Ontology can be thought of as the definition of entities in a domain of interest. It is useful, however, to talk about the word definition in a little more depth as it is a word with a range of usages within the discipline.
[Typedef] id: OBO_REL:part_of alt_id: OBO_REL:0000002 name: part_of def: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874] comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. inverse_of_on_instance_level: OBO_REL:has_part is_reflexive: true is_anti_symmetric: true is_transitive: true
Is the definition from the Relations Ontology for the part_of relationship. Simply put, this definition is what this particular relationship means. Note that there is a logical definition (written as plain text, not a computational form) as well as a natural language comment on the definition.
The same goes for class definitions; it states what the class means. Such definitions are usually in termrs of characteristics of the entities being described.
Within the OBO community, a definition means a natural language or textual description of that class. The OBO Foundry principles advocate a particular style for these textual definitions of genus and differentia along Aristotelian lines. The genus can be thought of as stating what characteristics are inherited from the more general class. The differentae are those characteristics that differentiate members of that class from other members of the superclass. A very general form of such a definition would be “X is a y that z …”.
"A planned process with the objective to produce information about some evaluant."
this states that an assay is a kind of planned process and that it is differentiated from other planned processes by having the objective of producing information about something being evaluated.
As a contrast we can look at a sibling of "assay": data transformation (OBI_0200000). It has the textual definition "A data transformation is a process which produces output data from input data". this states that a data transformation is a kind of planned process and is differentiated by having a data input and output.
These definitions tell a human reader what it means to be a member or instance of the assay or data transformation class.
One can also have a logical definition of a concept. Here, at least in OWL speak, definition has a narrower meaning; that of necessity and sufficiency. A necessary condition is a condition that an instance must fulfill to be a member of that class. Meeting that condition is, however, not enough to recognise that an instance is a member of a class. For example, having an x-chromosome is a necessary condition for being a member of the (cannonical) class of human male – it is not however sufficient because members of the class human female also have an x-chromosome. Having an x-chromosome is not enough to recognise a particular human as being a Man, even though a man must necessarily have an x-chromosome.
A necessary and sufficient condition is one, that when fulfilled (perhaps along with others), is enough to recognise that an instance is a member of a class. For example, being
Person and having a y-chromosome is a necessary and sufficient condition for being a member of the class of (cannonical) human male. A person with a y-chromosome is a Man or male human. Having two x-chromosomes is enough to recognise a person as being a (cannonical) woman or female human.
we can take the same OBI class of
assay for which we saw a text definition; its logical description is:
Class: 'assay' EquivalentTo: 'planned process', achieves_planned_objective some 'assay objective' SubClassOf: 'planned process', and has_specified_input some (material_entity and (has_role some 'evaluant role')) and has_specified_output some ('information content entity' and ('is about' some (continuant and (has_role some 'evaluant role')))) and realizes some 'evaluant role' and has_specified_output only 'information content entity'
This logical description in OWL has both necessity and sufficiency conditions, together with those that are just necessary. The text definition corresponds here to the "equivalence" axiom; that is, the logical definition. The conditions that are only necessary do not come in to the definition.
The textual definition in this case does correspond to the logical definition (the equivalence axiom). However, many textual definitions do seem to contain both necessary and sufficient conditions and those that are just necessary.
In the OWL world, Necessary and sufficient conditions are also called complete. Classes with only necessary conditions are called partial or primitive descriptions. Defined classes in OWL are a way of exploiting the reasoners that are available for OWL.
A definition is the criteria or conditions by which members of a class may be recognised. Labels for classes are not enough; it is possible to be misled by simple words—after all, that is one of the problems that ontologies attempt to overcome. A text definition is necessary for humans to understand what it means to be a member of that class (or other entity). A logical definition does the same, but for computers (and humans, but in a less accessible manner).
School of Computer Science,
The University of Manchester,
EMBL Outstation – Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,