computer science Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to Applied science, practical discipli ...

information science Information science (also known as information studies) is an academic field which is primarily concerned with analysis, collection, classification, manipulation, storage, retrieval, movement, dissemination, and protection of information. ...

and

systems engineering Systems engineering is an interdisciplinary field of engineering and engineering management that focuses on how to design, integrate, and manage complex systems over their life cycles. At its core, systems engineering utilizes systems thinki ...

, ontology engineering is a field which studies the methods and methodologies for building

ontologies In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...

, which encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities. In a broader sense, this field also includes a knowledge construction of the domain using formal ontology representations such as OWL/RDF. A large-scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering. Ontology engineering is one of the areas of

applied ontology Applied ontology involves the practical application of ontological resources to specific domains, such as management, relationships, biomedicine, information science or geography. Much work in applied ontology is carried out within the framework ...

, and can be seen as an application of philosophical ontology. Core ideas and objectives of ontology engineering are also central in

conceptual modeling A conceptual model is a representation of a system. It consists of concepts used to help people knowledge, know, understanding, understand, or simulation, simulate a subject the model represents. In contrast, physical models are physical object su ...

. Automated processing of information not interpretable by

software agents In computer science, a software agent or software AI is a computer program that acts for a user or other program in a relationship of agency, which derives from the Latin ''agere'' (to do): an agreement to act on one's behalf. Such "action on behal ...

can be improved by adding rich

semantics Semantics (from grc, σημαντικός ''sēmantikós'', "significant") is the study of reference, meaning, or truth. The term can be used to refer to subfields of several distinct disciplines, including philosophy, linguistics and comput ...

to the corresponding resources, such as video files. One of the approaches for the formal

conceptualization In information science a conceptualization is an abstract simplified view of some selected part of the world, containing the objects, concepts, and other entities that are presumed of interest for some particular purpose and the relationships betw ...

of represented

knowledge domain Knowledge can be defined as awareness of facts or as practical skills, and may also refer to familiarity with objects or situations. Knowledge of facts, also called propositional knowledge, is often defined as true belief that is distinc ...

s is the use of machine-interpretable ontologies, which provide

structured data A data model is an abstract model that organizes elements of data and standardizes how they relate to one another and to the properties of real-world entities. For instance, a data model may specify that the data element representing a car be c ...

in, or based on, RDF,

RDFS RDF Schema (Resource Description Framework Schema, variously abbreviated as RDFS, , RDF-S, or RDF/S) is a set of classes with certain properties using the RDF extensible knowledge representation data model, providing basic elements for the descr ...

, and

OWL Owls are birds from the order Strigiformes (), which includes over 200 species of mostly solitary and nocturnal birds of prey typified by an upright stance, a large, broad head, binocular vision, binaural hearing, sharp talons, and feathers a ...

. Ontology engineering is the design and creation of such ontologies, which can contain more than just the list of terms (

controlled vocabulary Control may refer to: Basic meanings Economics and business * Control (management), an element of management * Control, an element of management accounting * Comptroller (or controller), a senior financial officer in an organization * Control ...

); they contain terminological, assertional, and relational

axioms An axiom, postulate, or assumption is a statement that is taken to be true, to serve as a premise or starting point for further reasoning and arguments. The word comes from the Ancient Greek word (), meaning 'that which is thought worthy or f ...

to define concepts (classes), individuals, and roles (properties) ( TBox,

ABox In computer science, the terms TBox and ABox are used to describe two different types of statements in knowledge bases. TBox statements are the "terminology component", and describe a domain of interest by defining classes and properties as a d ...

, and RBox, respectively). Ontology engineering is a relatively new field of study concerning the ontology development process, the ontology life cycle, the methods and methodologies for building ontologies,Asunción Gómez-Pérez, Mariano Fernández-López, Oscar Corcho (2004).
Ontological Engineering: With Examples from the Areas of Knowledge Management, E-commerce and the Semantic Web
'. Springer, 2004. and the tool suites and languages that support them. A common way to provide the logical underpinning of ontologies is to formalize the axioms with description logics, which can then be translated to any serialization of RDF, such as

RDF/XML RDF/XML is a syntax,RDF/XML Syntax Specification
Turtle Turtles are an order of reptiles known as Testudines, characterized by a special shell developed mainly from their ribs. Modern turtles are divided into two major groups, the Pleurodira (side necked turtles) and Cryptodira (hidden necked t ...

