Specification of a conceptualization
The following outline is provided as an overview of and topical guide to ontologies:
Ontology – type of knowledge base that includes the concepts of a subject and the relationships between those concepts. In a formal ontology, each concept is represented by its own unique term (that is, each term has only one meaning), to eliminate ambiguity and guessing. The relationships recorded in formal ontologies support making automatic inferences about the world and the things in it. Thus, formal ontologies are models of reality that computer programs can use for automated reasoning, and are an important part of reasoning systems (in artificial intelligence, or AI). By contrast, an informal or natural ontology is one written using natural language, and it is more difficult to write programs for processing one (but no less important). In the jargon of the field, an ontology is a linguistic knowledge representation structure of the types, parts, properties, and interrelationships of the entities for a particular domain of discourse. Ontologies are a way to describe subject areas using taxonomies and classification networks, essentially defining the structure of knowledge for various domains.
What type of thing is an ontology?
Ontologies can be described as all of the following:
- A type of tool of knowledge representation and reasoning (KR) – KR is a field of artificial intelligence (AI) dedicated to representing information about the world in a form that a computer system can utilize to solve complex tasks such as diagnosing a medical condition or having a dialog in a natural language. Examples of knowledge representation formalisms include semantic nets, frames, rules, and ontologies.
Examples of ontologies
- BabelNet – very large multilingual semantic network and ontology, lexicalized in many languages
- BMO,[2] – e-Business Model Ontology based on a review of enterprise ontologies and business model literature
- CContology (Customer Complaint Ontology)[3] – e-business ontology to support online customer complaint management
- CIDOC Conceptual Reference Model – ontology for cultural heritage[4]
- Dublin Core – simple ontology for documents and publishing
- Foundational, Core and Linguistic Ontologies[5]
- Friend of a Friend – ontology for describing persons, their activities and their relations to other people and objects
- Gellish English dictionary – 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. See also Gellish as Open Source project on SourceForge.
- Geopolitical ontology – describes 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 <http://www.fao.org/countryprofiles/webservices.asp?lang=en> of geopolitical ontology and a module maker <http://www.fao.org/countryprofiles/geoinfo/modulemaker/index.html> to download modules of the geopolitical ontology into different formats (RDF, XML, and EXCEL). See more information on the FAO Country Profiles geopolitical ontology web page <http://www.fao.org/countryprofiles/geoinfo.asp?lang=en>.
- IDEAS Group[6] – formal ontology for enterprise architecture being developed by the Australian, Canadian, UK and U.S. Defence Depts.
- Indiana Philosophy Ontology Project – model of the discipline of philosophy, made available https://inpho.cogs.indiana.edu online which makes it possible to search and navigate via relations among philosophical ideas, scholars, and their works.
- Linkbase[7] – formal representation of the biomedical domain, founded upon Basic Formal Ontology.
- OMNIBUS Ontology[8] – ontology of learning, instruction, and instructional design
- Ontology for Biomedical Investigations – open access, integrated ontology for the description of biological and clinical investigations
- PRO[9] – Protein Ontology of the Protein Information Resource, Georgetown University
- Program abstraction taxonomy program abstraction taxonomy
- Protein Ontology[10] – for proteomics
- ThoughtTreasure –
- UMBEL – lightweight reference structure of 20,000 subject concept classes and their relationships derived from OpenCyc
- WikiTaxonomy – hierarchy of classes and instances automatically generated from Wikipedia's category system
- WordNet – lexical reference system
- YAGO (Yet Another Great Ontology) – knowledge base developed at the Max Planck Institute for Computer Science in Saarbrücken. It is automatically extracted from Wikipedia and other sources. It includes knowledge about more than 10 million entities and contains more than 120 million facts about these entities.
Examples of biological and biomedical ontologies
- Gene Ontology for genomics
- BioPAX[11] – ontology for the exchange and interoperability of biological pathway (cellular processes) data
- CCO and GexKB[12] – Application Ontologies (APO) that integrate diverse types of knowledge with the Cell Cycle Ontology (CCO) and the Gene Expression Knowledge Base (GexKB)
- Disease Ontology[13] – ontology designed to facilitate the mapping of diseases and associated conditions to particular medical codes. It was originally developed at Northwestern University and is associated with the Open Biomedical Ontologies Foundry.
- Foundational Model of Anatomy[14] – reference ontology for the domain of anatomy. It is a symbolic representation of the canonical, phenotypic structure of an organism; a spatial-structural ontology of anatomical entities and relations which form the physical organization of an organism at all salient levels of granularity.
- NCBO Bioportal,[15] 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. See http://neuinfo.org
- OBO-Edit,[16] an ontology browser for most of the Open Biological and Biomedical Ontologies
- OBO Foundry,[17] a suite of interoperable reference ontologies in biology and biomedicine
- ONSTR,[18] Ontology for Newborn Screening Follow-up and Translational Research [1], Newborn Screening Follow-up Data Integration Collaborative, Emory University, Atlanta, GA. See also https://nbsdc.org/projectmission.php
- Plant Ontology[19] for plant structures and growth/development stages, etc.
- POPE, Purdue Ontology for Pharmaceutical Engineering
- SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms)
- Systems Biology Ontology (SBO) – for computational models in biology
- SWEET[20] – Semantic Web for Earth and Environmental Terminology
- TIME-ITEM, Topics for Indexing Medical Education
- Uberon[21] – representing animal anatomical structures
Examples of upper ontologies
Upper ontology – ontology which describes very general concepts that are the same across all knowledge domains. Examples of upper ontologies include:
- Basic Formal Ontology,[22] a formal upper ontology designed to support scientific research
- COSMO,[23] 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.
- DOLCE, a Descriptive Ontology for Linguistic and Cognitive Engineering
- GOLD,[24] General Ontology for Linguistic Description
- GUM (Generalized Upper Model),[25] a linguistically motivated ontology for mediating between clients systems and natural language technology
- Suggested Upper Merged Ontology (SUMO) – formal upper ontology
- YAMATO,[26] Yet Another More Advanced Top-level Ontology
Ontology languages
Ontology language – formal language used to construct ontologies, that allows the encoding of knowledge about specific domains. An ontology language may include reasoning rules that support the processing of that knowledge.
- RDF Schema (Resource Description Framework Schema) – set of classes with certain properties using the RDF extensible knowledge representation data model, providing basic elements for the description of ontologies, otherwise called RDF vocabularies, intended to structure RDF web resources.
- Web Ontology Language (OWL) – family of knowledge representation languages for authoring ontologies.
Ontology engineering
Ontology engineering – building ontologies, and the field that studies the methods and methodologies for building ontologies.
Ontology learning
Ontology learning –