Chapter 5 AN ONTOLOGY FOR TB ADHERENCE FACTORS
5.1 Overview of the Ontology
5.1.2 The Adherence Factor Ontology Classes
5.1.2.1 TABInfluencing Factor
The TABInfluencingFactor class represents a characteristic or a group of characteristics of a TB patient that have been identified as influential on adherence and is informed by research studies on one or more communities. TABInfluencingFactor is the representation of the theme/factor type dimension of the model. The new factor type theme categorisation that was developed into the conceptual model (see section 4.3.1) is implemented as TABInfluencingFactor class hierarchy. The reformed categories are implemented as a three level sub-class hierarchy under the TABInfluencingFactor class. The hierarchical classes are used to represent factors as categories and sub-categories.
It is important to note that a specific factor may belong to multiple theme categories (TABInfluencingFactor sub-classes) in order to allow for ambiguity and different stances to be taken in the literature to be considered. Although the theme categories from these were reformulated to eliminate concept overlaps and misrepresented factors, there is still the possibility of a factor belonging to more than one theme. Formalising the model with an ontology allows for multiple association of factors with more than one class. The hierarchical representation of the TABInfluencingFactor with the 7 themes (factor type) is shown in Table 5.1 below.
Main Class Middle Class Bottom Class
Patient-centred Demographic Age group
Gender Marital status
Knowledge Knowledge of TB
Education level
Psychology Emotional state
Psychiatric condition Depression
Economic Finance Income class
Poverty
Employment Job class
Employment status Basic amenities Lack of food
Homelessness
Social Social network Family support
Community network Stigma related Perceived stigma
Experienced stigma
Belief Wellness perceived as cured
Treatment efficacy belief Health system Healthcare facility Opening hour favourability
Drug availability Healthcare staff Staff friendliness
Communication gap experience
Therapy Therapy effect Drug adverse effect
Symptoms persistence Co-morbidity HIV co-infection
Treatment Defaulting History
Treatment Alternative
Lifestyle Substance abuse Alcohol consumption
Tobacco use
Healthy living Diet
Exercise
Geographical access Location Distance to facility Dwelling region Transportation Travel time
Transportation cost Table 5.1: Three level hierarchy of TB adherence influencing factors
In representing the TABInfluencingFactor class, a design decision was made to represent influencing factors as the main subject of the model and not as characteristics of a person. This decision is to facilitate structuring of the facts from scientific publications for construction of a predictive model. This is also in line with the approaches taken by all three existing categorisation systems [1] [28] [8], which have been proposed by domain experts in this area. The three hierarchy levels under the TABInfluencingFactor class represent sub-categories of factors, while the bottom classes represent the concrete observable factors. For example, Gender falls under the Demographic sub-category and Patient-Centred the main category (see Figure 5.3). The instances of the Gender factor that can be observed in patients are “Male” and “Female”. This design decision is also significant for the conversion of the factors into useful primitives for mapping to Bayesian Network variables (see Chapter 6).
Figure 5.3: Example of hierarchical class of the ontology
5.1.2.2 The Evidence
Evidence is formal or informal information supporting the influence of a factor on adherence behaviour. It includes expert knowledge from scientific studies and other scientific documents.
Evidence is key to the identification of influencing factors and their interrelationships. It provides information about the characteristics of factors that influence TB adherence in various communities. Evidence, in this concept, refers to studies carried out to identify significant factors and their associated properties. The types of properties evidence asserts are described as the assertion relationship between the evidence and influencing factors.
The Evidence Ontology (ECO) was adopted as the base ontology for describing the Evidence class. ECO is a controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation and other means [99].
ECO consists of several evidence classifications, some of which were used as a base concept for designing the Evidence class for the ontology. Figure 5.5 shows the classes that are included in the Evidence class as sub-classes. ClinicalStudyEvidence is an empirical scientific study/research carried out in a region on a certain population and is a useful representation of the studies that assert the influencing factors.
Figure 5.4: Extract of ECO ontology used as a base concept for the ontology
Data properties are associated with the Evidence class for validation of evidence to be stored in the ontology. They are hasYear which defines the manifestation year of the Evidence and hasSampleSize which describes the sample size of the cohort or survey. The isCarriedOutAt property is a sub-property of isAtRegion, which describes the region that the study area represents. Lastly, the isDocumentedAs property is for the purpose of including the information about the scientific publication of the study.
5.1.2.3 The Work
A Work class is included in the ontology to include additional information for the Evidence class in the ontology. It represents any published document that is produced from a scientific study or other scientific work. Its properties include the name of the author(s), year of publication, URL
of the document online, and the digital object identifier (doi) for the document (See Figure 5.6 below).
The Work class is based on the concept of FaBiO18 ontology [108], which is an ontology for recording and publishing bibliographical records of scholarly endeavours on the Semantic Web.
The Work object-properties such as hasPublicationYear, hasIdentifier, hasAuthor, hasRealisation, hasResourceLocation were modelled on the FaBiO ontology.
The hasRealisation is an important property of the Work class as it links the study to the kind of expressions of the work; an Expression can be an article, a conference proceeding, a conference paper or technical report.
Figure 5.5: Extract of FaBiO ontology used as a base concept for the ontology
5.1.2.4 The Place
A Place refers to the region where the study was carried out (study location), and may be the town, city, province or country of the study. It is the formal representation of the region dimension of the model. The Place class is related to the Evidence class and was designed according to the object properties and classes from the GeoNames ontology [109].
18 http://www.essepuntato.it/lode/http://purl.org/spar/fabio
The Place class was extended to include socio-economic properties than can be used to describe the characteristics of the study location. This allows for users to search for a place of interest, using the characteristics as a guide. Some of the data properties that were included are the economic classification, population characteristics and spatial information. Also included are data properties to describe the incidence and prevalence of TB and HIV/AIDS in various places or locations.
The spatial relationship among the place entities was enhanced using GeoVocab19 ontology as base concept. GeoVocab ontology specifies the regional connections between spatial entities.
This is useful for the refinement of spatial searches for influencing factors in the ontology. The hierarchy of the administrative boundaries was based on the concept of GeoVocab ontology. For instance, the parentFeature property allows for an individual place to be identified with its parent administrative boundaries.
Figure 5.6: GeoNames ontology extract used as a base concept for the ontology
19 http://geovocab.org/
The Place class is also extended to include socio-economic properties than can be used to describe the characteristics of the study location (see Figure 5.4). This allows for users to search for a place of interest using the characteristics as a guide. Some of the data properties that were included are the economic classification, population characteristics and spatial information. Also included are hasTBprevalence, and hasHIVprevalence data properties to describe the prevalence of TB and HIV/AIDS in various places or locations.
5.1.2.5 The Interdependency
The Interdependency class is used to represent a finding of interdependency between factors.
Suppose, for example, a scientific publication finds the following: “Being male is a negative influencing factor that is influenced by the unfavourable working conditions that most males experience at work.” This would indicate a causal relationship between gender-related influencing factors and working condition.
Representing interdependency as a class provides the possibility of relating it to the evidence (studies) that asserts (finds) the existence of any interdependency. It also allows for multiple dependency relationships between influencing factors and different interdependencies found in different studies.