. Beyond the description logic axioms, ontologies might also contain SWRL rules. The concept definitions can be mapped to any kind of resource or resource segment in RDF, such as images, videos, and regions of interest, to annotate objects, persons, etc., and interlink them with related resources across

knowledge base A knowledge base (KB) is a technology used to store complex structured and unstructured information used by a computer system. The initial use of the term was in connection with expert systems, which were the first knowledge-based systems. ...

s, ontologies, and LOD datasets. This information, based on human experience and knowledge, is valuable for reasoners for the automated interpretation of sophisticated and ambiguous contents, such as the visual content of multimedia resources. Application areas of ontology-based reasoning include, but are not limited to,

information retrieval Information retrieval (IR) in computing and information science is the process of obtaining information system resources that are relevant to an information need from a collection of those resources. Searches can be based on full-text or other c ...

, automated scene interpretation, and

knowledge discovery Knowledge extraction is the creation of knowledge from structured (relational databases, XML) and unstructured (text, documents, images) sources. The resulting knowledge needs to be in a machine-readable and machine-interpretable format and must r ...

Ontology languages

An ontology language is a

formal language In logic, mathematics, computer science, and linguistics, a formal language consists of words whose letters are taken from an alphabet and are well-formed according to a specific set of rules. The alphabet of a formal language consists of sym ...

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

Common logic Common Logic (CL) 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. The CL definition permits and encourages the development o ...

is ISO standard 24707, a specification for a family of ontology languages that can be accurately translated into each other. * The Cyc project has its own ontology language called

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 varian ...

, based on

first-order predicate calculus First-order logic—also known as predicate logic, quantificational logic, and first-order predicate calculus—is a collection of formal systems used in mathematics, philosophy, linguistics, and computer science. First-order logic uses quan ...

with some higher-order extensions. * The

Gellish Gellish is an ontology language for data storage and communication, designed and developed by Andries van Renssen since mid-1990s. It started out as an engineering modeling language ("Generic Engineering Language", giving it the name, "Gellish") bu ...

language includes rules for its own extension and thus integrates an ontology with an ontology language. *

IDEF5 IDEF5 (''Integrated Definition for Ontology Description Capture Method'') is a software engineering method to develop and maintain usable, accurate domain ontologies.Perakath C. Benjamin et al. (1994)''IDEF5 Method Report''. Knowledge Based System ...

is a

software engineering Software engineering is a systematic engineering approach to software development. A software engineer is a person who applies the principles of software engineering to design, develop, maintain, test, and evaluate computer software. The term '' ...

method to develop and maintain usable, accurate, domain ontologies. * KIF is a syntax for

first-order logic First-order logic—also known as predicate logic, quantificational logic, and first-order predicate calculus—is a collection of formal systems used in mathematics, philosophy, linguistics, and computer science. First-order logic uses quantifie ...

that is based on

S-expression In computer programming, an S-expression (or symbolic expression, abbreviated as sexpr or sexp) is an expression in a like-named notation for nested list (tree-structured) data. S-expressions were invented for and popularized by the programming la ...

s. *

Rule Interchange Format The Rule Interchange Format (RIF) is a W3C Recommendation. RIF is part of the infrastructure for the semantic web, along with (principally) SPARQL, RDF and OWL. Although originally envisioned by many as a "rules layer" for the semantic web, ...

(RIF),

F-Logic F-logic (frame 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 ...

and its successor ObjectLogic combine ontologies and rules. *

is a language for making ontological statements, developed as a follow-on from RDF and

, as well as earlier ontology language projects including

OIL An oil is any nonpolar chemical substance that is composed primarily of hydrocarbons and is hydrophobic (does not mix with water) & lipophilic (mixes with other oils). Oils are usually flammable and surface active. Most oils are unsaturated ...

