- A controlled vocabulary is an established list of standardized
use in indexing and retrieval of information. In a controlled
vocabulary, every object has an agreed-upon name, for which there may
be many synonyms. Regardless of the synonym used, it is possible to
find the name used by the controlled vocabulary.
Ontology - "... an explicit
specification of some topic. For our
purposes, it is a formal and declarative representation which includes
the vocabulary (or names) for referring to the terms in that subject
area and the logical statements that describe what the terms are, how
they are related to each other, and how they can or cannot be related
to each other. Ontologies therefore provide a vocabulary for
representing and communicating knowledge about some topic and a set of
relationships that hold among the terms in that vocabulary (From the
Stanford Knowledge Systems Lab)."
Ontologies are designed as Directed Acyclic Graphs
(DAG). DAGs have the following properties:
Hierarchical tree-like structure
Vertices (branches) are unidirectional, from less specific to
Any node may have multiple parents
Cross-branching may occur between objects at different levels
Any path from a node must not lead back to that node (ie. acyclic)
In an ontology, relationships betwrelationshipseen nodes are
defined. Usually, only a small number of relationships need to be
defined. This will be illustrated using Gene Ontology as an example.
The goal of Gene Ontology is to create a formal description of the
relationships among genes and proteins and their cellular roles. The
current GO defines three high-level categories: Biological Process,
Molecular Function and Cell Component.
As illustrated above, relationships between objects are also