In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to 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 terms and relational expressions that represent the entities in that subject area. The field which studies ontologies so conceived is sometimes referred to as ''applied ontology''. Every

academic discipline An academic discipline or academic field is a subdivision of knowledge that is taught and researched at the college or university level. Disciplines are defined (in part) and recognized by the academic journals in which research is published, a ...

or field, in creating its terminology, thereby lays the groundwork for an ontology. Each uses ontological assumptions to frame explicit theories, research and applications. Improved ontologies may improve problem solving within that domain,

interoperability Interoperability is a characteristic of a product or system to work with other products or systems. While the term was initially defined for information technology or systems engineering services to allow for information exchange, a broader de ...

of data systems, and discoverability of data. Translating research papers within every field is a problem made easier when experts from different countries maintain a

controlled vocabulary A controlled vocabulary provides a way to organize knowledge for subsequent retrieval. Controlled vocabularies are used in subject indexing schemes, subject headings, thesauri, taxonomies and other knowledge organization systems. Controlled v ...

jargon Jargon, or technical language, is the specialized terminology associated with a particular field or area of activity. Jargon is normally employed in a particular Context (language use), communicative context and may not be well understood outside ...

between each of their languages. For instance, the definition and ontology of economics is a primary concern in

Marxist economics Marxian economics, or the Marxian school of economics, is a Heterodox economics, heterodox school of political economic thought. Its foundations can be traced back to Karl Marx, Karl Marx's Critique of political economy#Marx's critique of politi ...

, but also in other subfields of economics. 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 asset A capital asset is defined as property of any kind held by an assessee. It need not be connected to the assesse’s business or profession. The term encompasses all kinds of property, movable or immovable, tangible or intangible, fixed or circula ...

s are at risk and by how much (see

risk management Risk management is the identification, evaluation, and prioritization of risks, followed by the minimization, monitoring, and control of the impact or probability of those risks occurring. Risks can come from various sources (i.e, Threat (sec ...

). What ontologies in both information science and

philosophy Philosophy ('love of wisdom' in Ancient Greek) is a systematic study of general and fundamental questions concerning topics like existence, reason, knowledge, Value (ethics and social sciences), value, mind, and language. It is a rational an ...

have in common is the attempt to represent entities, including both objects 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 In computer science, information science and systems engineering, ontology engineering is a field which studies the methods and methodologies for building Ontology (information science), ontologies, which encompasses a representation, formal nami ...

(e.g.,

Quine Quine may refer to: * Quine (computing), a program that produces its source code as output * Quine's paradox, in logic * Quine (surname), people with the surname ** Willard Van Orman Quine (1908–2000), American philosopher and logician See al ...

and

Kripke Kripke is a surname. Notable people with the surname include: * Dorothy K. Kripke (1912–2000), American author of Jewish educational books, and the mother of Saul Kripke * Eric Kripke (born 1974), American television writer, director, and produc ...

in philosophy,

Sowa The SoWa Art & Design District (South of Washington) in the South End of Boston, Massachusetts, USA, is a community of artist studios, contemporary art galleries, boutiques, design showrooms, and restaurants. It features the SoWa Open Market, t ...

and Guarino in information science), and debates concerning to what extent

normative Normativity is the phenomenon in human societies of designating some actions or outcomes as good, desirable, or permissible, and others as bad, undesirable, or impermissible. A Norm (philosophy), norm in this sense means a standard for evaluatin ...

ontology is possible (e.g.,

foundationalism Foundationalism concerns philosophical theories of knowledge resting upon non-inferential justified belief, or some secure foundation of certainty such as a conclusion inferred from a basis of sound premises.Simon Blackburn, ''The Oxford Dict ...

and

coherentism In philosophical epistemology, there are two types of coherentism: the coherence theory of truth, and the coherence theory of justification (also known as epistemic coherentism). Coherent truth is divided between an anthropological approach, w ...

in philosophy, BFO and

Cyc Cyc (pronounced ) is a long-term artificial intelligence (AI) project that aims to assemble a comprehensive ontology and knowledge base that spans the basic concepts and rules about how the world works. Hoping to capture common sense knowledge ...

in artificial intelligence). Applied ontology is considered by some as a successor to prior work in philosophy. However many current efforts are more concerned with establishing

controlled vocabularies A controlled vocabulary provides a way to organize knowledge for subsequent retrieval. Controlled vocabularies are used in subject indexing schemes, subject headings, thesauri, taxonomies and other knowledge organization systems. Controlled vo ...

of narrow domains than with philosophical

first principles In philosophy and science, a first principle is a basic proposition or assumption that cannot be deduced from any other proposition or assumption. First principles in philosophy are from first cause attitudes and taught by Aristotelians, and nuan ...

, or with questions such as the mode of existence of fixed essences or whether enduring objects (e.g.,

perdurantism Perdurantism or perdurance theory is a philosophical theory of persistence and identity.Temporal parts

and

endurantism Endurantism or endurance theory is a philosophical theory of persistence and identity. According to the endurantist view, material objects are persisting three-dimensional individuals wholly present at every moment of their existence, which goes ...