, DAML and

DAML+OIL The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies. Ontologies are a formal way to describe taxonomies and classification networks, essentially defining the structure of knowledge for vari ...

. OWL is intended to be used over the

World Wide Web The World Wide Web (WWW), commonly known as the Web, is an information system enabling documents and other web resources to be accessed over the Internet. Documents and downloadable media are made available to the network through web ...

, and all its elements (classes, properties and individuals) are defined as RDF

resource Resource refers to all the materials available in our environment which are technologically accessible, economically feasible and culturally sustainable and help us to satisfy our needs and wants. Resources can broadly be classified upon thei ...

s, and identified by URIs. * OntoUML is a well-founded language for specifying reference ontologies. *

SHACL Shapes Constraint Language (SHACL) is a World Wide Web Consortium (W3C) standard language for describing Resource Description Framework (RDF) graphs. SHACL has been designed to enhance the semantic and technical interoperability layers of ontolog ...

(RDF SHapes Constraints Language) is a language for describing structure of RDF data. It can be used together with RDFS and OWL or it can be used independently from them. *

XBRL XBRL (eXtensible Business Reporting Language) is a freely available and global framework for exchanging business information. XBRL allows the expression of semantic meaning commonly required in business reporting. The language is XML-based an ...

(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 may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined ** Domain of definition of a partial function ** Natural domain of a partial function **Domain of holomorphy of a function * ...

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

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...

(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 In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...

, these optimizations can be automated to produce a principled and scalable architecture to restructure ontologies such as GO.

Open Biomedical Ontologies The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a ...

(OBO), a 2006 initiative of the U.S. National Center for Biomedical Ontology, provides a common 'foundry' for various ontology initiatives, amongst which are: *The Generic Model Organism Project (GMOD) *

Consortium *Sequence Ontology *Ontology Lookup Service *The

Plant Ontology Plant ontology (PO) is a collection of ontologies developed by the Plant Ontology Consortium. These ontologies describe anatomical structures and growth and developmental stages across Viridiplantae. The PO is intended for multiple applications, ...

Consortium *Standards and Ontologies for

Functional Genomics Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencing ...

and more

Methodologies and tools for ontology engineering

DOGMA Dogma is a belief or set of beliefs that is accepted by the members of a group without being questioned or doubted. It may be in the form of an official system of principles or doctrines of a religion, such as Roman Catholicism, Judaism, Islam ...

* DogmaModeler *

KAON KAON (Karlsruhe ontology) is an ontology infrastructure developed by the University of Karlsruhe and the Research Center for Information Technologies in Karlsruhe. Its first incarnation was developed in 2002 and supported an enhanced version of ...

OntoClean OntoClean is a methodology for analyzing ontologies based on formal, domain-independent properties of classes (the metaproperties) developed by Nicola Guarino and Chris Welty Christopher A. Welty is an American computer scientist, who works at ...

* HOZO *

Protégé (software) Protégé is a free, open source ontology editor and a knowledge management system. The Protégé meta-tool was first built by Mark Musen in 1987 and has since been developed by a team at Stanford University. The software is the most popular and w ...

* Gra.fo (http://gra.fo) * SABiO * TopBraid Composer * TopBraid EDG * HCOME: Human-centered collaborative ontology engineering methodology (http://semanticweb.org/wiki/SharedHCONE.html an
HCOME-3O

References

External links

Ontopia.net: Metadata? Thesauri? Taxonomies? Topic Maps! Making Sense of it All
by Lars Marius Garshol, 2004.
OntologyEngineering.org: Ontology Engineering With Diagrams
{{DEFAULTSORT:Ontology Engineering Knowledge engineering Technical communication Information science Semantic Web Ontology (information science) Bioinformatics

Ontology languages

Ontology engineering in life sciences

Methodologies and tools for ontology engineering

See also

References

Further reading

External links