ArticleScientific data2023
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas.
Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights.bioRxiv : the preprint server for biology · 2026Article
- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
- SenNet Portal: Build, Optimization and Usage.bioRxiv : the preprint server for biology · 2026Article
- A general strategy for generating expert-guided, simplified views of ontologies.Scientific data · 2026Article
- Article
- A general strategy for generating expert-guided, simplified views of ontologies.bioRxiv : the preprint server for biology · 2025Article
- Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph.Scientific data · 2025Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.Nature methods · 2025Article
- Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data.bioRxiv : the preprint server for biology · 2025Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage.bioRxiv : the preprint server for biology · 2024Article
- Publication, funding, and experimental data in support of Human Reference Atlas construction and usage.Scientific data · 2024Article
- Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas.Scientific data · 2023Article
- The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality.bioRxiv : the preprint server for biology · 2023Article
- Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models.BMC medical informatics and decision making · 2023Article
- The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality.Frontiers in bioinformatics · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.