) may be ontologically more primary than

process A process is a series or set of activities that interact to produce a result; it may occur once-only or be recurrent or periodic. Things called a process include: Business and management * Business process, activities that produce a specific s ...

es.

Artificial intelligence Artificial intelligence (AI) is the capability of computer, computational systems to perform tasks typically associated with human intelligence, such as learning, reasoning, problem-solving, perception, and decision-making. It is a field of re ...

has retained considerable attention regarding applied ontology in subfields like

natural language processing Natural language processing (NLP) is a subfield of computer science and especially artificial intelligence. It is primarily concerned with providing computers with the ability to process data encoded in natural language and is thus closely related ...

within

machine translation Machine translation is use of computational techniques to translate text or speech from one language to another, including the contextual, idiomatic and pragmatic nuances of both languages. Early approaches were mostly rule-based or statisti ...

and

knowledge representation Knowledge representation (KR) aims to model information in a structured manner to formally represent it as knowledge in knowledge-based systems whereas knowledge representation and reasoning (KRR, KR&R, or KR²) also aims to understand, reason, and ...

, but ontology editors are being used often in a range of fields, including biomedical informatics,Bioportal
/ref> industry. Such efforts often use ontology editing tools such as

Protégé Mentorship is the patronage, influence, guidance, or direction given by a mentor. A mentor is someone who teaches or gives help and advice to a less experienced and often younger person. In an organizational setting, a mentor influences the perso ...

Ontology in Philosophy

Ontology Ontology is the philosophical study of existence, being. It is traditionally understood as the subdiscipline of metaphysics focused on the most general features of reality. As one of the most fundamental concepts, being encompasses all of realit ...

is a branch of

and intersects areas such as

metaphysics Metaphysics is the branch of philosophy that examines the basic structure of reality. It is traditionally seen as the study of mind-independent features of the world, but some theorists view it as an inquiry into the conceptual framework of ...

epistemology Epistemology is the branch of philosophy that examines the nature, origin, and limits of knowledge. Also called "the theory of knowledge", it explores different types of knowledge, such as propositional knowledge about facts, practical knowle ...

, and

philosophy of language Philosophy of language refers to the philosophical study of the nature of language. It investigates the relationship between language, language users, and the world. Investigations may include inquiry into the nature of Meaning (philosophy), me ...

, as it considers how knowledge, language, and perception relate to the nature of reality.

Metaphysics Metaphysics is the branch of philosophy that examines the basic structure of reality. It is traditionally seen as the study of mind-independent features of the world, but some theorists view it as an inquiry into the conceptual framework of ...

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

particular In metaphysics, particulars or individuals are usually contrasted with ''universals''. Universals concern features that can be exemplified by various different particulars. Particulars are often seen as concrete, spatiotemporal entities as opposed ...

s and

universals In metaphysics, a universal is what particular things have in common, namely characteristics or qualities. In other words, universals are repeatable or recurrent entities that can be instantiated or exemplified by many particular things. For exa ...

intrinsic and extrinsic properties In science and engineering, an intrinsic property is a property of a specified subject that exists itself or within the subject. An extrinsic property is not essential or inherent to the subject that is being characterized. For example, mass i ...

, or

essence Essence () has various meanings and uses for different thinkers and in different contexts. It is used in philosophy and theology as a designation for the property (philosophy), property or set of properties or attributes that make an entity the ...

and

existence Existence is the state of having being or reality in contrast to nonexistence and nonbeing. Existence is often contrasted with essence: the essence of an entity is its essential features or qualities, which can be understood even if one does ...

. Metaphysics has been an ongoing topic of discussion since recorded history.

Etymology

The

compound Compound may refer to: Architecture and built environments * Compound (enclosure), a cluster of buildings having a shared purpose, usually inside a fence or wall ** Compound (fortification), a version of the above fortified with defensive struc ...

word ''ontology'' combines ''

onto In mathematics, a surjective function (also known as surjection, or onto function ) is a function such that, for every element of the function's codomain, there exists one element in the function's domain such that . In other words, for a f ...

-'', from the

Greek Greek may refer to: Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group *Greek language, a branch of the Indo-European language family **Proto-Greek language, the assumed last common ancestor of all kno ...

ὄν, ''on'' ( gen. ὄντος, ''ontos''), i.e. "being; that which is", which is the

present The present is the period of time that is occurring now. The present is contrasted with the past, the period of time that has already occurred; and the future, the period of time that has yet to occur. It is sometimes represented as a hyperplan ...

participle In linguistics, a participle (; abbr. ) is a nonfinite verb form that has some of the characteristics and functions of both verbs and adjectives. More narrowly, ''participle'' has been defined as "a word derived from a verb and used as an adject ...

of the

verb A verb is a word that generally conveys an action (''bring'', ''read'', ''walk'', ''run'', ''learn''), an occurrence (''happen'', ''become''), or a state of being (''be'', ''exist'', ''stand''). In the usual description of English, the basic f ...

εἰμί, ''eimí'', i.e. "to be, I am", and -λογία, ''

-logia ''-logy'' is a suffix in the English language, used with words originally adapted from Ancient Greek ending in ('). The earliest English examples were anglicizations of the French '' -logie'', which was in turn inherited from the Latin '' -lo ...

