Frequently Asked Questions


  1. What is an Ontology?
  2. What is Gene Ontology?
  3. What is OntoMarker?


  1. How do I install Java Runtime Environment?
  2. How do I install OntoMarker?
What is an Ontology?
By Ontology.Org
    The main purpose of an ontology is to enable communication between computer systems in in a way that is independent of the individual system technologies, information architectures and application domain.    The key ingredients that make up an ontology are a vocabulary of basic terms and a precise specification of what those terms mean.

The term ‘ontology’ has been used in this way for a number of years by the artificial intelligence and knowledge representation community, but is now becoming part of the standard terminology of a much wide community including object modelling and XML.

An ontology is more than an agreed vocabulary

  • An ontology provides a set of well-founded constructs that can be leveraged to build meaningful higher level knowledge. The terms in an ontology are selected with great care, ensuring that the most basic (abstract) foundational concepts and distinctions are defined and specified. The terms chosen form a complete set, whose relationship one to another is defined using formal techniques. It is these formally defined relationships that provide the semantic basis for the terminology chosen.

An ontology is more than a taxonomy or classification of terms

  • Although taxonomy contributes to the semantics of a term in a vocabulary, ontologies include richer relationships between terms. It is these rich relationships that enable the expression of domain-specific knowledge, without the need to include domain-specific terms.

In agent based systems, such as proposed for next generation electronic commerce, the adoption of a shared ontology allows commerce agents to simultaneously:

  • interoperate without misunderstanding,
  • retain a high degree of autonomy, flexibility and agility.

Commerce agents can therefore be highly adaptable yet are able to meaningfully communicate domain-specific knowledge. They do this by using only the basic terms and relationships defined in the ontology. It is the precise definitions of the basic terms that allows those terms to be combined to form meaningful higher level knowledge.

What is Gene Ontology?
By GeneOntology.org
    The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, we write and maintain the ontologies themselves; second, we make cross-links between the ontologies and the genes and gene products in the collaborating databases, and third, we develop tools that facilitate the creation, maintainence and use of ontologies.
    The use of GO terms by several collaborating databases facilitates uniform queries across them. The controlled vocabularies are structured so that you can query them at different levels: for example, you can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or you can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.
What is OntoMarker?
OntoMarker is a tool for Gene Ontology.
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