Ontology (information science)

In 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. Each uses ontological assumptions to frame explicit theories, research and applications.
New ontologies may 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] For instance, the definition and ontology of economics is a
primary concern in Marxist economics,[2] but also in other subfields of economics.[3] 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).

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),[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 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. Artificial intelligence has retained the most attention regarding
applied ontology in subfields like natural language processing within machine translation and knowledge
representation, but ontology editors are being used often in a range of fields like education without the
intent to contribute to AI.[5]

Ontology in Philosophy
Ontology is a branch of philosophy and intersects areas such as metaphysics, epistemology, and philosophy
of language, as it considers how knowledge, language, and perception relate to the nature of reality.
Metaphysics 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.

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.[6][7]
While the etymology is Greek, the oldest extant record of the word itself, the Neo-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
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 (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]

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 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 is 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 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.

Aspects of ontology editors 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]

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.[31]

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
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:

Common Algebraic Specification Language 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 is ISO standard 24707, a specification of a family of ontology languages that
can be accurately translated into each other.
The Cyc project has its own ontology language called CycL, based on first-order predicate
calculus with some higher-order extensions.
DOGMA (Developing Ontology-Grounded Methods and Applications) adopts the fact-
oriented modeling approach to provide a higher level of semantic stability.
The Gellish language includes rules for its own extension and thus integrates an ontology
with an ontology language.
IDEF5 is a software engineering method to develop and maintain usable, accurate, domain
ontologies.
KIF is a syntax for first-order logic that is based on S-expressions. SUO-KIF is a derivative
version supporting the Suggested Upper Merged Ontology.
MOF and UML are standards of the OMG
Olog is a category theoretic approach to ontologies, emphasizing translations between
ontologies using functors.
OBO, a language used for biological and biomedical ontologies.
OntoUML is an ontologically well-founded profile of UML for conceptual modeling of domain
ontologies.
OWL is a language for making ontological statements, developed as a follow-on from RDF
and RDFS, as well as earlier ontology language projects including OIL, DAML, and
DAML+OIL. OWL is intended to be used over the World Wide Web, and all its elements
(classes, properties and individuals) are defined as RDF resources, and identified by URIs.
Rule Interchange Format (RIF) and F-Logic combine ontologies and rules.
Semantic Application Design Language (SADL)[32] captures a subset of the expressiveness
of OWL, using an English-like language entered via an Eclipse Plug-in.
SBVR (Semantics of Business Vocabularies and Rules) is an OMG standard adopted in
industry to build ontologies.
TOVE Project, TOronto Virtual Enterprise project