'', i.e. "logical discourse", see

classical compound Neoclassical compounds are compound words composed from combining forms (which act as affixes or stems) derived from Classical_language#Classical_studies, classical languages (classical Latin or ancient Greek) root (linguistics), roots. Neo-Lati ...

s for this type of word formation. While the

etymology Etymology ( ) is the study of the origin and evolution of words—including their constituent units of sound and meaning—across time. In the 21st century a subfield within linguistics, etymology has become a more rigorously scientific study. ...

is Greek, the oldest extant record of the word itself, the

Neo-Latin Neo-LatinSidwell, Keith ''Classical Latin-Medieval Latin-Neo Latin'' in ; others, throughout. (also known as New Latin and Modern Latin) is the style of written Latin used in original literary, scholarly, and scientific works, first in Italy d ...

form ''ontologia'', appeared in 1606 in the work ''

Ogdoas Scholastica Jacob Lorhard (; 1561 – 19 May 1609) was a German philosopher and pedagogue based in St. Gallen, Switzerland. Biography Lorhard was born in Münsingen, in the Duchy of Württemberg. He studied at the University of Tübingen. In 1603 he b ...

'' by

Jacob Lorhard Jacob Lorhard (; 1561 – 19 May 1609) was a German philosopher and pedagogue based in St. Gallen, Switzerland. Biography Lorhard was born in Münsingen, in the Duchy of Württemberg. He studied at the University of Tübingen. In 1603 he be ...

(''Lorhardus'') and in 1613 in the '' Lexicon philosophicum'' by

Rudolf Göckel Rudolph Goclenius the Elder (; born ''Rudolf Gockel'' or ''Göckel''; 1 March 1547 – 8 June 1628) was a German scholastic philosopher. He is sometimes credited with coining the term ''psychology'' in 1590, though the term had been used by Pier ...

(''Goclenius''). The first occurrence in English of ''ontology'' as recorded by the ''OED'' (''

Oxford English Dictionary The ''Oxford English Dictionary'' (''OED'') is the principal historical dictionary of the English language, published by Oxford University Press (OUP), a University of Oxford publishing house. The dictionary, which published its first editio ...

'', online edition, 2008) came in '' Archeologia Philosophica Nova'' or ''New Principles of Philosophy'' by Gideon Harvey.

Formal Ontology

Since the mid-1970s, researchers in the field of

artificial intelligence Artificial intelligence (AI) is the capability of computer, computational systems to perform tasks typically associated with human intelligence, such as learning, reasoning, problem-solving, perception, and decision-making. It is a field of re ...

(AI) have recognized that

knowledge engineering Knowledge engineering (KE) refers to all aspects involved in knowledge-based systems. Background Expert systems One of the first examples of an expert system was MYCIN, an application to perform medical diagnosis. In the MYCIN example, the ...

is the key to building large and powerful AI systems. AI researchers argued that they could create new ontologies as

computational model A computational model uses computer programs to simulate and study complex systems using an algorithmic or mechanistic approach and is widely used in a diverse range of fields spanning from physics, engineering, chemistry and biology to economics ...

s that enable certain kinds of

automated reasoning In computer science, in particular in knowledge representation and reasoning and metalogic, the area of automated reasoning is dedicated to understanding different aspects of reasoning. The study of automated reasoning helps produce computer progr ...

, 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 A knowledge-based system (KBS) is a computer program that reasons and uses a knowledge base to solve complex problems. Knowledge-based systems were the focus of early artificial intelligence researchers in the 1980s. The term can refer to a b ...

. In particular, David Powers introduced the word ''ontology'' to AI to refer to real world or robotic grounding, 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. Some researchers, drawing inspiration from philosophical ontologies, viewed computational ontology as a kind of applied philosophy. In 1993, the widely cited web page and paper "Toward Principles for the Design of Ontologies Used for Knowledge Sharing" by

Tom Gruber Thomas Robert Gruber (born 1959) is an American computer scientist, inventor, and entrepreneur with a focus on systems for knowledge sharing and collective intelligence. He did foundational work in ontology engineering and is well known for his de ...

used ''ontology'' as a technical term in

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

closely related to earlier idea of

semantic networks A semantic network, or frame network is a knowledge base that represents semantic relations between concepts in a network. This is often used as a form of knowledge representation. It is a directed or undirected graph consisting of vertices, ...

and

taxonomies image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme o ...

. 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.

Attempting to distance ontologies from taxonomies and similar efforts in

knowledge modeling Knowledge modeling is a process of creating a computer interpretable model of knowledge or standard specifications about a kind of process and/or about a kind of facility or product. The resulting knowledge model can only be computer interpretable ...

that rely on classes and

inheritance Inheritance is the practice of receiving private property, titles, debts, entitlements, privileges, rights, and obligations upon the death of an individual. The rules of inheritance differ among societies and have changed over time. Offi ...

, 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 (Enderton, 1972). To specify a conceptualization, one needs to state axioms that ''do'' constrain the possible interpretations for the defined terms.

