Creating ontological definitions for use in science

Ontologies aim to represent the world in terms of uniquely defined classes and their properties which are expressed as relationships with other classes. They are becoming widely used in science to improve clarity, searching, inference and the ability to link data from different sources. Ontological definitions are descriptions that represent the essential properties of classes of entities (which include objects, object attributes and processes) that distinguish them from other classes. Classes have unique IRIs (Internationalised Resource Identifiers) that can be used for searching; they also have labels which are words of phrases that people can use to identify the class in passages of text or tables. This article provides a brief guide to help with writing good ontological definitions. The standard format of such a definition of a class, A, is: ‘a B that C’ or its semantic equivalent, where A is the class being defined, B is a parent class and C describes a set of properties of A that distinguish it from other members of B.


Definitions Addiction
Defined by Addiction Ontology

Ontologies and entities
Ontologies are ways of representing the world in a form that can be used for searching, data aggregation and inference by people and computers [1] .They increase clarity of conceptualisation and provide a basis for the development of an integrated, cumulative knowledge base [2] .
Although different formalisms of ontologies can have different features, in the most general sense they represent the world as classes of entities and their properties.The properties of a class are expressed as dyadic relationships of that class with other classes.Relationships link classes together (e.g., 'is a' in 'craving is a mental process' and 'causes condition' in 'tobacco smoking causes condition lung cancer').Thus ontologies can be thought of as collections of relationships between classes forming a network in which every class and relationship is fully defined, labelled and uniquely identified.
A successful example of ontologies of this kind is the Gene Ontology [3] , which was introduced to unify the description of gene functions to enable cross-species comparisons, and which has gone a long way to bringing together the field of molecular biology.
Entities also include immaterial things that contain information (e.g., data items, documents).

Dictionary definitions versus ontological definitions
At the heart of good ontologies are clear definitions of the classes of entities contained in them.In order to write good ontological definitions it is important to understand the distinction between these and dictionary definitions.
Dictionary definitions are statements of the conventional meanings of words or phrases as used in language.Thus they start with a word or phrase such as 'science' and they seek to capture its conventional usage, e.g., 'the study of the nature and behaviour of natural things and the knowledge that we obtain about them'.Dictionaries can offer multiple definitions.
For example, alternative definitions of 'science' might include 'a particular branch of knowledge,' which captures the sense in which we can refer to 'a science' rather than just 'science' as a process.Even within a single dictionary definition there may be multiple meanings embedded, which is the case for the first definition above: both the process of studying, and the knowledge obtained from such study, are referred to, despite the fact that these are different types of thing.Since multiple sorts of things are picked out by these dictionary definitions, corresponding to different senses in which the word can be used, such definitions can be a source of confusion and disagreement.
Ontological definitions are different in that they aim to uniquely and unambiguously delineate a single class of entity that is then given a unique identifier.It is also given a label that we can use to refer to in discourse.The label is a word or phrase that is unique within a given ontology.For example, we can delineate a class defined as 'A human activity that involves the systematic study of the structures and processes in the world through observation and the development of models and theories'.We can then give this class the label 'scientific activity' to avoid confusion with the more general term 'science' in common usage which can include both the activities and topics of study.
The primacy of the definition over the label in ontologies is particularly important in areas of science where strong preferences exist for conceptualising the subject matter in different ways.Thus different researchers may want to use labels such as 'anxiety' to mean somewhat different things, e.g., as a mental process versus as a disposition to experience a mental process, but it is crucial to be clear as to what it is that one is referring to.Ontological definitions do this, and labels can be framed to help with this, for example using the label 'anxiety feeling' for the mental process and 'anxiety disposition' for the disposition.
The same word or phrase may be attached to different ontological definitions by different people or teams if they are using The publishing platform, Qeios, is particularly well suited for writing articles that use ontological definitions because it has the facility to tag terms used in articles with their definitions that are published in Qeios.The Addiction Ontology has made use of this facility by setting up, with Qeios, an automated process whereby classes that have reached a certain stability within the ontology are sent to Qeios to be published as definitions (e.g., addiction).An advantage of this approach is that authors can use terms that are stylistically appropriate within the text but ambiguous and tag them with a definition to make it easy for readers to identify the precise class being referred to.

Writing good ontological definitions
Writing good ontological definitions is difficult, as is evidenced by the fact that a large proportion of the ones found on the Ontology Lookup Service website (https://www.ebi.ac.uk/ols/index) have important limitations.To help with writing good ontological definitions we have taken an existing set of guidelines and extended them and attempted to make them clearer for non-specialist users [5] .We list nine matters of substance, and six of style.unifying upper level ontology such as 'process' in Basic Formal Ontology [6] .

Example
Label: Perceptual process Good definition: A mental process which is a) produced by a causal process involving a part of the environment of the organism, and b) is experienced by the organism as being so caused, and c) in which the relevant part of the environment is thereby represented to the organism.http://purl.obolibrary.org/obo/MF_0000019(Mental process is the parent class and as such carries a lot of the meaning.Its definition in this case is 'A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour.'http://purl.obolibrary.org/obo/MF_0000020) Qeios, CC-BY 4.0 • Article, March 31, 2022 Qeios ID: YGIF9B.2 • https://doi.org/10.32388/YGIF9B.2 2/8 different ontologies.Thus no one ontology has a hegemony of the usage of a term.The different usages are made clear by the fact that the classes will have different IRIs consisting of a designation of the ontology, known as as the 'namespace', and the identifier within that ontology.Thus 'cell nucleus' in the Gene Ontology is 'GO:0005634' with the namespace GO while the same term in the Foundational Model of Anatomy Ontology has the identifier 'FMA:63840'.This avoids fruitless arguments about the 'true' meaning of labels and allows different perspectives to co-exist while ensuring that they are clearly expressed.