Ontology (information science)

This article is about ontology in information science. For the study of the nature of being, see Ontology.

In computer science and information science, an ontology is a formal naming and definition of the types, properties, and interrelationships of the entities that really or fundamentally exist for a particular domain of discourse. It is thus a practical application of philosophical ontology, with a taxonomy.

An ontology compartmentalizes the variables needed for some set of computations and establishes the relationships between them.[1][2]

The fields of artificial intelligence, the Semantic Web, systems engineering, software engineering, biomedical informatics, library science, enterprise bookmarking, and information architecture all create ontologies to limit complexity and to organize information. The ontology can then be applied to problem solving.

Etymology and definition

The term ontology has its origin in philosophy and has been applied in many different ways. The word element onto- comes from the Greek ὤν, ὄντος, ("being", "that which is"), present participle of the verb εἰμί ("be"). The core meaning within computer science is a model for describing the world that consists of a set of types, properties, and relationship types. There is also generally an expectation that the features of the model in an ontology should closely resemble the real world (related to the object).[3]

Overview

What many ontologies have in common in both computer science and in philosophy is the representation of entities, ideas, and events, along with their properties and relations, according to a system of categories. In both fields, there is considerable work on problems of ontological relativity (e.g., Quine and Kripke in philosophy, Sowa and Guarino in computer science),[4] and debates concerning whether a normative ontology is viable (e.g., debates over foundationalism in philosophy, and over the Cyc project in AI). Differences between the two are largely matters of focus. Computer scientists are more concerned with establishing fixed, controlled vocabularies, while philosophers are more concerned with first principles, such as whether there are such things as fixed essences or whether enduring objects must be ontologically more primary than processes.

Other fields make ontological assumptions that are sometimes explicitly elaborated and explored. For instance, the definition and ontology of economics (also sometimes called the political economy) is hotly debated especially in Marxist economics[5] where it is a primary concern, but also in other subfields.[6] Such concerns intersect with those of information science when a simulation or model is intended to enable decisions in the economic realm; for example, to determine what capital assets are at risk and if so by how much (see risk management). Some claim all social sciences have explicit ontology issues because they do not have hard falsifiability criteria like most models in physical sciences and that indeed the lack of such widely accepted hard falsification criteria is what defines a social or soft science.

History

Historically, ontologies arise out of the branch of philosophy known as metaphysics, which deals with the nature of reality – of what exists. This fundamental branch is concerned with analyzing various types or modes of existence, often with special attention to the relations between particulars and universals, between intrinsic and extrinsic properties, and between essence and existence. The traditional goal of ontological inquiry in particular is to divide the world "at its joints" to discover those fundamental categories or kinds into which the world’s objects naturally fall.[7]

During the second half of the 20th century, philosophers extensively debated the possible methods or approaches to building ontologies without actually building any very elaborate ontologies themselves. By contrast, computer scientists were building some large and robust ontologies, such as WordNet and Cyc, with comparatively little debate over how they were built.

Since the mid-1970s, researchers in the field of artificial intelligence (AI) have recognized that capturing knowledge 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. 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 systems. Some researchers, drawing inspiration from philosophical ontologies, viewed computational ontology as a kind of applied philosophy.[8]

In the early 1990s, the widely cited Web page and paper "Toward Principles for the Design of Ontologies Used for Knowledge Sharing" by Tom Gruber[9] is credited with a deliberate definition of ontology as a technical term in computer science. Gruber introduced the term to mean 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.[10]

According to Gruber (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.[11] To specify a conceptualization, one needs to state axioms that do constrain the possible interpretations for the defined terms.[1]

Components

Main article: Ontology components

Contemporary ontologies share many structural similarities, regardless of the language in which they are expressed. As mentioned above, 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:

Ontologies are commonly encoded using ontology languages.

