Ontology (information science)

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 of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject.

Every academic discipline or field creates ontologies to limit complexity and organize data into information and knowledge. New ontologies improve problem solving within that domain. Translating research papers within every field is a problem made easier when experts from different countries maintain a controlled vocabulary of jargon between each of their languages.[1]

Etymology[]

The compound word ontology combines onto-, from the Greek ὄν, on (gen. ὄντος, ontos), i.e. "being; that which is", which is the present participle of the verb εἰμί, eimí, i.e. "to be, I am", and -λογία, -logia, i.e. "logical discourse", see classical compounds for this type of word formation.[2][3]

While the etymology is Greek, the oldest extant record of the word itself, the New Latin form ontologia, appeared in 1606 in the work Ogdoas Scholastica by Jacob Lorhard (Lorhardus) and in 1613 in the Lexicon philosophicum by Rudolf Göckel (Goclenius).

The first occurrence in English of ontology as recorded by the OED (Oxford English Dictionary, online ion, 2008) came in Archeologia Philosophica Nova or New Principles of Philosophy by Gideon Harvey.

Overview[]

What ontologies in both information science and philosophy have in common is the attempt to represent entities, ideas and events, with all their interdependent properties and relations, according to a system of categories. In both fields, there is considerable work on problems of ontology engineering (e.g., Quine and Kripke in philosophy, Sowa and Guarino in computer science),[4] and debates concerning to what extent normative ontology is possible (e.g., foundationalism and coherentism in philosophy, BFO and Cyc in artificial intelligence). Applied ontology is considered a spiritual successor to prior work in philosophy, however many current efforts are more concerned with establishing controlled vocabularies of narrow domains than first principles, the existence of fixed essences or whether enduring objects (e.g., perdurantism and endurantism) may be ontologically more primary than processes.

Every field uses ontological assumptions to frame explicit theories, research and applications. For instance, the definition and ontology of economics is a primacy concern in Marxist economics,[5] but also in other subfields of economics.[6] An example of economics relying on information science occurs in cases where a simulation or model is intended to enable economic decisions, such as determining what capital assets are at risk and by how much (see risk management).

Artificial intelligence has retained the most attention regarding applied ontology in subfields like natural language processing within machine translation and knowledge representation, but ontology ors are being used often in a range of fields like education without the intent to contribute to AI.[7]

History[]

Ontologies arise out of the branch of philosophy known as metaphysics, which deals with questions like "what exists?" and "what is the nature of reality?". One of five traditional branches of philosophy, metaphysics, is concerned with exploring existence through properties, entities and relations such as those between particulars and universals, intrinsic and extrinsic properties, or essence and existence. Metaphysics has been an ongoing topic of discussion since recorded history.

Since the mid-1970s, researchers in the field of artificial intelligence (AI) have recognized that knowledge engineering is the key to building large and powerful AI systems. AI researchers argued that they could create new ontologies as computational models that enable certain kinds of automated reasoning, which was only marginally successful. In the 1980s, the AI community began to use the term ontology to refer to both a theory of a modeled world and a component of knowledge-based systems. In particular, David Powers introduced the word ontology to AI to refer to real world or robotic grounding,[8][9][10] publishing in 1990 literature reviews emphasizing grounded ontology in association with the call for papers for a AAAI Summer Symposium Machine Learning of Natural Language and Ontology, with an expanded version published in SIGART Bulletin and included as a preface to the proceedings.[11] Some researchers, drawing inspiration from philosophical ontologies, viewed computational ontology as a kind of applied philosophy.[12]

In 1993, the widely cited web page and paper "Toward Principles for the Design of Ontologies Used for Knowledge Sharing" by Tom Gruber[13] used ontology as a technical term in computer science closely related to earlier idea of semantic networks and taxonomies. Gruber introduced the term as a specification of a conceptualization:

An ontology is a description (like a formal specification of a program) of the concepts and relationships that can formally exist for an agent or a community of agents. This definition is consistent with the usage of ontology as set of concept definitions, but more general. And it is a different sense of the word than its use in philosophy.[14]

