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Cited by 750Biomedical Text Mining and OntologiesSemantic Web and OntologiesBioinformatics and Genomic Networks

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Uberon, an integrative multi-species anatomy ontology

Open access
Mungall, Christopher J, Torniai, Carlo, Gkoutos, Georgios V, Lewis, Suzanna E, Haendel, Melissa A·2012·Genome biology
DOI 10.1186/gb-2012-13-1-r5PMC PMC3334586
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Abstract

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org.

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Figures

Figure 1 Uberon integrates anatomical ontologies. Anatomical representation of 'lung' and related types and processes are siloed in various ontologies with no connections. EHDAA/EHDAA2, Edinburgh Human Developmental Anatomy, abstract version/abstract version 2; FMA, Foundational Model of Anatomy; GO, Gene Ontology; MA, Mouse Anatomy Ontology; MPO, Mammalian Phenotype Ontology.
Figure 1 Uberon integrates anatomical ontologies. Anatomical representation of 'lung' and related types and processes are siloed in various ontologies with no connections. EHDAA/EHDAA2, Edinburgh Human Developmental Anatomy, abstract version/abstract version 2; FMA, Foundational Model of Anatomy; GO, Gene Ontology; MA, Mouse Anatomy Ontology; MPO, Mammalian Phenotype Ontology.CC BY · PubMed Central
Figure 2 Illustration of how Uberon relates anatomical silos into a unified view. Uberon classes are shown in gray and classes from external ontologies are indicated with their respective prefix. Classes in light gray have computable definitions, which are indicated by the relations shown. For example, 'alveolus of lung' is_a 'alveolus' that is part_of some 'lung'. 'Respiration organ' is_a organ that is capable_of GO:respiratory gaseous exchange. The blue circle indicates what would be included in a mammal-restricted subset of Uberon, as swim bladder is not found in mammals. Use of Uberon together with taxon-specific anatomy ontologies enables bridging of the data with full reasoning capabilities. In this example, Uberon 'lung' subsumes the lung classes from the mouse and human anatomy ontologies. Classes in the blue circle plus the blue classes at the bottom would be available in uberon-collected-mammal.owl. Note that some relationships have been trimmed for illustration purposes.
Figure 2 Illustration of how Uberon relates anatomical silos into a unified view. Uberon classes are shown in gray and classes from external ontologies are indicated with their respective prefix. Classes in light gray have computable definitions, which are indicated by the relations shown. For example, 'alveolus of lung' is_a 'alveolus' that is part_of some 'lung'. 'Respiration organ' is_a organ that is capable_of GO:respiratory gaseous exchange. The blue circle indicates what would be included in a mammal-restricted subset of Uberon, as swim bladder is not found in mammals. Use of Uberon together with taxon-specific anatomy ontologies enables bridging of the data with full reasoning capabilities. In this example, Uberon 'lung' subsumes the lung classes from the mouse and human anatomy ontologies. Classes in the blue circle plus the blue classes at the bottom would be available in uberon-collected-mammal.owl. Note that some relationships have been trimmed for illustration purposes.CC BY · PubMed Central
Figure 3 Import chain of taxonomically arranged Uberon modules. Each combined module at different taxonomic levels imports the relevant native ontologies as well as bridge files that specify the logical definitions. The number of equivalent class (EC) or SubClass (SC) axioms in each bridge file are shown, illustrating the contributions of each ontology to the total infrastructure. The files linked with dotted lines represent the mechanism by which a new chicken anatomy ontology (and similarly, archosaur) would be integrated.
Figure 3 Import chain of taxonomically arranged Uberon modules. Each combined module at different taxonomic levels imports the relevant native ontologies as well as bridge files that specify the logical definitions. The number of equivalent class (EC) or SubClass (SC) axioms in each bridge file are shown, illustrating the contributions of each ontology to the total infrastructure. The files linked with dotted lines represent the mechanism by which a new chicken anatomy ontology (and similarly, archosaur) would be integrated.CC BY · PubMed Central
Figure 4 Strategy for applying taxonomic constraints. If the fruitfly class FBbt:tibia (representing a segment of an insect leg) were accidentally placed as a child of UBERON:0000979 'tibia', the reasoner would flag this as an error because 'tibia' is_a 'bone' in Uberon, bones are found only in vertebrates, and FBbt:tibia is a Drosophila structure.
Figure 4 Strategy for applying taxonomic constraints. If the fruitfly class FBbt:tibia (representing a segment of an insect leg) were accidentally placed as a child of UBERON:0000979 'tibia', the reasoner would flag this as an error because 'tibia' is_a 'bone' in Uberon, bones are found only in vertebrates, and FBbt:tibia is a Drosophila structure.CC BY · PubMed Central
Figure 5 Expression of Distal-less (Dll) and Dll orthologs (Dlx) in 'legs'. (a) Three-day Molgula occidentalis ascidian larva from which an ampulla is extending. (b) Polychaete annelid Chaetopterus variopedatus, ventral view of larva just prior to metamorphosis (anterior to left). Dll expressing cells are visible in parapodial rudiments (arrows), antennae (out of focus on opposite dorsal surface), and in prospective feeding organs (bracket). (c) Metamorphosing Strongylocentrotus droebachiensis sea urchin larvae, aboral view. Cells at the distal tip of the tube feet (arrows) express Dll prior to and during extension from the body wall. (d) Expression in nine-day mouse embryo, lateral view, head top; arrows point to medial border of cells expressing one or more Dlx genes in the presumptive forelimb. (e) The evolutionary appearance of the various appendages for which Dll expression data are indicated in (a-d) are shown on this cladogram (branch lengths are not scaled). Reprinted with modification and permission from [49].
Figure 5 Expression of Distal-less (Dll) and Dll orthologs (Dlx) in 'legs'. (a) Three-day Molgula occidentalis ascidian larva from which an ampulla is extending. (b) Polychaete annelid Chaetopterus variopedatus, ventral view of larva just prior to metamorphosis (anterior to left). Dll expressing cells are visible in parapodial rudiments (arrows), antennae (out of focus on opposite dorsal surface), and in prospective feeding organs (bracket). (c) Metamorphosing Strongylocentrotus droebachiensis sea urchin larvae, aboral view. Cells at the distal tip of the tube feet (arrows) express Dll prior to and during extension from the body wall. (d) Expression in nine-day mouse embryo, lateral view, head top; arrows point to medial border of cells expressing one or more Dlx genes in the presumptive forelimb. (e) The evolutionary appearance of the various appendages for which Dll expression data are indicated in (a-d) are shown on this cladogram (branch lengths are not scaled). Reprinted with modification and permission from [49].CC BY · PubMed Central

