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.
翻译:国家卫生研究所(NIH) 人类生物分子图集(HuBMAP) 国家卫生研究所(NIH) 人类生物分子图集方案(HuBMAP) 旨在建立一个包含健康人体中所有细胞的全面高分辨率肾脏图集。 美国各地的多个实验室正在收集来自不同捐赠者器官的组织样本,这些器官在性别、年龄和身体大小方面各不相同。 整合和统一这些样本产生的数据,并将其“ 映射” 进入一个共同的三维( 3D) 空间空间空间。 实现这个目标的关键是“ Commonond 协调框架 ” (CCF), 它为整个身体提供一个配有附加注释的 3D 参考系统。 CCF CMT (CC) 提供 HUBMAP 的捐赠者在共同的空间参考系统中“ register' 标本和数据集 ” 。 它支持一种标准化的查询和“Explore ” 数据方法, 通过空间和语义清晰的方式。 [.] 本文描述了人体的计算和分子数据库的初始数据库(On ) 和捐赠的系统(由Semal deal se) 和分子用户 提供数据流流流数据,由Sendal 和分子流数据结构的系统(由Semald) 、由Semal) 、由Semal 和分子流流数据系统提供一个内部的系统进行一个数据库的输入和分子流数据结构的输入和体数据库的版本。