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This glossary is to help communication within the NCBO by standardizing the terms we use internally

Many of the terms here are sourced from: Media:SmithCeusters.pdf

Meanings of terms used in NCBO

Levels of Reality:

1 - Physical Reality

2 - Psychological Reality = our knowledge and beliefs about 1.

3 - Propositions, Theories, Texts = formalizations of those ideas and beliefs



Anything which exists, including things and processes, functions and qualities, beliefs and actions, documents and software (Levels 1, 2 and 3)

Note that sometimes in software engineering the term "entity" refers solely to a the digital representation itself rather than the thing being represented. Within NCBO we use "entity" to mean anything that exists, but typically for level 1 entities.


portion of reality that forms the subject-matter of a single science or technology or mode of study.


An image, idea, map, picture, name or description ... of some entity or entities external to the representation.

Representational Units

Terms, icons, alphanumeric identifiers ... which refer, or are intended to refer, to entities in a representational artifact. Daniel S: Should we add 'representations of universals', 'definitions' and 'properties' to the examples of RUs above ?


A representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent types in reality and those relations between these types which obtain universally (universally = for all instances)

From Reference Terminology Paper: An ONTOLOGY is a representational artifact, comprising a taxonomy as proper part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them.

Comment: In ontologies nodes from a CV (each of which is associated with an identifier, term, definition, and an optional set of synonyms.) are linked by directed edges, thus forming a graph. This graph represents a counterpart structure on the side of entities (classes, universals) in reality, and its edges represent the relations (e.g. is-a or part-of) which hold between these entities. If a node has a parent node in the is-a hierarchy, then we say that the corresponding class is subsumed by this parent node.

Application vs Reference Ontology

There is a good summary here:

 Reference Ontologies - Application Ontologies: Either/Or or Both/And?
 Christopher Menzel
 Texas AM University


Mapping vs. Alignment

Mapping = Refers to the process of creation of a relationship b/w terms in separate ontologies

Alignment = Refers to the process of creation of a near-synonymy relation b/w terms in separate ontologies

Universal (type, natural kind)

From Reference Terminology paper:

General terms such as ‘DNA’, ‘fracture’, ‘cat’, which represent structures or characteristics in reality which are exemplified – the very same structures or characteristics; over and over again – in an open-ended collection of particulars in arbitrarily disconnected regions of space and time, e.g. as a certain DNA structure is instantiated as a transcript (RNA-structure) over and over again in cells of our body. A universal is something that is shared in common by all those particulars which are its INSTANCES. The universal itself then exists in Level 1 reality as a result of existing in its particular instances. It is overwhelmingly universals which are the entities represented in scientific texts and which are used for classifications. Comment: Universals in a taxonomy stand in an is_a relation

Particular (instance)

From Reference Terminology paper:

No def, Examples: individual patients, their lesions, diseases, and bodily reactions, some of which receive PROPER NAMES. In the paper 'individuals' and 'tokens' were called synonyms also. This should be reslved more clearly I guess.

Aristotelian Definition

Also known as genus-differentia definition (but not limited to species taxonomies).