Types

Domain ontology

A domain ontology (or domain-specific ontology) represents concepts which belong to part of the world. Particular meanings of terms applied to that domain are provided by domain ontology. 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 represent concepts in very specific and often eclectic ways, they are often incompatible. As systems that rely on domain ontologies expand, they often need to merge domain ontologies into a more general representation. 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 foundation ontology is a largely manual process and therefore time-consuming and expensive. Domain ontologies that use the same foundation ontology to provide a set of basic elements with which to specify the meanings of the domain ontology elements can be merged automatically. There are studies on generalized techniques for merging ontologies,[12] but this area of research is still largely theoretical.

Upper ontology

Main article: Upper ontology

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

There are several standardized upper ontologies available for use, including BFO, BORO method, Dublin Core, GFO, OpenCyc/ResearchCyc, SUMO, the Unified Foundational Ontology (UFO),[13] and DOLCE.[14][15] WordNet, while considered an upper ontology by some, is not strictly an ontology. However, it has been employed as a linguistic tool for learning domain ontologies.[16]

Hybrid ontology

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

Visualization

A survey of ontology visualization techniques is presented by Katifori et al.[17] An evaluation of two most established ontology visualization techniques: indented tree and graph is discussed in.[18] A visual language for ontologies represented in OWL is specified by the Visual Notation for OWL Ontologies (VOWL).

Engineering

Main article: Ontology engineering

Ontology engineering (or ontology building) is a subfield of knowledge engineering. It studies the ontology development process, the ontology life cycle, the methods and methodologies for building ontologies, and the tool suites and languages that support them.[19][20]

Ontology engineering aims to make explicit the knowledge contained within software applications, and within enterprises and business procedures for a particular domain. Ontology engineering offers a direction towards solving the interoperability problems brought about by semantic obstacles, such as the obstacles related to the definitions of business terms and software classes. Ontology engineering is a set of tasks related to the development of ontologies for a particular domain.[21]

Editor

Ontology editors are applications designed to assist in the creation or manipulation of ontologies. They often express ontologies in one of many ontology languages. Some provide export to other ontology languages however.

Among the most relevant criteria for choosing an ontology editor are the degree to which the editor abstracts from the actual ontology representation language used for persistence and the visual navigation possibilities within the knowledge model. Next come built-in inference engines and information extraction facilities, and the support of meta-ontologies such as OWL-S, Dublin Core, etc. Another important feature is the ability to import & export foreign knowledge representation languages for ontology matching. Ontologies are developed for a specific purpose and application.

Learning

Main article: Ontology 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 methods have been explored to automatically link ontologies to documents, e.g. in the context of the BioCreative challenges.[22]

Languages

Main article: Ontology language

An ontology language is a formal language used to encode the 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 for the Web has led to the emergence of services providing lists or directories of ontologies with search facility. Such directories have been called ontology libraries.

The following are libraries of human-selected ontologies.

The following are both directories and search engines. They include crawlers searching the Web for well-formed ontologies.

Examples of applications

In general, ontologies can be used beneficially in

Criticisms

Werner Ceusters has noted the confusion caused by the significant differences in the meaning of word ontology when used by philosophy compared with the use of the word ontology in computer science, and advocates for greater precision in use of the word ontology so that members of the various disciplines using various definitions of the word ontology can communicate. He writes 'before one is able to answer the question 'what is an ontology?', one must provide first an answer to the question 'what does the word ontology mean?'.[61]

It's also not clear how ontology fits with Schema on Read (NoSQL) databases.

