Glossary
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[edit] About
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
[edit] 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
[edit] Definitions
[edit] Entity
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.
[edit] Domain
portion of reality that forms the subject-matter of a single science or technology or mode of study.
[edit] Representation
An image, idea, map, picture, name or description ... of some entity or entities external to the representation.
[edit] 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 ?
[edit] Ontology
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.
[edit] Application vs Reference Ontology
There is a good summary here:
Reference Ontologies - Application Ontologies: Either/Or or Both/And? Christopher Menzel Texas AM University
[edit] 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
[edit] 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
[edit] 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.
[edit] Aristotelian Definition
Also known as genus-differentia definition (but not limited to species taxonomies).