Published examples
Arabic Ontology, a linguistic ontology for Arabic, which can be used as an Arabic Wordnet
but with ontologically-clean content.
AURUM - Information Security Ontology,[33] An ontology for information security 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, a very large multilingual semantic network and ontology, lexicalized in many
languages
Basic Formal Ontology,[34] a formal upper ontology designed to support scientific research
BioPAX,[35] an ontology for the exchange and interoperability of biological pathway (cellular
processes) data
BMO,[36] an e-Business Model Ontology based on a review of enterprise ontologies and
business model literature
SSBMO,[37] 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,[38] 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),[39] an e-business ontology to support online
customer complaint management
CIDOC Conceptual Reference Model, an ontology for cultural heritage[40]
COSMO,[41] 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.
Computer Science Ontology, an automatically generated ontology of research topics in the
field of computer science
Cyc, a large Foundation Ontology for formal representation of the universe of discourse
Disease Ontology,[42] designed to facilitate the mapping of diseases and associated
conditions to particular medical codes
DOLCE, a Descriptive Ontology for Linguistic and Cognitive Engineering[20][21]
Drammar, ontology of drama[43]
Dublin Core, a simple ontology for documents and publishing
Financial Industry Business Ontology (FIBO), a business conceptual ontology for the
financial industry[44]
Foundational, Core and Linguistic Ontologies[45]
Foundational Model of Anatomy,[46] an ontology for human anatomy
Friend of a Friend, an ontology for describing persons, their activities and their relations to
other people and objects
Gene Ontology for genomics
Gellish English dictionary, an ontology that includes a dictionary and taxonomy that includes
an upper ontology and a lower ontology that focusses on industrial and business
applications in engineering, technology and procurement.
Geopolitical ontology, an ontology describing geopolitical information created by Food and
Agriculture Organization(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.
GAO (General Automotive Ontology) - an ontology for the automotive industry that includes
'car' extensions[47]
GOLD,[48] General Ontology for Linguistic Description
GUM (Generalized Upper Model),[49] a linguistically motivated ontology for mediating
between clients systems and natural language technology
IDEAS Group,[50] a formal ontology for enterprise architecture being developed by the
Australian, Canadian, UK and U.S. Defence Depts.
Linkbase,[51] a formal representation of the biomedical domain, founded upon Basic Formal
Ontology.
LPL, Landmark Pattern Language[52]
NCBO Bioportal,[53] biological and biomedical ontologies and associated tools to search,
browse and visualise
NIFSTD Ontologies from the Neuroscience Information Framework: a modular set of
ontologies for the neuroscience domain.
OBO-Edit,[54] an ontology browser for most of the Open Biological and Biomedical
Ontologies
OBO Foundry,[55] a suite of interoperable reference ontologies in biology and biomedicine
OMNIBUS Ontology,[56] an ontology of learning, instruction, and instructional design
Ontology for Biomedical Investigations, an open-access, integrated ontology of biological
and clinical investigations
ONSTR,[57] Ontology for Newborn Screening Follow-up and Translational Research,
Newborn Screening Follow-up Data Integration Collaborative, Emory University, Atlanta.
Plant Ontology[58] for plant structures and growth/development stages, etc.
POPE, Purdue Ontology for Pharmaceutical Engineering
PRO,[59] the Protein Ontology of the Protein Information Resource, Georgetown University
ProbOnto, knowledge base and ontology of probability distributions.[60][61]
Program abstraction taxonomy
Protein Ontology[62] for proteomics
RXNO Ontology, for name reactions in chemistry
SCDO, the Sickle Cell Disease Ontology,[63] facilitates data sharing and collaborations
within the SDC community, amongst other applications (see list on SCDO website ([Link]
[Link]/)).
Sequence Ontology,[64] for representing genomic feature types found on biological
sequences
SNOMED CT (Systematized Nomenclature of Medicine—Clinical Terms)
Suggested Upper Merged Ontology,[65] a formal upper ontology
Systems Biology Ontology (SBO), for computational models in biology
SWEET,[66] Semantic Web for Earth and Environmental Terminology
SSN/SOSA,[67] 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,[68] representing animal anatomical structures
UMBEL, a lightweight reference structure of 20,000 subject concept classes and their
relationships derived from OpenCyc
WordNet, a lexical reference system
YAMATO,[69] Yet Another More Advanced Top-level Ontology

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.

COLORE[70] is an open repository of first-order ontologies in Common Logic with formal

links between ontologies in the repository.
DAML Ontology Library[71] maintains a legacy of ontologies in DAML.
Ontology Design Patterns portal[72] is a wiki repository of reusable components and
practices for ontology design, and also maintains a list of exemplary ontologies.
Protégé Ontology Library[73] contains a set of OWL, Frame-based and other format
ontologies.
SchemaWeb[74] is a directory of RDF schemata expressed in RDFS, OWL and DAML+OIL.

The following are both directories and search engines.

OBO Foundry is a suite of interoperable reference ontologies in biology and

biomedicine.[75][76]
Bioportal (ontology repository of NCBO)[77]
OntoSelect[78] Ontology Library offers similar services for RDF/S, DAML and OWL
ontologies.
Ontaria[79] 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[80]
ROMULUS is a foundational ontology repository aimed at improving semantic
interoperability. Currently there are three foundational ontologies in the repository: DOLCE,
BFO and GFO.[81]

Examples of applications
In general, ontologies can be used beneficially in several fields.
 Enterprise applications.[82] A more concrete example is SAPPHIRE (Health care) or
Situational Awareness and Preparedness for Public Health Incidences and Reasoning
Engines which is a semantics-based health information system capable of tracking and
evaluating situations and occurrences that may affect public health.
Geographic information systems bring together data from different sources and benefit
therefore from ontological metadata which helps to connect the semantics of the data.[83]
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.[84] 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.[85]

See also
Commonsense knowledge bases
Concept map
Controlled vocabulary
Classification scheme (information science)
Folksonomy
Formal concept analysis
Formal ontology
Knowledge graph
Lattice
Ontology
Ontology alignment
Ontology chart
Open Semantic Framework
Semantic technology
Soft ontology
Terminology extraction
Weak ontology
Web Ontology Language

Related philosophical concepts

Alphabet of human thought

Characteristica universalis
Interoperability
Level of measurement
Metalanguage
Natural semantic metalanguage