See also

Related philosophical concepts

References

  1. 1 2 Gruber, Thomas R. (June 1993). "A translation approach to portable ontology specifications" (PDF). Knowledge Acquisition 5 (2): 199–220. doi:10.1006/knac.1993.1008.
  2. ↑ Arvidsson, F.; Flycht-Eriksson, A. "Ontologies I" (PDF). Retrieved 26 November 2008.
  3. ↑ Garshol, L. M. (2004). "Metadata? Thesauri? Taxonomies? Topic Maps! Making sense of it all". Retrieved 13 October 2008.
  4. ↑ Sowa, J. F. (1995). "Top-level ontological categories". International Journal of Human-Computer Studies 43 (5-6 (November/December)): 669–85. doi:10.1006/ijhc.1995.1068.
  5. ↑ Giulio Palermo* (2007-01-10). "The ontology of economic power in capitalism: mainstream economics and Marx". Cje.oxfordjournals.org. Retrieved 2013-06-16.
  6. ↑ Zuniga, Gloria L. (1999-02-02). "An Ontology Of Economic Objects". Ideas.repec.org. Retrieved 2013-06-16.
  7. ↑ Benjamin, Perakath C.; Menzel, Christopher P.; Mayer, Richard J.; Fillion, Florence; Futrell, Michael T.; deWitte, Paula S.; Lingineni, Madhavi (September 21, 1994). "IDEF5 Method Report" (PDF). Knowledge Based Systems, Inc.
  8. ↑ Gruber, T. (2008). Liu, Ling; Özsu, M. Tamer, eds. Ontology. Encyclopedia of Database Systems (Springer-Verlag). ISBN 978-0-387-49616-0.
  9. ↑ Gruber, T. (1995). "Toward Principles for the Design of Ontologies Used for Knowledge Sharing". International Journal of Human-Computer Studies 43 (5-6): 907–928. doi:10.1006/ijhc.1995.1081.
  10. ↑ Gruber, T. (2001). "What is an Ontology?". Stanford University. Retrieved 2009-11-09.
  11. ↑ Enderton, H. B. (1972-05-12). A Mathematical Introduction to Logic (1 ed.). San Diego, CA: Academic Press. p. 295. ISBN 978-0-12-238450-9 2nd edition; January 5, 2001, ISBN 978-0-12-238452-3
  12. ↑ "Project: Dynamic Ontology Repair". University of Edinburgh Department of Informatics. Retrieved 2 January 2012.
  13. ↑ Giancarlo Guizzardi & Gerd Wagner. "A Unified Foundational Ontology and some Applications of it in Business Modeling" (PDF). Retrieved 31 March 2014.
  14. 1 2 "Laboratory for Applied Ontology - DOLCE". Laboratory for Applied Ontology (LOA). Retrieved 10 February 2011.
  15. 1 2 "OWL version of DOLCE+DnS". Semantic Technology Lab. Retrieved 21 February 2013.
  16. ↑ Navigli, Roberto; Velardi, Paola (2004). "Learning Domain Ontologies from Document Warehouses and Dedicated Web Sites" (PDF). Computational Linguistics (MIT Press) 30 (2): 151–179. doi:10.1162/089120104323093276.
  17. ↑ Katifori, A., Halatsis, C., Lepouras, G., Vassilakis, C., Giannopoulou, E.: Ontology Visualization Methods - A Survey. ACM Computing Surveys, 39, 4, Article 10 (2007)
  18. ↑ Bo Fu, Natalya F. Noy, Margaret-Anne Storey, Indented Tree or Graph? A Usability Study of Ontology Visualization Techniques in the Context of Class Mapping Evaluation. In Proceedings of the 12th International Semantic Web Conference (ISWC 2013), LNCS 8218, 117-134
  19. ↑ Gómez-Pérez, Ascunion; Fernández-López, Mariano; Corcho, Oscar (2004). Ontological Engineering: With Examples from the Areas of Knowledge Management, E-commerce and the Semantic Web (1 ed.). Springer. p. 403. ISBN 978-1-85233-551-9.
  20. ↑ De Nicola, Antonio; Missikoff, Michele; Navigli, Roberto (2009). "A Software Engineering Approach to Ontology Building" (PDF). Information Systems (Elsevier) 34 (2): 258–275. doi:10.1016/j.is.2008.07.002.
  21. ↑ Pouchard, Line; Ivezic, Nenad; Schlenoff, Craig (March 2000). "Ontology Engineering for Distributed Collaboration in Manufacturing" (PDF). Proceedings of the AIS2000 conference.