Recent experimental ontology frameworks have also explored resonance-based AI-human co-evolution structures, such as IAMF (Illumination AI Matrix Framework). Though not yet widely adopted in academic discourse, such models propose phased approaches to ethical harmonization and structural emergence. 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."

Formal Ontology 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.

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 Card or The Card may refer to: Common uses * Plastic cards of various types: **Bank card **Credit card **Debit card **Payment card * Playing card, used in games * Printed circuit board, or card * Greeting card, given on special occasions Arts an ...

'' has many different meanings. An ontology about the domain of

poker Poker is a family of Card game#Comparing games, comparing card games in which Card player, players betting (poker), wager over which poker hand, hand is best according to that specific game's rules. It is played worldwide, with varying rules i ...

would model the "

playing card A playing card is a piece of specially prepared card stock, heavy paper, thin cardboard, plastic-coated paper, cotton-paper blend, or thin plastic that is marked with distinguishing motifs. Often the front (face) and back of each card has a f ...

" meaning of the word, while an ontology about the domain of

computer hardware Computer hardware includes the physical parts of a computer, such as the central processing unit (CPU), random-access memory (RAM), motherboard, computer data storage, graphics card, sound card, and computer case. It includes external devices ...

would model the "

punched card A punched card (also punch card or punched-card) is a stiff paper-based medium used to store digital information via the presence or absence of holes in predefined positions. Developed over the 18th to 20th centuries, punched cards were widel ...

" and "

video card A graphics card (also called a video card, display card, graphics accelerator, graphics adapter, VGA card/VGA, video adapter, display adapter, or colloquially GPU) is a computer expansion card that generates a feed of graphics output to a displa ...

" 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 In information science, an upper ontology (also known as a top-level ontology, upper model, or foundation ontology) is an ontology (in the sense used in information science) that consists of very general terms (such as "object", "property", "rel ...

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, but this area of research is still ongoing, and it is a recent event to see the issue sidestepped by having multiple domain ontologies using the same upper ontology like the

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

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 A glossary (from , ''glossa''; language, speech, wording), also known as a vocabulary or clavis, is an alphabetical list of Term (language), terms in a particular domain of knowledge with the definitions for those terms. Traditionally, a gloss ...

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 BORO (Business Objects Reference Ontology) is an approach to developing ontological or semantic models for large complex operational applications that consists of a top ontology as well as a process for constructing the ontology. It was originally ...

Dublin Core 140px, Logo of DCMI, maintenance agency for Dublin Core Terms The Dublin Core vocabulary, also known as the Dublin Core Metadata Terms (DCMT), is a general purpose metadata vocabulary for describing resources of any type. It was first developed ...

, GFO,

SUMO is a form of competitive full-contact wrestling where a ''rikishi'' (wrestler) attempts to force his opponent out of a circular ring (''dohyō'') or into touching the ground with any body part other than the soles of his feet (usually by th ...

UMBEL UMBEL (Upper Mapping and Binding Exchange Layer) is a logically organized knowledge graph of 34,000 concepts and entity types that can be used in information science for relating information from disparate sources to one another. It was retired ...

, and

DOLCE Dolce may refer to: Places *Dolcè, a municipality in Italy *Dolce (Plzeň-South District), a municipality and village in the Czech Republic *Dolce, a village and part of Jesenice (Příbram District) in the Czech Republic People * Dolce (sur ...

WordNet WordNet is a lexical database of semantic relations between words that links words into semantic relations including synonyms, hyponyms, and meronyms. The synonyms are grouped into ''synsets'' with short definitions and usage examples. It can thu ...

has been considered an upper ontology by some and has been used as a linguistic tool for learning domain ontologies.

Hybrid ontology

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") b ...

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. An updated survey of ontology visualization methods and tools was published by Dudás et al. The most established ontology visualization methods, namely indented tree and graph visualization are evaluated by Fu et al. A visual language for ontologies represented in

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 ...

is specified by the ''Visual Notation for OWL Ontologies (VOWL)''.

Engineering

Ontology engineering (also called ontology building) is a set of tasks related to the development of ontologies for a particular domain. It is a subfield of

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. 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: # Ensuring the ontology is ''current'' with

domain knowledge Domain knowledge is knowledge of a specific discipline or field in contrast to general (or domain-independent) knowledge. The term is often used in reference to a more general discipline—for example, in describing a software engineer who has ge ...

and term use # Providing ''sufficient specificity and concept coverage'' for the domain of interest, thus minimizing the content completeness problem # Ensuring the ontology can support its use cases

Editors

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

ontology languages Ontology is the philosophical study of being. It is traditionally understood as the subdiscipline of metaphysics focused on the most general features of reality. As one of the most fundamental concepts, being encompasses all of reality and every ...

