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Cited by 73Biomedical Text Mining and OntologiesNeonatal Respiratory Health ResearchMedical and Biological Sciences

Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung

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Pan, Huaqin, Deutsch, Gail H., Wert, Susan E., On behalf of the Ontology Subcommittee, Ambalavanan, Namasivayam, Ansong, Charles, Ardini-Poleske, Maryanne E., Bagwell, Jacqueline +16 more·2019·Journal of Biomedical Semantics
DOI 10.1186/s13326-019-0209-1PMC PMC6814058
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Abstract

Background: Although the mouse is widely used to model human lung development, function, and disease, our understanding of the molecular mechanisms involved in alveolarization of the peripheral lung is incomplete. Recently, the Molecular Atlas of Lung Development Program (LungMAP) was funded by the National Heart, Lung, and Blood Institute to develop an integrated open access database (known as BREATH) to characterize the molecular and cellular anatomy of the developing lung. To support this effort, we designed detailed anatomic and cellular ontologies describing alveolar formation and maturation in both mouse and human lung. Description: While the general anatomic organization of the lung is similar for these two species, there are significant variations in the lung’s architectural organization, distribution of connective tissue, and cellular composition along the respiratory tract. Anatomic ontologies for both species were constructed as partonomic hierarchies and organized along the lung’s proximal-distal axis into respiratory, vascular, neural, and immunologic components. Terms for developmental and adult lung structures, tissues, and cells were included, providing comprehensive ontologies for application at varying levels of resolution. Using established scientific resources, multiple rounds of comparison were performed to identify common, analogous, and unique terms that describe the lungs of these two species. Existing biological and biomedical ontologies were examined and cross-referenced to facilitate integration at a later time, while additional terms were drawn from the scientific literature as needed. This comparative approach eliminated redundancy and inconsistent terminology, enabling us to differentiate true anatomic variations between mouse and human lungs. As a result, approximately 300 terms for fetal and postnatal lung structures, tissues, and cells were identified for each species. Conclusion: These ontologies standardize and expand current terminology for fetal and adult lungs, providing a qualitative framework for data annotation, retrieval, and integration across a wide variety of datasets in the BREATH database. To our knowledge, these are the first ontologies designed to include terminology specific for developmental structures in the lung, as well as to compare common anatomic features and variations between mouse and human lungs. These ontologies provide a unique resource for the LungMAP, as well as for the broader scientific community.

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  • Rodent exposures in early infancy (i.e., the neonatal period) mimic human 3rd trimester exposures for several organs, including the lung and brain.

    “This is based on developmental endpoints, since rodent exposures in early infancy (i.e., the neonatal period) mimic human 3rd trimester exposures for several organs, including the lung [50] and brain [51].”

    From Air pollution and children’s health—a review of adverse effects associated with prenatal exposure from fine to ultrafine particulate matter (2021) · cites this paper as [50]

    The Background and ‘Development of the human lung ontology’ sections place comparable lung-maturation stages before birth in humans (around 36 weeks’ gestation) and after birth in mice (beginning around postnatal day 4). This supports the developmental-timing rationale for the lung, which is the part attached to this citation. The paper does not establish that neonatal exposures mimic third-trimester exposures, and its comparison is of mice rather than rodents generally; the brain is cited separately. (LLM, conf=0.85)

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Sorted by citations

Authors
Pan, H., Deutsch, G. H., Wert, S. E., Subcommittee, O. B. O. T. O., Ambalavanan, N., Ansong, C., Ardini-Poleske, M. E., Bagwell, J., Chan, C., Deutsch, G. H., Frevert, C., Gabriel, D., Hagood, J. S., Hill, C. B., Holden-Wiltse, J., Jegga, A. G., Mariani, T. J., Masci, A. M., Pan, H., Shi, W., Warburton, D., Wert, S. E., A, K., & NHLBI Molecular Atlas of Lung Development Program Consortium
ORCID
Venue
Journal of Biomedical Semantics
Publisher
Springer Science and Business Media LLC
Published
2019-10-24
Volume
10
Issue
1
Pages
18-18
ISSN
2041-1480 (ISSN-L)
DOI
10.1186/s13326-019-0209-1
PMC
PMC6814058
OpenAlex
W2982089810
Cited by
73
References
4
Citations by year
2026: 5 · 2025: 13 · 2024: 13 · 2023: 10 · 2022: 14 · 2021: 14 · 2020: 4
FWCI
2.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Biomedical Semantics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
National Heart, Lung, and Blood Institute (U01-HL-122638, U01-HL-122642, U01-HL-122703, U01HL122700, U01-HL-122626, U01-HL-122681)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Neonatal Respiratory Health Research
  • Health Sciences › Medicine › Anatomy › Medical and Biological Sciences
Keywords
lung development, alveolarization, mouse lung, human lung, comparative anatomy, terminology standardization, proximal-distal axis
MeSH terms
Animals, Humans, Pulmonary Alveoli, Mice, Biological Ontologies

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