  22. ↑ Krallinger, M; Leitner, F; Vazquez, M; Salgado, D; Marcelle, C; Tyers, M; Valencia, A; Chatr-Aryamontri, A (2012). "How to link ontologies and protein-protein interactions to literature: Text-mining approaches and the Bio Creative experience". Database 2012: bas017. doi:10.1093/database/bas017. PMC 3309177. PMID 22438567.
  23. ↑ "SADL". Sourceforge. Retrieved 10 February 2011.
  24. ↑ "AURUM - Information Security Ontology". Retrieved 29 January 2016.
  25. ↑ "Basic Formal Ontology (BFO)". Institute for Formal Ontology and Medical Information Science (IFOMIS).
  26. ↑ "BioPAX". Retrieved 10 February 2011.
  27. ↑ Osterwalder, Alexander; Pigneur, Yves (June 17–19, 2002). "An e-Business Model Ontology for Modeling e-Business" (PDF). 15th Bled eConference, Slovenia.
  28. ↑ "About CCO and GexKB". Semantic Systems Biology.
  29. ↑ "CContology". Retrieved 10 February 2011.
  30. ↑ "The CIDOC Conceptual Reference Model (CRM)". Retrieved 10 February 2011.
  31. ↑ "COSMO". MICRA Inc. Retrieved 10 February 2011.
  32. ↑ "Disease Ontology". Sourceforge. Retrieved 10 February 2011.
  33. ↑ "Foundational, Core and Linguistic Ontologies". Retrieved 10 February 2011.
  34. ↑ "Foundational Model of Anatomy". Retrieved 10 February 2011.
  35. ↑ "GOLD". Retrieved 10 February 2011.
  36. ↑ "Generalized Upper Model". Retrieved 10 February 2011.
  37. ↑ "The IDEAS Group Website". Retrieved 10 February 2011.
  38. ↑ "Linkbase". Retrieved 10 February 2011.
  39. ↑ "Bioportal". National Center for Biological Ontology (NCBO).
  40. ↑ "Ontology browser for most of the Open Biological and Biomedical Ontologies". Berkeley Bioinformatics Open Source Project (BBOP).
  41. ↑ "The Open Biological and Biomedical Ontologies". Berkeley Bioinformatics Open Source Project (BBOP).
  42. ↑ "OMNIBUS Ontology". Retrieved 10 February 2011.
  43. ↑ "ONSTR". Retrieved 16 April 2014.
  44. ↑ "Plant Ontology". Retrieved 10 February 2011.
  45. ↑ "PRO". Retrieved 10 February 2011.
  46. ↑ "Protein Ontology". Retrieved 10 February 2011.
  47. ↑ "SWEET". Retrieved 10 February 2011.
  48. ↑ "UBERON". Retrieved 10 July 2012.
  49. ↑ "YAMATO". Retrieved 10 February 2011.
  50. ↑ "COLORE". Retrieved 4 May 2011.
  51. ↑ "DAML Ontology Library". Retrieved 10 February 2011.
  52. ↑ "ODP Library". Retrieved 21 February 2013.
  53. ↑ "Protege Ontology Library". Retrieved 10 February 2011.
  54. ↑ "SchemaWeb". Retrieved 10 February 2011.
  55. ↑ "OBO Foundry". Retrieved 10 February 2011.
  56. ↑ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K.; Ireland, A.; Mungall, C. J.; Leontis, N.; Rocca-Serra, P.; Ruttenberg, A.; Sansone, S. A.; Scheuermann, R. H.; Shah, N.; Whetzel, P. L.; Lewis, S. (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology 25 (11): 1251–1255. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687.
  57. ↑ "OntoSelect". Retrieved 10 February 2011.
  58. ↑ "Ontaria". Retrieved 10 February 2011.
  59. ↑ Daniel Oberle, How ontologies benefit enterprise applications, Semantic Web Journal, IOS Press, 2013. DOI 10.3233/SW-130114
  60. ↑ Andrew U. Frank (2001), "Tiers of ontology and consistency constraints in geographical information systems", International Journal of Geographical Information Science 15 (7): 667–678
  61. ↑ http://www.referent-tracking.com/RTU/sendfile/?file=CeustersCommentaryOnMaojoLongVersion.pdf

Further reading

External links

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