El segundo nivel de la Agenda Setting

The specialised domain model is a subset of the concrete domain model. It cannot contain elements which contradict the concrete domain model and thus the underlying domain ontology. Domain expert users create a specialised domain model for individual projects utilising the Specialisation I/F to effectively edit the concrete domain model as seen in figure 5.1. The specialised domain model is thus simply the transformed concrete domain model containing only the descriptive elements of relevance to a particular project.

A data entry interface based on the whole angiosperm domain ontology would be too large in terms of its usability and would cover a much larger number of ‘Structures’ and characteristics than a taxonomist would utilise in any one taxonomic project. Individual projects are typically restricted to only a small subset of the angiosperm group of plants. As was seen in chapter 2, taxonomists are interested in different sets of specimen characteristics dependent on the focus of their work. The exact data requirements of a given taxonomic project must therefore be established. Normally, taxonomists do this by creating paper-based proforma templates for each project, which have entries for the major describable characteristics of the specimens that they wish to record. In the approach in chapter 4, taxonomists specified an electronic proforma to this end. The ontology-based system provides an equivalent to this process by allowing taxonomists to edit the concrete domain model. Interface constraints on users ensure the edited model does not contradict the underlying ontology.

These specialised domain models enable the system to present data entry forms based solely on the data and semantics relevant for the users’ particular project. Below some nuances of the specialised domain model that can be specified by users are discussed 5.3.4.2 Identified descriptive data elements of interest

In order to generate a data entry interface based only upon the descriptive elements of interest to a particular project, the relevant data elements must be identified by taxonomists.

Description objects to be included in the specialised domain model must be identified by users. The logic of the description object hierarchy means that there must be a path of included description objects from any included description object up to the root. For each included description object, any attributes of interest also require to be identified. Likewise where those attributes have a value domain composed of value objects, the value objects to be included in the value domain require to be identified.

5.3.4.3 Concrete description instances

By default the description objects being instantiated are considered to be abstract concepts (for example the description object ‘leaf’ refers to leaves in general on a plant). Description objects can also be declared to be concrete instances as opposed to being abstract. In this case the eventual entered data refers to an individual specific instance of the description object, and all its instantiated attributes are grouped for that one instance. For example the concrete description object ‘leaf’ refers to a specific leaf on a plant specimen. At the data entry stage, multiple instances of the one concrete description object can be captured. The exact number of concrete instances to be captured is determined at data entry and not at the specialisation stage.

The data entered for the attributes of the concrete instance are grouped together. This allows users to record a volume of related numerical data suitable for later statistical analysis. Recording concrete data also avoids the loss of data through the amalgamation of results which can occur in the more abstract case. For example a user could record that leaf #1 was rough and 16mm in length; leaf #2 was smooth and 5mm in length; leaf #3 was rough and 21mm in length; leaf #4 was rough and 17mm in length; leaf #5 was rough and 19mm in length; leaf #6 was smooth and 3mm in length. The abstract data recorded would simply be that the leaves were rough or smooth with a length in the range of 3-21mm.

Concrete status does not however affect other description objects by dint of their relationships to the concrete one. So that the data for description objects that are children of a concrete description object is not related to the individual concrete instances. Where there is a desire to relate the data from different description objects in such a manner, another mechanism, cloning, exists.

5.3.4.4 Clones

Normally a description object is instantiated once. There are however occasions where two or more description objects with the same ontology based composition (i.e. path to root) and description (same possible related attributes, values and related child description objects) are useful.

The primary example is where the user knows in advance of data entry that there is more than one distinctive type of the description object. For example, the user, specialising the angiosperm ontology for a project looking at the Alyxia group of plants, knew there were two distinct types of ‘flower’ in the plant specimens that they were interested in. These plants, the user knew, often had small ‘terminal’ (situated at the apex) flowers in addition to the main ones. In addition to many characteristics of the main flowers, the user was interested in the number of these terminal flowers and in the presence of ‘bracteoles’ (a sub-structure of ‘flower’, i.e. a child description object of the ‘flower’ description object). In order for clarity, the user thus required two separate description objects for ‘flower’.

The domain model accommodates this by allowing the use of clones. A cloned description object has all the possible attributes, values and child description objects of the original, but can be independently specialised, for example by including different description elements.

Cloning description objects differs from using a concrete concept. Clones can have different description possibilities defined for each of the clones at the specialisation stage, whereas concrete instances all have the same description possibilities. Additionally, the description of the child description objects is linked to the relevant clone. In the concrete concept case, the child description objects of the original abstract concept are not affected and do not have data recorded for them separately for each concrete instance.

Figure 5.6 shows an example of cloning. Each box represents one description object with its own unique path to the root (those with the same identifying letter are based on the same defined term, but are different description objects because of their different composition). The user clones the description object F with the compositional path I – F. This results in a clone F2, which has the compositional path I – F2. The child

description objects of F are the same as those of F2, except that their compositional path includes F2 rather than F, e.g. I – F2- B rather than I – F – B. The included status of attributes and child description objects of F2 is inherited from F at the point of creation, but thereafter F2 is independent of F.

F

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Clone of I - F

Figure 5.6 Cloning description objects.

5.3.4.5 Ratios and Relative Characteristics

The specialisation process allows users to build some complex descriptive concepts that involve more than one attribute or description object. The primary reason for these more complex descriptive concepts is to allow the recording of ratios and other concepts that relate two attributes of the same or different description objects. There are a number of common uses for these descriptive concepts. For example, in a system test with the ‘Ranunculus’ group of plants, the expert user wished to record the relative colour hue of the upper surface of the leaf as opposed to the lower surface. An example of the use of ratios appears in the ‘Alyxia’ group of plants where the user wished to record the ratio of leaf length to leaf width.

The specialised domain model allows attributes to be related to other attributes, using a set of relative modifiers that are included in the ontology. These modifiers can alter the attribute’s value domain, for example to change numerical entry to a domain of relative values such as greater-than, less-than, etc. The value domains of relative modifier altered attributes are determined by the imported ontology. Not all ontologies will have such terms depending upon their nature.

A related complex descriptive alteration of attributes is spatial modified attributes. In this case the user uses a spatial modifier to form a link to another description object, in order to clarify the attribute’s position in relation to the description object. An example of this would be to note where a measurement should be taken on a plant structure e.g. in the ‘Alyxia’ group of plants the user wished to record the presence of ‘bracts’ at the ‘base’ of the ‘pedicel’ and their presence ‘below’ the ‘calyx’. This involves 2 specialised attributes, each with a spatial modifier (e.g. description object ‘flower – bracts’, attribute ‘presence’, spatial modifier ‘at’ with target description object ‘flower - pedicel – base’). The allowed spatial modifiers are also taken from the imported ontology.

5.3.4.6 Preferred Units

Attributes with numerical value domains can have a preferred unit term attached to them (see figure 5.2). Users are able to access and alter this aspect of the specialised domain model. The underlying ontology may have default preferred units of measurement for attribute terms that would be reflected in the specialised domain model, although the angiosperm ontology does not. The units of measurement are also taken form the imported ontology. If the base underlying ontology does not have unit terms, the IT expert performing the initial mapping of the ontology for the system, would require to add units of measurement either themselves or from a secondary source.