. Aspects of ontology editors include: visual navigation possibilities within the

knowledge model Knowledge representation (KR) aims to model information in a structured manner to formally represent it as knowledge in knowledge-based systems whereas knowledge representation and reasoning (KRR, KR&R, or KR²) also aims to understand, reason, and ...

inference engine In the field of artificial intelligence, an inference engine is a software component of an intelligent system that applies logical rules to the knowledge base to deduce new information. The first inference engines were components of expert systems ...

s and information extraction; support for modules; the import and export of foreign

languages for ontology matching; and the support of meta-ontologies such as

OWL-S OWL-S is an ontology built on top of Web Ontology Language (OWL) by the DARPA The Defense Advanced Research Projects Agency (DARPA) is a research and development agency of the United States Department of Defense responsible for the development ...

, etc.

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 Text mining, text data mining (TDM) or text analytics is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extracting information from differe ...

have been explored to automatically link ontologies to documents, for example in the context of the BioCreative challenges.

Research

Epistemological assumptions, which in research asks "What do you know? or "How do you know it?", creates the foundation researchers use when approaching a certain topic or area for potential research. As epistemology is directly linked to knowledge and how we come about accepting certain truths, individuals conducting academic research must understand what allows them to begin theory building. Simply, epistemological assumptions force researchers to question how they arrive at the knowledge they have.

Languages

ontology language In computer science and artificial intelligence, ontology languages are formal languages used to construct ontologies. They allow the encoding of knowledge about specific domains and often include reasoning rules that support the processing of ...

is a

formal language In logic, mathematics, computer science, and linguistics, a formal language is a set of strings whose symbols are taken from a set called "alphabet". The alphabet of a formal language consists of symbols that concatenate into strings (also c ...

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

Common Algebraic Specification Language The Common Algebraic Specification Language (CASL) is a general-purpose specification language based on first-order logic with induction. Partial functions and subsorting are also supported. Overview CASL has been designed by CoFI, the Common ...

is a general logic-based specification language developed within the IFIP working group 1.3 "Foundations of System Specifications" and is a ''de facto'' standard language for software specifications. It is now being applied to ontology specifications in order to provide modularity and structuring mechanisms. *

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 ...

is ISO standard 24707, a specification of a family of ontology languages that can be accurately translated into each other. * The

project has its own ontology language called

CycL CycL in computer science and artificial intelligence, is an ontology language used by Douglas Lenat's Cyc artificial intelligence project. Ramanathan V. Guha was instrumental in designing early versions of the language. A close CycL variant exi ...

, based on

first-order predicate calculus First-order logic, also called predicate logic, predicate calculus, or quantificational logic, is a collection of formal systems used in mathematics, philosophy, linguistics, and computer science. First-order logic uses quantified variables over ...

with some higher-order extensions. *

DOGMA Dogma, in its broadest sense, is any belief held definitively and without the possibility of reform. It may be in the form of an official system of principles or doctrines of a religion, such as Judaism, Roman Catholicism, Protestantism, or Islam ...

(Developing Ontology-Grounded Methods and Applications) adopts the fact-oriented modeling approach to provide a higher level of semantic stability. * The

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 Systems ...

is a

software engineering Software engineering is a branch of both computer science and engineering focused on designing, developing, testing, and maintaining Application software, software applications. It involves applying engineering design process, engineering principl ...

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

first-order logic First-order logic, also called predicate logic, predicate calculus, or quantificational logic, is a collection of formal systems used in mathematics, philosophy, linguistics, and computer science. First-order logic uses quantified variables over ...

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 (computing), list (Tree (data structure), tree-structured) data. S-expressions were invented ...

s. SUO-KIF is a derivative version supporting the

Suggested Upper Merged Ontology The Suggested Upper Merged Ontology (SUMO) is an upper ontology intended as a foundation ontology for a variety of computer information processing systems. SUMO defines a hierarchy of ''classes'' and related rules and relationships. These are exp ...

. * MOF and UML are standards of the

OMG OMG may refer to: Abbreviations * ''Oh my God!'' (sometimes also ''Oh my Goodness!'' or ''Oh my Gosh!'') is a common abbreviation meaning shock or surprise, often used in SMS messages and Internet communications * OMG is the IATA code for Omega ...

* Olog is a

category theoretic Category theory is a general theory of mathematical structures and their relations. It was introduced by Samuel Eilenberg and Saunders Mac Lane in the middle of the 20th century in their foundational work on algebraic topology. Category theory ...

approach to ontologies, emphasizing translations between ontologies using

functor In mathematics, specifically category theory, a functor is a Map (mathematics), mapping between Category (mathematics), categories. Functors were first considered in algebraic topology, where algebraic objects (such as the fundamental group) ar ...

s. * OBO, a language used for biological and biomedical ontologies. * OntoUML is an ontologically well-founded profile of UML for conceptual modeling of domain ontologies. *

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

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 ...

, 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) and lipophilic (mixes with other oils). Oils are usually flammable and surface active. Most oils are unsaturate ...

, 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 vario ...

. OWL is intended to be used over the

World Wide Web The World Wide Web (WWW or simply the Web) is an information system that enables Content (media), content sharing over the Internet through user-friendly ways meant to appeal to users beyond Information technology, IT specialists and hobbyis ...

