Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
27 03 2023
27 03 2023
Historique:
received:
27
09
2022
accepted:
30
01
2023
medline:
29
3
2023
entrez:
27
3
2023
pubmed:
28
3
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36973309
doi: 10.1038/s41597-023-01993-8
pii: 10.1038/s41597-023-01993-8
pmc: PMC10043028
doi:
Types de publication
Dataset
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
171Subventions
Organisme : NIDDK NIH HHS
ID : U24 DK135157
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA242936
Pays : United States
Organisme : NIDDK NIH HHS
ID : U2C DK114886
Pays : United States
Organisme : NIH HHS
ID : OT2 OD026671
Pays : United States
Organisme : NIH HHS
ID : OT2 OD033756
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL145608
Pays : United States
Organisme : NIH HHS
ID : OT2 OD030545
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA268108
Pays : United States
Informations de copyright
© 2023. The Author(s).
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