Nose to tail, roots to shoots: Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Wasila M. Dahdul, Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, Melissa Haendel

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Background: Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species. We developed the Biological Spatial Ontology (BSPO) to standardize the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes. Results: BSPO currently contains 146 classes and 58 relations representing anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Spatial reasoning is further enhanced in anatomy ontologies by integrating spatial relations such as dorsal_to into class descriptions (e.g., 'dorsolateral placode' dorsal_to some 'epibranchial placode').Conclusions: The BSPO is currently used by projects that require standardized anatomical descriptors for phenotype annotation and ontology integration across a diversity of taxa. Anatomical location classes are also useful for describing phenotypic differences, such as morphological variation in position of structures resulting from evolution within and across species.

Original languageEnglish (US)
Article number34
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
StatePublished - Aug 11 2014

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Biological Ontologies
Nose
Ontology
Anatomy
Phenotype
Terminology
Fungi
Animals

Keywords

  • Anatomy
  • Axes
  • BSPO
  • Ontology
  • Phenotype
  • Position
  • Reasoning
  • Spatial relationships

ASJC Scopus subject areas

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

Cite this

Nose to tail, roots to shoots : Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. / Dahdul, Wasila M.; Cui, Hong; Mabee, Paula M.; Mungall, Christopher J.; Osumi-Sutherland, David; Walls, Ramona L.; Haendel, Melissa.

In: Journal of Biomedical Semantics, Vol. 5, No. 1, 34, 11.08.2014.

Research output: Contribution to journalArticle

Dahdul, Wasila M. ; Cui, Hong ; Mabee, Paula M. ; Mungall, Christopher J. ; Osumi-Sutherland, David ; Walls, Ramona L. ; Haendel, Melissa. / Nose to tail, roots to shoots : Spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. In: Journal of Biomedical Semantics. 2014 ; Vol. 5, No. 1.
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