, 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 Technology, technologically accessible, Economics, economically feasible and Culture, culturally Sustainability, sustainable and help us to satisfy our needs and want ...

s, and identified by

URI Uri may refer to: Places * Canton of Uri, a canton in Switzerland * Úri, a village and commune in Hungary * Uri, Iran, a village in East Azerbaijan Province * Uri, Jammu and Kashmir, a town in India * Uri (island), off Malakula Island in V ...

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, in r ...

(RIF) and

F-Logic F-logic (Frame logic) is a knowledge representation and ontology language. It combines the advantages of conceptual modeling with Object-oriented programming, object-oriented, Frame (artificial intelligence), frame-based languages, and offers a Decl ...

combine ontologies and rules. * Semantic Application Design Language (SADL) captures a subset of the expressiveness of

, using an English-like language entered via an

Eclipse An eclipse is an astronomical event which occurs when an astronomical object or spacecraft is temporarily obscured, by passing into the shadow of another body or by having another body pass between it and the viewer. This alignment of three ...

Plug-in. *

SBVR The Semantics of Business Vocabulary and Business Rules (SBVR) is an adopted standard of the Object Management Group (OMG) intended to be the basis for formal and detailed natural language declarative description of a complex entity, such as a bus ...

(Semantics of Business Vocabularies and Rules) is an OMG standard adopted in industry to build ontologies. *

TOVE Project The TOVE project ("Toronto Virtual Enterprise") is a project to develop an ontology (information science), ontological framework for enterprise integration (EI) based on and suited for enterprise modeling.Terje Totland (1997)5.2.3 Toronto Virtual ...

, TOronto Virtual Enterprise project

Published examples

Arabic Ontology Arabic Ontology is a linguistic ontology for the Arabic language, which can be used as an Arabic WordNet with ontologically clean content. People use it also as a tree (i.e. classification) of the concepts/meanings of the Arabic terms. It is a f ...

, a linguistic ontology for Arabic, which can be used as an Arabic Wordnet but with ontologically-clean content. * AURUM – Information Security Ontology, An ontology for

information security Information security is the practice of protecting information by mitigating information risks. It is part of information risk management. It typically involves preventing or reducing the probability of unauthorized or inappropriate access to data ...

knowledge sharing, enabling users to collaboratively understand and extend the domain knowledge body. It may serve as a basis for automated information security risk and compliance management. *

BabelNet BabelNet is a multilingual lexical-semantic knowledge graph, ontology and encyclopedic dictionary developed at the NLP group of the Sapienza University of Rome under the supervision of Roberto Navigli.R. Navigli and S. P Ponzetto. 2012BabelNet: ...

, a very large multilingual semantic network and ontology, lexicalized in many languages *

Basic Formal Ontology Basic Formal Ontology (BFO) is a Upper ontology, top-level ontology developed by Barry Smith (academic), Barry Smith and his associates for the purposes of promoting interoperability among domain ontologies built in its terms through a process of ...

, a formal upper ontology designed to support scientific research * BioPAX, an ontology for the exchange and interoperability of biological pathway (cellular processes) data * BMO, an e-Business Model Ontology based on a review of enterprise ontologies and business model literature * SSBMO, a Strongly Sustainable Business Model Ontology based on a review of the systems based natural and social science literature (including business). Includes critique of and significant extensions to the Business Model Ontology (BMO). * CCO and GexKB, Application Ontologies (APO) that integrate diverse types of knowledge with the Cell Cycle Ontology (CCO) and the Gene Expression Knowledge Base (GexKB) * CContology (Customer Complaint Ontology), an e-business ontology to support online customer complaint management *

CIDOC Conceptual Reference Model The CIDOC Conceptual Reference Model (CRM) provides an extensible ontology for concepts and information in cultural heritage and museum documentation. It is the international standard (ISO 21127:2023) for the controlled exchange of cultural he ...

, an ontology for

cultural heritage Cultural heritage is the heritage of tangible and intangible heritage assets of a group or society that is inherited from past generations. Not all heritages of past generations are "heritage"; rather, heritage is a product of selection by socie ...

* COSMO, a Foundation Ontology (current version in OWL) that is designed to contain representations of all of the primitive concepts needed to logically specify the meanings of any domain entity. It is intended to serve as a basic ontology that can be used to translate among the representations in other ontologies or databases. It started as a merger of the basic elements of the OpenCyc and SUMO ontologies, and has been supplemented with other ontology elements (types, relations) so as to include representations of all of the words in the Longman dictionary

defining vocabulary A defining vocabulary is a list of words used by lexicographers to write dictionary definitions. The underlying principle goes back to Samuel Johnson's notion that words should be defined using 'terms less abstruse than that which is to be explain ...

. *

Computer Science Ontology The Computer Science Ontology (CSO) is an automatically generated Taxonomy_(general), taxonomy of research topics in the field of Computer Science. It was produced by the Open University in collaboration with Springer Nature by running an informa ...

, an automatically generated ontology of research topics in the field of

, a large Foundation Ontology for formal representation of the universe of discourse *

Disease Ontology The Disease Ontology (DO) is a formal ontology of human disease. ThDisease Ontology projectis hosted at thInstitute for Genome Sciencesat the University of Maryland School of Medicine. The Disease Ontology project was initially developed in 2003 ...

