Ontologies

Ontologies - relationships beteween data objects

SGD Tutorial: GO Annotations [http://www.yeastgenome.org/help/gotutorial.html]
Open Biomedical Ontologies [http://obo.sourceforge.net]
Gene Ontology [http://www.geneontology.org/]
Wilkinson M (2004) Biobabel: Issues and tools for integration of Biological data from disparate sources. Presentation, Genome Canada Applied Computational Biology Course, Halifax, Canada.

Controlled vocabulary - A controlled vocabulary is an established list of standardized terminology for 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 more specific
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.

Gene Ontology

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 defined.
Example:

The entire GO tree can be viewed or searched using the AmiGO browser at http://www.godatabase.org/cgi-bin/amigo/go.cgi.

http://home.cc.umanitoba.ca/~frist/Seminars/iims07/iims07.html