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Subcellular Anatomy Ontology

Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

URL: http://ccdb.ucsd.edu/SAO

Resource ID: nif-0000-00206     Resource Type: Resource     Version: Latest Version

Keywords

electron microscopy, cellular structure, glial cell, light microscopy, macromolecule, nervous system, neuroanatomy, neuronal cell, neuropil, subcellular anatomy, subcellular structure, supracellular structure, synapse, owl, anatomy, sub-cellular, cellular component, cell, mesoscale

Additional Resource Types

Ontology

Alternate URLs

http://ccdb.ucsd.edu/SAO/1.2/SAO.owl, http://ccdb.ucsd.edu/CCDBWebSite/sao.html, http://bioportal.bioontology.org/ontologies/SAO

Supercategory

Resource

Abbreviation

SAO, NIF Subcellular

Funding Information

NIH,

Parent Organization

Comment

Contact: Maryann Martone, mmartone (at) ucsd.edu

OBO Foundry: No
Status: Production and review
Contact: Stephen Larson: slarson (at) ncmir.ucsd.edu
(Info provided by OBO Foundry)

Listed By

BioPortal, OBO

Alternate IDs

sao

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

  • Description was changed
  • Funding Information was changed
  • Comment was changed
  • Additional Resource Types was changed

Version 2

Created 2 weeks ago by Christie Wang

Version 1

Created 5 years ago by Anonymous

A formal ontology of subcellular neuroanatomy.

  • Larson SD
  • Front Neuroinform
  • 2007 31

The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.