, designed to facilitate the mapping of diseases and associated conditions to particular medical codes *

, a Descriptive Ontology for Linguistic and Cognitive Engineering * Drammar, ontology of drama *

, a simple ontology for documents and publishing * Financial Industry Business Ontology (FIBO), a business conceptual ontology for the financial industry * Foundational, Core and Linguistic Ontologies *

Foundational Model of Anatomy The Foundational Model of Anatomy Ontology (FMA) is a reference ontology for the domain of human anatomy. It is a symbolic representation of the canonical, phenotypic structure of an organism; a spatial-structural ontology of anatomical entities an ...

, an ontology for human anatomy *

Friend of a Friend In sociology, a friend of a friend is a human contact that exists because of a mutual friend. Person C is a friend of a friend of person A when there is a person B that is a friend of both A and C. Thus the human relation "friend of a friend" is ...

, an ontology for describing persons, their activities and their relations to other people and objects *

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 ...

for

genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...

Gellish English dictionary The Gellish English Dictionary-Taxonomy is an example of an open-source “smart” electronic dictionary, in which concepts are arranged in a subtype-supertype hierarchy, thus forming a taxonomy. The dictionary-taxonomy is machine readable. It is ...

, an ontology that includes a dictionary and taxonomy that includes an upper ontology and a lower ontology that focuses on industrial and business applications in engineering, technology and procurement. * Geopolitical ontology, an ontology describing geopolitical information created by

Food and Agriculture Organization The Food and Agriculture Organization of the United Nations; . (FAO) is a specialized agency of the United Nations that leads international efforts to defeat hunger and improve nutrition and food security. Its Latin motto, , translates ...

(FAO). The geopolitical ontology includes names in multiple languages (English, French, Spanish, Arabic, Chinese, Russian and Italian); maps standard coding systems (UN, ISO, FAOSTAT, AGROVOC, etc.); provides relations among territories (land borders, group membership, etc.); and tracks historical changes. In addition, FAO provides web services of geopolitical ontology and a module maker to download modules of the geopolitical ontology into different formats (RDF, XML, and EXCEL). See more information at

FAO Country Profiles The FAO Country Profiles is a multilingual web portal that repackages the Food and Agriculture Organization of the United Nations (FAO) information archive on its global activities in agriculture and food security in a single area and catalogues ...

. * GAO (General Automotive Ontology) – an ontology for the automotive industry that includes 'car' extensions * GOLD, General Ontology for

Linguistic Description In the study of language, description or descriptive linguistics is the work of objectively analyzing and describing how language is actually used (or how it was used in the past) by a speech community. François & Ponsonnet (2013). All aca ...

* GUM (Generalized Upper Model), a linguistically motivated ontology for mediating between clients systems and natural language technology *

IDEAS Group The International Defence Enterprise Architecture Specification for exchange Group (IDEAS Group) is a project involving four nations (plus NATO as observers) and covering MODAF (UK), DoDAF (US), DNDAF (Canada) and the Australian Defence Architec ...

, a formal ontology for enterprise architecture being developed by the Australian, Canadian, UK and U.S. Defence Depts. * Linkbase, a formal representation of the biomedical domain, founded upon Basic Formal Ontology. * LPL, Landmark Pattern Language * NCBO Bioportal, biological and biomedical ontologies and associated tools to search, browse and visualise * NIFSTD Ontologies from the

Neuroscience Information Framework The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/ genomic resources and provides many aut ...

: a modular set of ontologies for the neuroscience domain. * OBO-Edit, an ontology browser for most of the Open Biological and Biomedical Ontologies *

, a suite of interoperable reference ontologies in biology and biomedicine * OMNIBUS Ontology, an ontology of learning, instruction, and instructional design *

Ontology for Biomedical Investigations The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used ...

, an open-access, integrated ontology of biological and clinical investigations * ONSTR, Ontology for Newborn Screening Follow-up and Translational Research, Newborn Screening Follow-up Data Integration Collaborative, Emory University, Atlanta. * Plant Ontology for plant structures and growth/development stages, etc. * POPE, Purdue Ontology for Pharmaceutical Engineering * PRO, the Protein Ontology of the Protein Information Resource, Georgetown University * ProbOnto, knowledge base and ontology of

probability distribution In probability theory and statistics, a probability distribution is a Function (mathematics), function that gives the probabilities of occurrence of possible events for an Experiment (probability theory), experiment. It is a mathematical descri ...

s. * Program abstraction taxonomy * Protein Ontology for

proteomics Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

* RXNO Ontology, for

name reaction A name reaction (or named reaction) is a chemical reaction named after its discoverer(s) or developer(s). Among the tens of thousands of organic reactions that are known, hundreds of such reactions are typically identified by the eponym. Well-know ...

s in chemistry *SCDO, the Sickle Cell Disease Ontology, facilitates data sharing and collaborations within the SDC community, amongst other applications (see list o
SCDO website
. * Schema.org, for embedding structured data into web pages, primarily for the benefit of search engines *

Sequence Ontology The Sequence Ontology (SO) is an ontology Ontology is the philosophical study of existence, being. It is traditionally understood as the subdiscipline of metaphysics focused on the most general features of reality. As one of the most fundamen ...

