The Cell Component Ontology

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Cell Component Ontology

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Introduction

The Cell Component Ontology (CCO) is a controlled vocabulary of terms describing cellular components and compartments, and relationships between these terms. CCO spans all domains of life, and includes terms such as cytoplasm, cell wall, and chloroplast. The ontology currently contains 160 terms.

Each term within CCO has a common-name (its preferred English name), and a definition. Many terms include synonyms, and a reference for the definition. Terms can also contain a 'sensu' slot that indicates one or more taxonomic classes of organisms to which they apply.

The CCO Class Hierarchy

The CCO terms are organized into a hierarchy of classes and instances according to the class-subclass relationship and the class-instance relationship (is-a). Classes correspond to types of biological entities, such as the class of all organelles. Instances correspond to specific biological entities, such as the mitochondrion. The class-subclass relationship defines a generalization relationship between a parent class and its child class (subclass), e.g., class membrane-bound-organelle is a subclass of class organelle because the latter defines a more general type of biological entity. The class-instance relationship defines a relationship between a class and an instance of that class, e.g., mitochondrion is an instance of membrane-bound organelle. The broader concepts (classes) appear on the upper levels of the hierarchy tree. More specific concepts are grouped under the broader concepts.

There are eight top-level class terms. Each term must and can only have a single top-level parent on the class hierarchy. Mitochondiral membrane has a single top-level parent membrane, whereas, mitochondrion has a single top-level parent organelle. However, a term may have multiple low-level parents which are all under the same single high-level parent. Golgi-ER transport vesicle is a child term of both Golgi vesicle and COPI-coated vesicle. The latter two are children terms of the single high-level term organelle.

Relationships within CCO

Two additional relationships, besides the is-a relationship, are used in CCO: component-of and surrounded-by. The component-of relationship (the inverse relationship is components) describes whether one term is a physical constituent of another term, e.g., mitochondrial membrane is a component of mitochondrion. The surrounded-by relationship (the inverse relationship surrounds) provides relative positional information of two terms within a cell, e.g., mitochondrial lumen is surrounded by mitochondrial envelope.

The surrounded-by relationship is used only for the terms that are immediately adjacent to each other physically within the cell. CCO states that mitochondrial inner membrane is surrounded-by mitochondrial inter-membrane space, and that mitochondrial inter-membrane space is surrounded-by mitochondrial outer membrane. CCO does not explicitly state that mitochondrial inner membrane is surrounded-by mitochondrial outer membrane, although this is implied transitively.

Relationship of CCO to GO

Many terms and their definitions in CCO were initially selected from the Gene Ontology (GO) Consortiumís cellular component terms. These terms have cross-reference links to GO and have GO IDs as external IDs. Additional terms, most notably class and subclass terms, had to be added to classify all the terms, which do not have the is-a relationship in GO. For example, the class term space was introduced to classify terms such as chloroplast stroma. A new relationship surrounded-by, is not used in GO and was introduced to describe relative positional information of two terms within a cell. Species-specific terms were created only if necessary such as when a term has different components in a specific taxon group. The naming style of the species-specific terms follows the convention used in GO. For example, cell envelope (sensu Gram-positive Bacteria) has components plasma membrane (sensu Gram-positive Bacteria) and cell wall (sensu Gram-positive Bacteria), whereas, cell envelope (sensu Gram-negative Bacteria) has components plasma membrane (sensu Gram-negative Bacteria), periplasmic space (sensu Gram-negative Bacteria), cell wall (sensu Gram-negative Bacteria), and outer membrane (sensu Gram-negative Bacteria).

CCO was developed using SRI Internationalís GKB Editor software.


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