The Common Coordinate Framework (CCF) Organ VR Gallery

Bueckle, Andreas; Browne, Kristen; Herr, Bruce W.; Börner, Katy

doi:10.31219/osf.io/z9gm3

Cited by 3 publications

(4 citation statements)

References 4 publications

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“…These interfaces are now available and provide an important base-level mechanism, but have a number of problems for a Gut Cell Atlas (GCA). The current HuBMAP SOP to register a tissue sample [44] provides a mechanism to define the tissue sample as a rectangular block enclosing the sample which is then registered with a 3D location using the registration interface. By this means the block acquires a precise location but with no measure of the spatial uncertainty of that placement.…”

Section: Discussionmentioning

confidence: 99%

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

Burger

Baldock

Adams

et al. 2022

Preprint

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Background: The Human Cell Atlas resource will deliver single cell transcriptome data spatially organised in terms of gross anatomy, tissue location and with images of cellular histology. This will enable the application of bioinformatics analysis, machine learning and data mining revealing an atlas of cell types, sub-types, varying states and ultimately cellular changes related to disease conditions. To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms. Methods: We describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut. This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patient's CT scan where the gut has been segmented. Results: The outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. All data and software is fully open-source and available online. Conclusions: Small and large intestines have a natural "gut coordinate" system best represented as a 1D centreline through the gut tube, reflecting functional differences. Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. This permits users to accurately locate samples for data comparison. Keywords: Human Cell Atlas, Human Gut Cell Atlas, Common Coordinate Framework

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Section: Discussionmentioning

confidence: 99%

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

Burger

Baldock

Adams

et al. 2022

Preprint

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“…Once the package is complete, data is added to the EUI for review by scientists to verify registration accuracy in terms of tissue size, placement, and orientation. SOPs detail millitome construction 110 and usage 111 .…”

Section: Tissue Collection and Rui Registrationmentioning

confidence: 99%

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

Börner,

Blood,

Silverstein

et al. 2024

Preprint

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The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials. Experts from more than 20 consortia are collaborating to construct the HRA's Common Coordinate Framework (CCF), knowledge graphs, and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes, and biomarkers) and to use the HRA to understand changes that occur at each of these levels with aging, disease, and other perturbations. The 6th release of the HRA v2.0 covers 36 organs with 4,499 unique anatomical structures, 1,195 cell types, and 2,089 biomarkers (e.g., genes, proteins, lipids) linked to ontologies. In addition, three workflows were developed to map new experimental data into the HRA's CCF. This paper describes the HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interface (APIs), flexible hybrid cloud infrastructure, and demonstrates first atlas usage applications and previews.

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“…The VR setup makes it possible to explore the HRA data across different scales—from encountering a whole body in real size (see Fig. 6d ), zooming into single organs and studying their many anatomical structures, or examining cell-type populations within specific anatomical structures 12 . The Organ Gallery utilizes the CCF API to retrieve all 53 reference organs published in the third HRA release and 306 HuBMAP tissue blocks publicly available on August 25, 2022 (see Table 3 ).…”

Section: Technical Validationmentioning

confidence: 99%

“…1a depicts how Visible Human Project data (VHP) 10 (a high-quality, whole-body dataset published by the National Library of Medicine) is used to create reference organs (different anatomical structures of a kidney are shown) and how resulting data is uniformly represented using the spatial and specimen ontology. All reference organs can be interactively explored in the Exploration User Interface (EUI) 11 and the Virtual Reality Organ Gallery 12 , both of which are detailed in the Applications section. The spatial size, shape, location, and rotation of experimental tissue data is captured relative to the organs in the 3D Reference Object Library.…”

Section: Background and Summarymentioning

confidence: 99%

Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

Herr

Hardi

Quardokus

et al. 2022

Preprint

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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 that develop standard terminologies linked 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 models in 3D editing tools. This paper introduces the Common Coordinate Framework Ontology (CCFO) v2.0.1 that interlinks specimen, biological structure, and spatial data together with the CCF API which makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCFO design and implementation, present CCFO classes and properties together with examples of their usage, and report on technical validation performed. The CCFO graph database and API are used in the HuBMAP portal, Virtual Reality Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources.

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The Common Coordinate Framework (CCF) Organ VR Gallery

Cited by 3 publications

References 4 publications

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

Towards a Clinically-based Common Coordinate Framework for the Human Gut Cell Atlas - The Gut Models

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

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