Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

Herr, Bruce W.; Hardi, Josef; Quardokus, Ellen M.; Bueckle, Andreas; Chen, Lu; Wang, Fusheng; Caron, Anita R.; Osumi-Sutherland, David; Musen, Mark A.; Börner, Katy

doi:10.1038/s41597-023-01993-8

Cited by 7 publications

(3 citation statements)

References 41 publications

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“…We use the CCF API v1.0.0 ( https://ccf-api.hubmapconsortium.org ) to access the biological structure, spatial, and specimen data needed to construct the 3D scene from the CCF.OWL 2.1.0 ( Herr et al, 2023 ).…”

Section: Methodsmentioning

confidence: 99%

“…Using the Registration User Interface (RUI) and the EUI ( Bueckle et al, 2021 ; Bueckle et al, 2022 ; Börner et al, 2022 ), 3D reference organs are used to register 3D tissue blocks from diverse donors into the HRA. The specimen data for each tissue block is tracked to support filter, search, and exploration by donor demographics using the CCF Ontology ( Herr et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

et al. 2023

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The Human Reference Atlas (HRA, https://humanatlas.io) funded by the NIH Human Biomolecular Atlas Program (HuBMAP, https://commonfund.nih.gov/hubmap) and other projects engages 17 international consortia to create a spatial reference of the healthy adult human body at single-cell resolution. The specimen, biological structure, and spatial data that define the HRA are disparate in nature and benefit from a visually explicit method of data integration. Virtual reality (VR) offers unique means to enable users to explore complex data structures in a three-dimensional (3D) immersive environment. On a 2D desktop application, the 3D spatiality and real-world size of the 3D reference organs of the atlas is hard to understand. If viewed in VR, the spatiality of the organs and tissue blocks mapped to the HRA can be explored in their true size and in a way that goes beyond traditional 2D user interfaces. Added 2D and 3D visualizations can then provide data-rich context. In this paper, we present the HRA Organ Gallery, a VR application to explore the atlas in an integrated VR environment. Presently, the HRA Organ Gallery features 55 3D reference organs, 1,203 mapped tissue blocks from 292 demographically diverse donors and 15 providers that link to 6,000+ datasets; it also features prototype visualizations of cell type distributions and 3D protein structures. We outline our plans to support two biological use cases: on-ramping novice and expert users to HuBMAP data available via the Data Portal (https://portal.hubmapconsortium.org), and quality assurance/quality control (QA/QC) for HRA data providers. Code and onboarding materials are available at https://github.com/cns-iu/hra-organ-gallery-in-vr.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

et al. 2023

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“…Each month, more than 80,000 papers are published in PubMed making it difficult to keep track of expertise, methods, data, or code. Scientific Data papers typically focus on ontologies 10 – 12 or experimental data 13 – 15 while science of science studies commonly focus on authors, their publications, and possibly the funding that supports the research 16 . The construction of a HRA benefits from interlinking expertise, publication, funding, and experimental datasets.…”

Section: Background and Summarymentioning

confidence: 99%

Publication, funding, and experimental data in support of Human Reference Atlas construction and usage

Kong,

Börner

2024

Sci Data

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Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage.

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Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

et al. 2023

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The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and ontology annotations for 26 organs. Experts access the HRA annotations via spreadsheets and view reference object models in 3D editing tools. This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCF Ontology design and implementation, present CCF Ontology classes and properties together with exemplary usage, and report on validation methods. The CCF Ontology graph database and API are used in the HuBMAP portal, HRA Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources.

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Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

Cited by 7 publications

References 41 publications

The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

Publication, funding, and experimental data in support of Human Reference Atlas construction and usage

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

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