A formal ontology of subcellular neuroanatomy

Abstract

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.

The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data

“…5. Details of its construction and content can be found in Fong et al (2007) and Larson et al (2007).…”

“…The first version of the SAO focuses on the subcellular anatomy of the nervous system, comprising neuronal and glial cells, their subcellular components, structural compartments and macromolecular constituents along with multicellular domains such as neuropil and the Node of Ranvier Larson et al, 2007). 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.…”

NeuroMorpho.Org Implementation of Digital Neuroscience: Dense Coverage and Integration with the NIF

“…For example, the terms “Purkinje cell” and “Granule cell” in NeuroMorpho.Org are respectively mapped to “birnlex 867-Purkinje” and “nifext_153-Dentate gyrus granule cell” in NIFSTD. NIFSTD also incorporates cell type relations and terms from other related efforts, such as the Open Biomedical Ontologies (OBO: Bard et al, 2005) and the sub-cellular anatomy ontology (SAO: Larson et al, 2007). The partially hierarchical organization of NeuroMorpho.Org metadata (e.g.…”

Feasibility of Automated Foundational Ontology Interchangeability

“…For DOLCE we select the following ontologies: DMOP.owl, which is an ontology about data mining optimisation [7], the Naive animal ontology2.owl ontology of animals 3 , OntoDerm 5.3.owl about dermatology [4], the SceneOntology.owl ontology of spatial scenes and objects specifically for visual recognition 4 , and SEGOv3.owl for describing relations between geographic occurrences and properties observed by sensors 5 . For BFO, we select the following ontologies: bco.owl about biological collections 6 , the epidemiology ontology.owl for the epidemiology and pub-lic health domain 7 , ero.owl intended for representing biomedical research resources 8 , IDO.9.19.07.owl representing infectious diseases [3], the proper name on -tology v1.8.owl that contains proper names for re-use in biomedical ontologies 9 , and the SAO.owl ontology about subcellular anatomy of the nervous system [12]. For GFO as s O f , we select the following ontologies: the pid.owl about primary immunodeficiency diseases [1] and two biological core ontologies, gfo-bio.…”