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) Consortium’s 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 International’s GKB Editor software.
|