Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology
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 asmore »
- Authors:
-
- Univ. of South Dakota, Vermillion, SD (United States). Dept. of Biology; National Evolutionary Synthesis Center, Durham, NC (United States)
- Univ. of Arizona, Tucson, AZ (United States). School of Information Resource and Library Science
- Univ. of South Dakota, Vermillion, SD (United States). Dept. of Biology
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Cambridge (United Kingdom). Dept. of Genetics
- Univ. of Arizona, Tucson, AZ (United States). Bio5 Inst. The iPlant Collaborative
- Oregon Health and Science Univ., Portland, OR (United States). Library. Dept. of Medical Informatics and Epidemiology
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1626678
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biomedical Semantics
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2041-1480
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; Mathematical & Computational Biology; Anatomy; Spatial relationships; Position; Axes; Reasoning; BSPO; Ontology; Phenotype
Citation Formats
Dahdul, Wasila M., Cui, Hong, Mabee, Paula M., Mungall, Christopher J., Osumi-Sutherland, David, Walls, Ramona L., and Haendel, Melissa A. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. United States: N. p., 2014.
Web. doi:10.1186/2041-1480-5-34.
Dahdul, Wasila M., Cui, Hong, Mabee, Paula M., Mungall, Christopher J., Osumi-Sutherland, David, Walls, Ramona L., & Haendel, Melissa A. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. United States. https://doi.org/10.1186/2041-1480-5-34
Dahdul, Wasila M., Cui, Hong, Mabee, Paula M., Mungall, Christopher J., Osumi-Sutherland, David, Walls, Ramona L., and Haendel, Melissa A. Wed .
"Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology". United States. https://doi.org/10.1186/2041-1480-5-34. https://www.osti.gov/servlets/purl/1626678.
@article{osti_1626678,
title = {Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology},
author = {Dahdul, Wasila M. and Cui, Hong and Mabee, Paula M. and Mungall, Christopher J. and Osumi-Sutherland, David and Walls, Ramona L. and Haendel, Melissa A.},
abstractNote = {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.},
doi = {10.1186/2041-1480-5-34},
journal = {Journal of Biomedical Semantics},
number = 1,
volume = 5,
place = {United States},
year = {Wed Jan 01 00:00:00 EST 2014},
month = {Wed Jan 01 00:00:00 EST 2014}
}
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