arXiv 2007.144742020-07-28q-bio.QMcs.CLcs.DL

包括临床、语义和空间本体的人体公共坐标框架的构建和使用

Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies

Indiana University（印第安纳大学）；University of Pittsburgh（匹兹堡大学）；National Institutes of Health（美国国立卫生研究院）；Washington University（华盛顿大学）；University of Florida（佛罗里达大学）；Vanderbilt University（范德堡大学）；Stanford University（斯坦福大学）；Harvard Medical School（哈佛医学院）

Katy Börner, Ellen M. Quardokus, Bruce W. Herr, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, … 展开作者

Katy Börner, Ellen M. Quardokus, Bruce W. Herr, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Mark A. Musen, Griffin M. Weber

备注：: 24 pages with SI, 6 figures, 5 tables

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摘要：

美国国立卫生研究院（NIH）的人类生物分子图谱计划（HuBMAP）旨在创建健康人体中所有细胞的全面高分辨率图谱。美国各地的多个实验室正在从不同性别、年龄和体型的捐赠者的不同器官中收集组织标本。整合和协调来自这些样本的数据，并将其“映射”到一个共同的三维（3D）空间是一个重大挑战。实现这一点的关键是“通用坐标框架”（CCF），它为整个身体提供了一个语义注释的3D参考系统。CCF使HuBMAP的贡献者能够在一个公共的空间参考系统中“注册”标本和数据集，并且它支持以空间和语义明确的方式查询和“探索”数据的标准化方式。[...]本文描述了一个人体CCF的构造和使用，以及它在HuBMAP中的参考实现。CCF包括（1）CCF临床本体，提供关于标本和供体（“谁”）的元数据;（2）CCF语义本体，描述样本来自身体的“什么”部分，并详细说明解剖结构、细胞类型和生物标志物（ASCT+B）;以及（3）CCF空间本体，指示组织样本位于3D坐标系中的“哪里”。所有三个CCF本体的初始版本都已在首个HuBMAP Portal版本中实现。它被组织映射中心成功地用于语义注释和空间配准48个肾脏和脾脏组织块。可以通过HuBMAP Portal中的CCF用户界面在其临床、语义和空间背景下查询和探索这些块。

英文摘要：

The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue specimens from different organs of donors who vary in sex, age, and body size. Integrating and harmonizing the data derived from these samples and 'mapping' them into a common three-dimensional (3D) space is a major challenge. The key to making this possible is a 'Common Coordinate Framework' (CCF), which provides a semantically annotated, 3D reference system for the entire body. The CCF enables contributors to HuBMAP to 'register' specimens and datasets within a common spatial reference system, and it supports a standardized way to query and 'explore' data in a spatially and semantically explicit manner. [...] This paper describes the construction and usage of a CCF for the human body and its reference implementation in HuBMAP. The CCF consists of (1) a CCF Clinical Ontology, which provides metadata about the specimen and donor (the 'who'); (2) a CCF Semantic Ontology, which describes 'what' part of the body a sample came from and details anatomical structures, cell types, and biomarkers (ASCT+B); and (3) a CCF Spatial Ontology, which indicates 'where' a tissue sample is located in a 3D coordinate system. An initial version of all three CCF ontologies has been implemented for the first HuBMAP Portal release. It was successfully used by Tissue Mapping Centers to semantically annotate and spatially register 48 kidney and spleen tissue blocks. The blocks can be queried and explored in their clinical, semantic, and spatial context via the CCF user interface in the HuBMAP Portal.

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