Attempting to distance ontologies from taxonomies and similar efforts in knowledge modeling that rely on classes and inheritance, Gruber stated (1993):

Ontologies are often equated with taxonomic hierarchies of classes, class definitions, and the subsumption relation, but ontologies need not be limited to these forms. Ontologies are also not limited to conservative definitions — that is, definitions in the traditional logic sense that only introduce terminology and do not add any knowledge about the world.[15] To specify a conceptualization, one needs to state axioms that do constrain the possible interpretations for the defined terms.[16]

As refinement of Gruber's definition Feilmayr and Wöß (2016) stated: "An ontology is a formal, explicit specification of a shared conceptualization that is characterized by high semantic expressiveness required for increased complexity."[17]

Components[]

Contemporary ontologies share many structural similarities, regardless of the language in which they are expressed. Most ontologies describe individuals (instances), classes (concepts), attributes and relations. In this section each of these components is discussed in turn.

Common components of ontologies include:

Individuals
Instances or objects (the basic or "ground level" objects)
Classes
Sets, collections, concepts, classes in programming, types of objects or kinds of things
Attributes
Aspects, properties, features, characteristics or parameters that objects (and classes) can have
Relations
Ways in which classes and individuals can be related to one another
Function terms
Complex structures formed from certain relations that can be used in place of an individual term in a statement
Restrictions
Formally stated descriptions of what must be true in order for some assertion to be accepted as input
Rules
Statements in the form of an if-then (antecedent-consequent) sentence that describe the logical inferences that can be drawn from an assertion in a particular form
Axioms
Assertions (including rules) in a logical form that together comprise the overall theory that the ontology describes in its domain of application. This definition differs from that of "axioms" in generative grammar and formal logic. In those disciplines, axioms include only statements asserted as a priori knowledge. As used here, "axioms" also include the theory derived from axiomatic statements
Events
The changing of attributes or relations

Ontologies are commonly encoded using ontology languages.

Types[]

Domain ontology[]

A domain ontology (or domain-specific ontology) represents concepts which belong to a realm of the world, such as biology or politics. Each domain ontology typically models domain-specific definitions of terms. For example, the word card has many different meanings. An ontology about the domain of poker would model the "playing card" meaning of the word, while an ontology about the domain of computer hardware would model the "punched card" and "video card" meanings.

Since domain ontologies are written by different people, they represent concepts in very specific and unique ways, and are often incompatible within the same project. As systems that rely on domain ontologies expand, they often need to merge domain ontologies by hand-tuning each entity or using a combination of software merging and hand-tuning. This presents a challenge to the ontology designer. Different ontologies in the same domain arise due to different languages, different intended usage of the ontologies, and different perceptions of the domain (based on cultural background, education, ideology, etc.).

At present, merging ontologies that are not developed from a common upper ontology is a largely manual process and therefore time-consuming and expensive. Domain ontologies that use the same upper ontology to provide a set of basic elements with which to specify the meanings of the domain ontology entities can be merged with less effort. There are studies on generalized techniques for merging ontologies,[18] but this area of research is still ongoing, and it's a recent event to see the issue sidestepped by having multiple domain ontologies using the same upper ontology like the OBO Foundry.

Upper ontology[]

An upper ontology (or foundation ontology) is a model of the commonly shared relations and objects that are generally applicable across a wide range of domain ontologies. It usually employs a core glossary that overarches the terms and associated object descriptions as they are used in various relevant domain ontologies.

Standardized upper ontologies available for use include BFO, BORO method, Dublin Core, GFO, Cyc, SUMO, UMBEL, the Unified Foundational Ontology (UFO),[19] and DOLCE.[20][21] WordNet has been considered an upper ontology by some and has been used as a linguistic tool for learning domain ontologies.[22]

Hybrid ontology[]

The Gellish ontology is an example of a combination of an upper and a domain ontology.

