ArticlebioRxiv : the preprint server for biology2025
A general strategy for generating expert-guided, simplified views of ontologies.
Anita R Caron, Aleix Puig-Barbe, Ellen M Quardokus, James P Balhoff, Jasmine Belfiore, Nana-Jane Chipampe, Josef Hardi, Bruce W Herr, Huseyin Kir, Paola Roncaglia and 5 more
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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0citing papers in PubMed
–field-weighted citation impact
What it found
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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.
2 · The registryThe trial behind it
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3 · Its place in the literatureWho cites it
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4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
15 authors.
Anita R CaronEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-6523-4866 Aleix Puig-BarbeEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0001-6677-8489 Ellen M QuardokusDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0001-7655-4833 Nana-Jane ChipampeWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.ORCID 0000-0002-8802-0473 Josef HardiStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, 94305 USA.ORCID 0000-0002-2533-6681 Bruce W HerrDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-6703-7647 Huseyin KirEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-3315-2794 Paola RoncagliaEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-2825-0621 Mark A MusenStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, 94305 USA.ORCID 0000-0003-3325-793X Helen ParkinsonEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0003-3035-4195 James A McLaughlinEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-8361-2795 Katy BörnerDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-3321-6137 David Osumi-SutherlandEuropean Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.ORCID 0000-0002-7073-9172 Funding
SenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI KRETZLER, MATTHIAS · 2017 to 2021
$21.0MKPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4M3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]OT2OD033756 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2022 to 2025
$7.4MThe Human Body Atlas: High-Resolution, Functional Mapping of Voxel, Vector, and Meta DatasetsOT2OD026671 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2018 to 2021
$3.5MNational Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and diseaseU24DK135157 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI JAIN, SANJAY, VALERIUS, MICHAEL TODD · 2022 to 2023
$3.4MNCI NIH HHS U24 CA268108NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIH HHS OT2 OD026671NIH HHS OT2 OD033756
6 · The paper itselfAbstract
Annotation of biomedical entities with widely used, well-structured ontologies and ontology-aware tools ensures data and analyses are Findable, Accessible, Interoperable, and Reusable (FAIR). Standardized terms with synonyms support lexical search, while ontology structure enables biologically meaningful grouping of annotations, such as by location and type. However, ontologies serving diverse communities are often more complex than needed for specific applications, creating barriers to adoption by researchers and resource developers. For example, cell atlases often attempt simplifications by manually building term hierarchies linking to cell type and anatomy ontologies, but these may include relationship types unsuitable for grouping annotations. We present tools for validating human expert curated term hierarchies, developed in two human reference atlas projects, against ontology structures. The tools provide tabular statistics plus graphical views of matching and non-matching terms and relationships to support discussion and conflict resolution. The HuBMAP Human Reference Atlas (HRA) effort is used to validate the approach and tools, and the Human Developmental Cell Atlas is featured as a use case.
Identifiers
PMID39763856
PMCPMC11702530
What OpenQuestion holds
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LicenceCC BY
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