, for representing genomic feature types found on biological sequences *

SNOMED CT SNOMED CT or SNOMED Clinical Terms is a systematically organized computer-processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. SNOMED CT is considered to be the mo ...

(Systematized Nomenclature of Medicine – Clinical Terms) *

, a formal upper ontology *

Systems Biology Ontology The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling. Motivation The rise of systems biology, seeking to comprehend biological ...

(SBO), for computational models in biology * SWEET, Semantic Web for Earth and Environmental Terminology * SSN/SOSA, The Semantic Sensor Network Ontology (SSN) and Sensor, Observation, Sample, and Actuator Ontology (SOSA) are W3C Recommendation and OGC Standards for describing sensors and their observations. * ThoughtTreasure ontology * TIME-ITEM, Topics for Indexing Medical Education * Uberon, representing

animal Animals are multicellular, eukaryotic organisms in the Biology, biological Kingdom (biology), kingdom Animalia (). With few exceptions, animals heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, ...

anatomical structures *

, a lightweight reference structure of 20,000 subject concept classes and their relationships derived from OpenCyc *

, a lexical reference system * YAMATO, Yet Another More Advanced Top-level Ontology * YSO – General Finnish Ontology The W3C Linking Open Data community project coordinates attempts to converge different ontologies into worldwide

Semantic Web The Semantic Web, sometimes known as Web 3.0, is an extension of the World Wide Web through standards set by the World Wide Web Consortium (W3C). The goal of the Semantic Web is to make Internet data machine-readable. To enable the encoding o ...

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. * COLORE is an open repository of first-order ontologies in

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 ...

with formal links between ontologies in the repository. * DAML Ontology Library maintains a legacy of ontologies in DAML. * Ontology Design Patterns portal is a wiki repository of reusable components and practices for ontology design, and also maintains a list of ''exemplary ontologies''. * Protégé Ontology Library contains a set of OWL, Frame-based and other format ontologies. * SchemaWeb is a directory of RDF schemata expressed in RDFS, OWL and DAML+OIL. The following are both directories and search engines. *

is a suite of interoperable reference ontologies in biology and biomedicine. * Bioportal (ontology repository of NCBO)
Linked Open Vocabularies
* OntoSelect Ontology Library offers similar services for RDF/S, DAML and OWL ontologies. * Ontaria is a "searchable and browsable directory of semantic web data" with a focus on RDF vocabularies with OWL ontologies. (NB Project "on hold" since 2004). * Swoogle is a directory and search engine for all RDF resources available on the Web, including ontologies. * Open Ontology Repository initiative * ROMULUS is a foundational ontology repository aimed at improving semantic interoperability. Currently there are three foundational ontologies in the repository:

, BFO and GFO.

Examples of applications

In general, ontologies can be used beneficially in several fields. * Enterprise applications. A more concrete example is SAPPHIRE (Health care) or ''Situational Awareness and Preparedness for Public Health Incidences and Reasoning Engines'' which is a

semantics Semantics is the study of linguistic Meaning (philosophy), meaning. It examines what meaning is, how words get their meaning, and how the meaning of a complex expression depends on its parts. Part of this process involves the distinction betwee ...

-based

health information system Health informatics combines communications, information technology (IT), and health care to enhance patient care and is at the forefront of the medical technological revolution. It can be viewed as a branch of engineering and applied science. ...

capable of tracking and evaluating situations and occurrences that may affect

public health Public health is "the science and art of preventing disease, prolonging life and promoting health through the organized efforts and informed choices of society, organizations, public and private, communities and individuals". Analyzing the de ...

. *

Geographic information systems A geographic information system (GIS) consists of integrated computer hardware and software that store, manage, analyze, edit, output, and visualize geographic data. Much of this often happens within a spatial database; however, this is not ...

bring together data from different sources and benefit therefore from ontological metadata which helps to connect the semantics of the data. * Domain-specific ontologies are extremely important in biomedical research, which requires named entity disambiguation of various biomedical terms and abbreviations that have the same string of characters but represent different biomedical concepts. For example, CSF can represent Colony Stimulating Factor or Cerebral Spinal Fluid, both of which are represented by the same term, CSF, in biomedical literature. This is why a large number of public ontologies are related to the life sciences. Life science data science tools that fail to implement these types of biomedical ontologies will not be able to accurately determine causal relationships between concepts.

References

External links

* Knowledge Representation at Open Directory Project
Library of ontologies (Archive, Unmaintained)

GoPubMed
using Ontologies for searching
ONTOLOG
(a.k.a.
Ontolog Forum
) - an Open, International, Virtual Community of Practice on Ontology, Ontological Engineering and Semantic Technology

Ontology Summit
- an annual series of events (first started in 2006) that involves the ontology community and communities related to each year's theme chosen for the summit.
Standardization of Ontologies
{{DEFAULTSORT:Ontology (Information Science) Knowledge engineering Technical communication Information science Semantic Web Knowledge representation Knowledge bases Ontology editors