/fmicb.2021.765268
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发表时间：
2021
影响因子：
5.2
通讯作者：
Hurwitz BL
中科院分区：
文献类型：
--
作者：
Blumberg KL;Ponsero AJ;Bomhoff M;Wood-Charlson EM;DeLong EF;Hurwitz BL
海洋微生物生态学需要对生物地球化学和序列数据进行系统比较，以分析环境对微生物群落分布和变异的影响。随着宏基因组数据数量的不断增加，越来越需要使数据集在不同的生态系统中可查找、可访问、可互操作和可重用（FAIR）。 FAIR 数据对于开发整合微生物学、基因组学、生态学、海洋学和计算方法的分析框架至关重要。尽管存在定义序列数据所需的最小元数据的社区标准，但它们并未在项目中得到一致使用，从而妨碍了互操作性。此外，这些数据无法由机器操作或被网络基础设施系统发现。通过使组学和物理化学数据集对机器系统公平，我们可以基于机器可读的环境或物理化学梯度描述来实现序列数据发现和重用。在这项工作中，我们开发了一种新颖的数据集封装技术规范，以便在网络基础设施系统中公平地重用海洋宏基因组和物理化学数据集。这包括使用富含环境和生命科学本体术语的无摩擦数据包来注释测量变量、其单位以及所使用的测量设备。这种方法已在网络基础设施平台和海洋宏基因组门户网站 Planet Microbe 中实施。在这里，我们讨论规范中内置的数据属性，以使全球海洋数据集在 Planet Microbe 门户中公平。我们还讨论了规范中使用的海洋科学本体的选择和贡献。最后，我们使用该系统发现数据，通过荟萃分析来回答有关环境、物理化学梯度和微生物群落的各种生物学问题。这项工作提出了 FAIR 数据集封装规范，代表了海洋宏基因组研究的未来方向，如果在网络基础设施系统中采用该规范，将自动发现、交换和重用所需数据，以回答比最初预期更广泛的问题。
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.