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Citations

Cites

Show all 67 references

Research works printed but not linked: 4

  1. Travillian R, Malone J, Pang C, Hancock J, Holland PW, Schofield P, Parkinson H: The Vertebrate Bridging Ontology (VBO). Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http://icbo.buffalo.edu/ICBO-2011_Proceedings.pdf]
  2. Osumi-Sutherland D: CARO 2.0. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http://icbo.buffalo.edu/ICBO-2011_Proceedings.pdf]
  3. Torniai C, Brush M, Vasilevsky N, Segerdell E, Wilson ML, Johnson T, Corday K, Shaffer C, Haendel M: Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. Proceedings of the Second International Conference on Biomedical Ontology: July 26-30, 2011; Buffalo, NY. 2011, [http://icbo.buffalo.edu/ICBO-2011_Proceedings.pdf]
  4. Segerdell E, Wilson ML, Bashor T, Bourges-Waldegg D, Corday K, Frost HR, Johnson T, Shaffer CJ, Stone L, Torniai C, Haendel MA: eagle-i: an ontology-driven framework for biomedical resource annotation and discovery. Nat Precedings. 2010, [http://precedings.nature.com/documents/5176/version/1/files/npre20105176-1.pdf]

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    “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
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    “…phase of apoptosis’ A version of the ontology containing all relationships, including information from the Uberon anatomy (or stage) ontology (7), the Chemical Entities of Biological Inter-est ontology (ChEBI; (8)), the Plant Ontology for plant structure / stage (PO; (9)), the Phenotypic…”

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    “Uberon (Mungall et al. 2012) for most vertebrates, other metazoan ontologies such as the Drosophila anatomy ontology (Costa et al.”
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  • The ChEMBL database in 2017

    Gaulton, A., Hersey, A., Nowotka, M., Bento, A. P., Chambers, J. K., Méndez, D., Mutowo, P., Atkinson, F. L., Bellis, L. J., Cibrián–Uhalte, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1074 · Cited by 2,394

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Related

Metadata

Authors
Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A.
Affiliations
  • Oregon Health & Science University (US)
  • University of Cambridge (GB)
  • Lawrence Berkeley National Laboratory (US)
ORCID
Venue
Genome biology
Publisher
Springer Science and Business Media LLC
Published
2012-01-31
Volume
13
Issue
1
Pages
R5-R5
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2012-13-1-r5
PMC
PMC3334586
OpenAlex
W2116034137
Cited by
732
References
67
Citations by year
2026: 60 · 2025: 69 · 2024: 55 · 2023: 66 · 2022: 55 · 2021: 51 · 2020: 46 · 2019: 45 · 2018: 55 · 2017: 46 · 2016: 49 · 2015: 50 · 2014: 34 · 2013: 28 · 2012: 21
FWCI
17.73
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
Funders
  • U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
  • National Institutes of Health (2p41hg002273-07, 5u24rr029825-02, DE-AC02–05CH11231)
  • Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
  • National Human Genome Research Institute (U41HG002273, R01HG004838, P41HG002273-09S1, P41-HG002273)
  • National Center for Research Resources (1U24RR029825-01)
  • Basic Energy Sciences (DE-AC02, DE-AC02-05CH11231., AC02–05CH11231)
Topics
  • Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
  • Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
UBERON, anatomy ontology, anatomical classification, taxonomic variation, human anatomy
MeSH terms
Anatomy, Comparative, Classification, Humans, Phenotype, Software, Species Specificity, Databases, Factual, Computational Biology

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