Ontology engineering - AbsoluteAstronomy.com

Ontology engineering in computer science

Computer science

Computer science or computing science is the study of the theoretical foundations of information and computation and of practical techniques for their implementation and application in computer systems...

and information science

Information science

-Introduction:Information science is an interdisciplinary science primarily concerned with the analysis, collection, classification, manipulation, storage, retrieval and dissemination of information...

is a new field, which studies the methods and methodologies for building ontologies: formal representations of a set of concepts within a domain and the relationships between those concepts.
A large scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering.

Overview

Ontologies provide a common vocabulary of an area and define, with different levels of formality, the meaning of the terms and the relationships between them. During the last decade, increasing attention has been focused on ontologies. Ontologies are now widely used in knowledge engineering

Knowledge engineering

Knowledge engineering was defined in 1983 by Edward Feigenbaum, and Pamela McCorduck as follows:At present, it refers to the building, maintaining and development of knowledge-based systems...

, artificial intelligence

Artificial intelligence

Artificial intelligence is the intelligence of machines and the branch of computer science that aims to create it. AI textbooks define the field as "the study and design of intelligent agents" where an intelligent agent is a system that perceives its environment and takes actions that maximize its...

and computer science

Computer science

; in applications related to areas such as knowledge management

Knowledge management

Knowledge management comprises a range of strategies and practices used in an organization to identify, create, represent, distribute, and enable adoption of insights and experiences...

, natural language processing

Natural language processing

Natural language processing is a field of computer science and linguistics concerned with the interactions between computers and human languages; it began as a branch of artificial intelligence....

, e-commerce, intelligent information integration, bio-informatics, education; and in new emerging fields like the semantic web

Semantic Web

The Semantic Web is a collaborative movement led by the World Wide Web Consortium that promotes common formats for data on the World Wide Web. By encouraging the inclusion of semantic content in web pages, the Semantic Web aims at converting the current web of unstructured documents into a "web of...

. Ontological engineering is a new field of study concerning the ontology development process, the ontology life cycle, the methods and methodologies for building ontologies, and the tool suites and languages that support them.

Ontology languages

An ontology language is a formal language

Formal language

A formal language is a set of words—that is, finite strings of letters, symbols, or tokens that are defined in the language. The set from which these letters are taken is the alphabet over which the language is defined. A formal language is often defined by means of a formal grammar...

used to encode the ontology. There are a number of such languages for ontologies, both proprietary and standards-based:

Common logic
Common logic
Common logic is a framework for a family of logic languages, based on first-order logic, intended to facilitate the exchange and transmission of knowledge in computer-based systems....

is ISO standard 24707, a specification for a family of ontology languages that can be accurately translated into each other.
The Cyc
Cyc
Cyc is an artificial intelligence project that attempts to assemble a comprehensive ontology and knowledge base of everyday common sense knowledge, with the goal of enabling AI applications to perform human-like reasoning....

project has its own ontology language called CycL
CycL
CycL in computer science and artificial intelligence is an ontology language used by Doug Lenat's Cyc artificial intelligence project. Ramanathan V. Guha was instrumental in the design of early versions of the language. There is a close variant of CycL known as MELD.The original version of CycL was...

, based on first-order predicate calculus with some higher-order extensions.
The Gellish
Gellish
Gellish is a controlled natural language, also called a formal language, in which information and knowledge can be expressed in such a way that it is computer-interpretable, as well as system-independent. Gellish is a structured subset of natural language that is suitable for information modelling...

language includes rules for its own extension and thus integrates an ontology with an ontology language.
IDEF5
IDEF5
IDEF5 is a software engineering method to develop and maintain usable, accurate, domain ontologies...

is a software engineering
Software engineering
Software Engineering is the application of a systematic, disciplined, quantifiable approach to the development, operation, and maintenance of software, and the study of these approaches; that is, the application of engineering to software...

method to develop and maintain usable, accurate, domain ontologies.
KIF
KIF
KIF may stand for:* Knowledge Interchange Format* Kingfisher Lake Airport's IATA code* Københavns Idræts Forening, Denmark's oldest athletics club* KIF Kolding, a team handball club based in Kolding, Denmark...

is a syntax for first-order logic
First-order logic
First-order logic is a formal logical system used in mathematics, philosophy, linguistics, and computer science. It goes by many names, including: first-order predicate calculus, the lower predicate calculus, quantification theory, and predicate logic...

that is based on S-expression
S-expression
S-expressions or sexps are list-based data structures that represent semi-structured data. An S-expression may be a nested list of smaller S-expressions. S-expressions are probably best known for their use in the Lisp family of programming languages...

s.
Rule Interchange Format
Rule Interchange Format
The Rule Interchange Format is a W3C Recommendation. RIF is part of the infrastructure for the semantic web, along with SPARQL, RDF and OWL...