Visualization[]

A survey of ontology visualization methods is presented by Katifori et al.[23] An updated survey of ontology visualization methods and tools was published by Dudás et al.[24] The most established ontology visualization methods, namely indented tree and graph visualization are evaluated by Fu et al.[25] A visual language for ontologies represented in OWL is specified by the Visual Notation for OWL Ontologies (VOWL).[26]

Engineering[]

Ontology engineering (also called ontology building) is a set of tasks related to the development of ontologies for a particular domain.[27] It is a subfield of knowledge engineering that studies the ontology development process, the ontology life cycle, the methods and methodologies for building ontologies, and the tools and languages that support them.[28][29]

Ontology engineering aims to make explicit the knowledge contained in software applications, and organizational procedures for a particular domain. Ontology engineering offers a direction for overcoming semantic obstacles, such as those related to the definitions of business terms and software classes. Known challenges with ontology engineering include:

  1. Ensuring the ontology is current with domain knowledge and term use
  2. Providing sufficient specificity and concept coverage for the domain of interest, thus minimizing the content completeness problem
  3. Ensuring the ontology can support its use cases

Editors[]

Ontology ors are applications designed to assist in the creation or manipulation of ontologies. It is common for ontology ors to use one or more ontology languages.

Aspects of ontology ors include: visual navigation possibilities within the knowledge model, inference engines and information extraction; support for modules; the import and export of foreign knowledge representation languages for ontology matching; and the support of meta-ontologies such as OWL-S, Dublin Core, etc.[30]