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Further reading
Oberle, D.; Guarino, N.; Staab, S. (2009). "What is an ontology?" ([Link]
cs/Guarino2009_What_is_an_Ontology.pdf) (PDF). Staab & Studer 2009. pp. 1–17.
doi:10.1007/978-3-540-92673-3_0 ([Link]
ISBN 978-3-540-70999-2.
Fensel, D.; van Harmelen, F.; Horrocks, I.; McGuinness, D.L.; Patel-Schneider, P.F. (2001).
"OIL: an ontology infrastructure for the Semantic Web". IEEE Intelligent Systems. 16 (2): 38–
45. doi:10.1109/5254.920598 ([Link]
Gangemi, A.; Presutti, V. "Ontology Design Patterns" ([Link]
070620/handbookchapter_odps.pdf) (PDF). Staab & Studer 2009.
Golemati, M.; Katifori, A.; Vassilakis, C.; Lepouras, G.; Halatsis, C. (2007). "Creating an
Ontology for the User Profile# Method and Applications" ([Link]
217030517/[Link] (PDF).
Proceedings of the First IEEE International Conference on Research Challenges in
Information Science (RCIS), Morocco 2007. CiteSeerX [Link].9399 ([Link]
[Link]/viewdoc/summary?doi=[Link].9399). Archived from the original ([Link]
[Link]/pened/papers/[Link]) (PDF) on 2008-12-17.
Mizoguchi, R. (2004). "Tutorial on ontological engineering: Part 3: Advanced course of
ontological engineering" ([Link]
[Link]/pub/miz/[Link]) (PDF). New Gener Comput. 22: 193–220.
doi:10.1007/BF03040960 ([Link] S2CID 23747079 (http
s://[Link]/CorpusID:23747079). Archived from the original ([Link]
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Gruber, T. R. (1993). "A translation approach to portable ontology specifications" ([Link]
[Link]/writing/[Link]) (PDF). Knowledge Acquisition. 5 (2): 199–220.
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Maedche, A.; Staab, S. (2001). "Ontology learning for the Semantic Web". IEEE Intelligent
Systems. 16 (2): 72–79. doi:10.1109/5254.920602 ([Link]
2). S2CID 1411149 ([Link]
Noy, Natalya F.; McGuinness, Deborah L. (March 2001). "Ontology Development 101: A
Guide to Creating Your First Ontology" ([Link]
[Link]/people/dlm/papers/[Link]).
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[Link]/people/dlm/papers/[Link]) on 2010-07-14.
Chaminda Abeysiriwardana, Prabath; Kodituwakku, Saluka R (2012). "Ontology Based
Information Extraction for Disease Intelligence". International Journal of Research in
Computer Science. 2 (6): 7–19. arXiv:1211.3497 ([Link]
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Razmerita, L.; Angehrn, A.; Maedche, A. (2003). "Ontology-Based User Modeling for
Knowledge Management Systems" ([Link]
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[Link]/CorpusID:2267593).
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[Link]/viewdoc/summary?doi=[Link].2599).
Staab, S.; Studer, R., eds. (2009). Handbook on Ontologies (2nd ed.). Springer.
doi:10.1007/978-3-540-92673-3_0 ([Link]
ISBN 978-3-540-92673-3.
Uschold, Mike; Gruninger, M. (1996). "Ontologies: Principles, Methods and Applications".
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([Link] S2CID 2618234 ([Link]
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Pidcock, W. "What are the differences between a vocabulary, a taxonomy, a thesaurus, an
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Yudelson, M.; Gavrilova, T.; Brusilovsky, P. (2005). "Towards User Modeling Meta-ontology".
User Modeling 2005. Lecture Notes in Computer Science. Vol. 3538. Springer. pp. 448–452.
CiteSeerX [Link].7079 ([Link]
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31878-1.
Movshovitz-Attias, Dana; Cohen, William W. (2012). "Bootstrapping Biomedical Ontologies
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[Link]) (PDF). Proceedings of the 2012 Workshop on Biomedical Natural
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CiteSeerX [Link].2874 ([Link]
2874).
External links
Knowledge Representation at Open Directory Project
Library of ontologies ([Link]
GoPubMed ([Link] using Ontologies for searching
ONTOLOG ([Link] (a.k.a. "Ontolog Forum ([Link]
m/ontolog-forum/)") - an Open, International, Virtual Community of Practice on Ontology,
Ontological Engineering and Semantic Technology
Use of Ontologies in Natural Language Processing ([Link]
[Link])
Ontology Summit ([Link] - 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 ([Link]
ologies_paper.pdf)

Retrieved from "[Link]