(RIF) and F-Logic
F-logic
F-logic is a knowledge representation- and ontology language. F-logic combines the advantages of conceptual modeling with object-oriented, frame-based languages and offers a declarative, compact and simple syntax, as well as the well-defined semantics of a logic-based language.Features include,...

combine ontologies and rules.
OWL
Web Ontology Language
The Web Ontology Language is a family of knowledge representation languages for authoring ontologies.The languages are characterised by formal semantics and RDF/XML-based serializations for the Semantic Web...

is a language for making ontological statements, developed as a follow-on from RDF
Resource Description Framework
The Resource Description Framework is a family of World Wide Web Consortium specifications originally designed as a metadata data model...

and RDFS, as well as earlier ontology language projects including OIL
Ontology Inference Layer
OIL can be regarded as an Ontology infrastructure for the Semantic Web. OIL is based on concepts developed in Description Logic and frame-based systems and is compatible with RDFS....

, DAML and DAML+OIL. OWL is intended to be used over the World Wide Web
World Wide Web
The World Wide Web is a system of interlinked hypertext documents accessed via the Internet...

, and all its elements (classes, properties and individuals) are defined as RDF resources
Resource (Web)
The concept of resource is primitive in the Web architecture, and is used in the definition of its fundamental elements. The term was first introduced to refer to targets of Uniform Resource Locators , but its definition has been further extended to include the referent of any Uniform Resource...

, and identified by URI
Uniform Resource Identifier
In computing, a uniform resource identifier is a string of characters used to identify a name or a resource on the Internet. Such identification enables interaction with representations of the resource over a network using specific protocols...

s.
XBRL
XBRL
XBRL is a freely available, market-driven, open, and global standard for exchanging business information. XBRL allows information modeling and the expression of semantic meaning commonly required in business reporting. XBRL is XML-based...

(Extensible Business Reporting Language) is a syntax for expressing business semantics.

Ontology Engineering In Life Sciences

Life sciences is flourishing with ontologies that biologists use to make sense of their experiments. For inferring correct conclusions from experiments, ontologies have to be structured optimally against the knowledge base they represent. The structure of an ontology needs to be changed continuously so that it is an accurate representation of the underlying domain

Domain model

A domain model in problem solving and software engineering can be thought of as a conceptual model of a domain of interest which describes the various entities, their attributes, roles and relationships, plus the constraints that govern the integrity of the model elements comprising that problem...

.

Recently, an automated method was introduced for engineering ontologies in life sciences such as Gene Ontology

Gene Ontology

The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...

(GO), one of the most successful and widely used biomedical ontology. Based on information theory, it restructures ontologies so that the levels represent the desired specificity of the concepts. Similar information theoretic approaches have also been used for optimal partition of Gene Ontology. Given the mathematical nature of such engineering algorithms, these optimizations can be automated to produce a principled and scalable architecture to restructure ontologies such as GO.

Open Biomedical Ontologies
Open Biomedical Ontologies
Open Biomedical Ontologies is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S...

(OBO), a 2006 initiative of the U.S. National Center for Biomedical Ontology, that provides a common 'foundry' for various ontology initiatives, amongst which are:

The Generic Model Organism Project
Generic Model Organism Database
The Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences...

(GMOD)
Gene Ontology
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...

Consortium
Sequence Ontology
Ontology Lookup Service
The Plant Ontology
Plant ontology
Plant ontology is a set of controlled vocabularies , developed by the Plant Ontology Consortium. These ontologies describe plant structures and growth and developmental stages, providing a semantic framework for cross-species queries across databases.-Core members of the Plant Ontology...

Consortium
Standards and Ontologies for Functional Genomics

and more

Tools for ontology engineering

DOGMA
DOGMA
DOGMA, short for Developing Ontology-Grounded Methods and Applications, is the name of research project in progress at Vrije Universiteit Brussel's STARLab, Semantics Technology and Applications Research Laboratory...
DogmaModeler
DogmaModeler
DogmaModeler is a free and open source, ontology modeling tool based on ORM. The philosophy of DogmaModeler is to enable non-IT experts to model ontologies with a little or no involvement of an ontology engineer. This challenge is tackled in DogmaModeler through well-defined methodological...
KAON
KAON
KAON is an ontology infrastructure developed by the University of Karlsruhe and the Research Center for Information Technologies in Karlsruhe....
OntoClean
OntoClean
OntoClean is a methodology for analyzing ontologies based on formal, domain-independent properties of classes due to Nicola Guarino and Chris Welty.-Overview and History:...
OnToContent
HOZO
Hozo
Hozo is a graphical ontology editor especially created to produce heavy-weight and well thought out ontologies. It was developed in Japan through a partnership between the Department of Knowledge Systems , ISIR-Osaka University, and Enegate Co, Ltd.-External links:* * *...
Protégé (software)
Protege (software)
Protégé is a free, open source ontology editor and a knowledge acquisition system. Like Eclipse, Protégé is a framework for which various other projects suggest plugins. This application is written in Java and heavily uses Swing to create the rather complex user interface...

External links

Metadata? Thesauri? Taxonomies? Topic Maps!.

The source of this article is wikipedia, the free encyclopedia. The text of this article is licensed under the GFDL.

Overview

Ontology languages

Ontology Engineering In Life Sciences

Tools for ontology engineering

See also

Further reading

External links