Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Melissa Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne Bradford, Aurelie Comte, Wasila M. Dahdul, Thomas A. Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Background: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. Results: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. Conclusions: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies.

Original languageEnglish (US)
Article number21
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
StatePublished - May 19 2014

Fingerprint

Comparative Anatomy
Ontology
Vertebrates
Anatomy
Troleandomycin
Phenotype
Molecular Sequence Annotation
Genes
Gene Ontology
Biodiversity
Amphibians
Obsolescence
Interoperability
Research
Animals

Keywords

  • Bio-ontology
  • Evolutionary biology
  • Morphological variation
  • Phenotype
  • Semantic integration

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Computer Networks and Communications
  • Health Informatics

Cite this

Haendel, M., Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. A., Bradford, Y., ... Mungall, C. J. (2014). Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics, 5(1), [21]. https://doi.org/10.1186/2041-1480-5-21

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. / Haendel, Melissa; Balhoff, James P.; Bastian, Frederic B.; Blackburn, David C.; Blake, Judith A.; Bradford, Yvonne; Comte, Aurelie; Dahdul, Wasila M.; Dececchi, Thomas A.; Druzinsky, Robert E.; Hayamizu, Terry F.; Ibrahim, Nizar; Lewis, Suzanna E.; Mabee, Paula M.; Niknejad, Anne; Robinson-Rechavi, Marc; Sereno, Paul C.; Mungall, Christopher J.

In: Journal of Biomedical Semantics, Vol. 5, No. 1, 21, 19.05.2014.

Research output: Contribution to journalArticle

Haendel, M, Balhoff, JP, Bastian, FB, Blackburn, DC, Blake, JA, Bradford, Y, Comte, A, Dahdul, WM, Dececchi, TA, Druzinsky, RE, Hayamizu, TF, Ibrahim, N, Lewis, SE, Mabee, PM, Niknejad, A, Robinson-Rechavi, M, Sereno, PC & Mungall, CJ 2014, 'Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon', Journal of Biomedical Semantics, vol. 5, no. 1, 21. https://doi.org/10.1186/2041-1480-5-21
Haendel, Melissa ; Balhoff, James P. ; Bastian, Frederic B. ; Blackburn, David C. ; Blake, Judith A. ; Bradford, Yvonne ; Comte, Aurelie ; Dahdul, Wasila M. ; Dececchi, Thomas A. ; Druzinsky, Robert E. ; Hayamizu, Terry F. ; Ibrahim, Nizar ; Lewis, Suzanna E. ; Mabee, Paula M. ; Niknejad, Anne ; Robinson-Rechavi, Marc ; Sereno, Paul C. ; Mungall, Christopher J. / Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. In: Journal of Biomedical Semantics. 2014 ; Vol. 5, No. 1.
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