Name Written in License Features Publisher/creator
a.k.a. software[31] Ontology, taxonomy and thesaurus management software The Synercon Group
Anzo for Excel[32] Includes an RDFS and OWL ontology or within Excel; generates ontologies from Excel spreadsheets Cambridge Semantics
Be Informed Suite Commercial tool for building large ontology based applications. Includes visual ors, inference engines, export to standard formats
CENtree Java Commercial Web based client-server ontology management tool for life sciences, supports OWL, RDFS, OBO SciBite
Chimaera Other web service Stanford University
CmapTools Java based Ontology Editor (COE) ontology or Supports numerous formats Florida Institute for Human and Machine Cognition
dot15926 Editor Python? Open source ontology or for data compliant to engineering ontology standard ISO 15926. Allows Python scripting and pattern-based data analysis. Supports extensions.
EMFText OWL2 Manchester Editor[33] Eclipse-based open-source Pellet integration
Enterprise Architect along with UML modeling, supports OMG's Ontology Definition MetaModel which includes OWL and RDF Sparx Systems
Fluent Editor ontology or for OWL and SWRL with Controlled Natural Language (Controlled English). Supports OWL, RDF, DL and Functional rendering, unlimited imports and built-in reasoning services.
Gra.fo[34] Free and Commercial A visual, collaborative and real time ontology and knowledge graph schema or. Features include sharing documents, commenting, search and tracking history. Support W3C Semantic Web standards: RDF, RDFS, OWL and also Property Graph schemas. Capsenta
HOZO Java graphical or especially created to produce heavy-weight and well thought out ontologies Osaka University and Enegate Co, ltd.
Java Ontology Editor (JOE)[35] Java Can be used to create and browse ontologies, and construct ontology based queries. Incorporates abstraction mechanisms that enable users to manage large ontologies Center for Information Technology, Department of Electrical and Computer Engineering, University of South Carolina
KAON open source single user and server based solutions possible FZI/AIFB Karlsruhe
KMgen Ontology or for the KM language. km: The Knowledge Machine
Knoodl Free web application/service that is an ontology or, wiki, and ontology registry. Supports creation of communities where members can collaboratively import, create, discuss, document and publish ontologies. Supports OWL, RDF, RDFS, and SPARQL queries. Revelytix, Inc..
Menthor Editor An ontology engineering tool for dealing with OntoUML. It also includes OntoUML syntax validation, Alloy simulation, Anti-Pattern verification, and transformations from OntoUML to OWL, SBVR and Natural Language (Brazilian Portuguese)
Model Futures IDEAS AddIn free A plug-in for Enterprise Architect] that allows IDEAS Group 4D ontologies to be developed using a UML profile
Model Futures OWL Editor Free Able to work with very large OWL files (e.g. Cyc) and has extensive import and export capabilities (inc. UML, Thesaurus Descriptor, MS Word, CA ERwin Data Modeler, CSV, etc.)
myWeb Java mySQL connection, bundled with applet that allows online browsing of ontologies (including OBO)
Neologism built on Drupal open source Web-based, supports RDFS and a subset of OWL
NeOn Toolkit Eclipse-based open source OWL support, several import mechanisms, support for reuse and management of networked ontologies, visualization, etc. NeOn Project
OBIS Web based user interface that allows users to input ontology instances that can be accessed via SPARQL endpoint
OBO-Edit Java open source downloadable, developed by the Gene Ontology Consortium for ing biological ontologies. OBO-Edit is no longer actively developed [36] Gene Ontology Consortium
Ontosight Free and Commercial Machine learning-based auto-scaling biomedical ontology combining all public biomedical ontologies[37] Innoplexus
OntoStudio Eclipse downloadable, support for RDF(S), OWL and ObjectLogic (derived from F-Logic), graphical rule or, visualizations semafora systems
Ontolingua Web service Stanford University
ONTOLIS[38] Commercial Collaborative web application for managing ontologies and knowledge engineering, web-browser-based graphical rules or, sophisticated search and export interface. Web service available to link ontology information to existing data ONTOLIS
Open Semantic Framework (OSF) an integrated software stack using semantic technologies for knowledge management, which includes an ontology or
OWLGrEd A graphical ontology or, easy-to-use
PoolParty Thesaurus Server Commercial ontology, taxonomy and thesaurus management software, fully based on standards like RDFS, SKOS and SPARQL, integrated with Virtuoso Universal Server Semantic Web Company
Protégé[39] Java open source downloadable, supports OWL, many sample ontologies Stanford University
ScholOnto[40] net-centric representations of research
Semantic Turkey[41][42] Firefox extension - based on Java for managing ontologies and acquiring new knowledge from the Web developed at University of Rome, Tor Vergata
Sigma knowledge engineering environment is a system primarily for development of the Suggested Upper Merged Ontology
Swoop[43] Java open source downloadable, OWL Ontology browser and or University of Maryland
Semaphore Ontology Manager Commercial ontology, taxonomy and thesaurus management software. Tool to manage the entire "build - enhance - review - maintain" ontology lifecycle. Smartlogic Semaphore Limited
Synaptica Ontology, taxonomy and thesaurus management software. Web based, supports OWL and SKOS. Synaptica, LLC.
TopBraid Composer Eclipse-based downloadable, full support for RDFS and OWL, built-in inference engine, SWRL or and SPARQL queries, visualization, import of XML and UML TopQuadrant
Transinsight Editor especially designed for creating text mining ontologies and part of GoPubMed.org
WebODE[44][45] Web service Technical University of Madrid
TwoUse Toolkit Eclipse-based open source model-driven ontology ing environment especially designed for software engineers
Thesaurus Master Manages creation and use of ontologies for use in data management and semantic enrichment by enterprise, government, and scholarly publishers.
TODE .Net Tool for Ontology Development and Editing
VocBench[46] Collaborative Web Platform for Management of SKOS thesauri, OWL ontologies and OntoLex lexicons, now in its third incarnation supported by the ISA2 program of the EU originally developed on a joint effort between University of Rome Tor Vergata and the Food and the Agriculture Organization of the United Nations: FAO

Learning[]

Ontology learning is the automatic or semi-automatic creation of ontologies, including extracting a domain's terms from natural language text. As building ontologies manually is extremely labor-intensive and time-consuming, there is great motivation to automate the process. Information extraction and text mining have been explored to automatically link ontologies to documents, for example in the context of the BioCreative challenges.[47]

Languages[]

An ontology language is a formal language used to encode an ontology. There are a number of such languages for ontologies, both proprietary and standards-based:

Published examples[]

The W3C Linking Open Data community project coordinates attempts to converge different ontologies into worldwide Semantic Web.

Libraries[]

The development of ontologies has led to the emergence of services providing lists or directories of ontologies called ontology libraries.

The following are libraries of human-selected ontologies.

The following are both directories and search engines.

Examples of applications[]

In general, ontologies can be used beneficially in several fields.

See also[]

Related philosophical concepts

References[]

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