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J Biomed Semantics. 2014 Aug 11;5:34. doi: 10.1186/2041-1480-5-34. eCollection 2014.

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

Author information

1
Department of Biology, University of South Dakota, Vermillion, SD, USA ; National Evolutionary Synthesis Center, Durham, NC, USA.
2
School of Information Resource and Library Science, University of Arizona, Tucson, AZ, USA.
3
Department of Biology, University of South Dakota, Vermillion, SD, USA.
4
Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
5
Department of Genetics, University of Cambridge, Cambridge, UK.
6
The iPlant Collaborative, Bio5 Institute, University of Arizona, Tucson, AZ, USA.
7
Library and Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA.

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.

KEYWORDS:

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

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