Ontology ranking based on the analysis of concept structures

In view of the need to provide tools to facilitate the re-use of existing knowledge structures such as ontologies, we present in this paper a system, AKTiveRank, for the ranking of ontologies. AKTiveRank uses as input the search terms provided by a knowledge engineer and, using the output of an ontology search engine, ranks the ontologies. We apply a number of metrics in an attempt to investigate their appropriateness for ranking ontologies, and compare the results with a questionnaire-based human study. Our results show that AKTiveRank will have great utility although there is potential for improvement.

Data driven ontology evaluation

The evaluation of ontologies is vital for the growth of the Semantic Web. We consider a number of problems in evaluating a knowledge artifact like an ontology. We propose in this paper that one approach to ontology evaluation should be corpus or data driven. A corpus is the most accessible form of knowledge and its use allows a measure to be derived of the ‘fit’ between an ontology and a domain of knowledge. We consider a number of methods for measuring this ‘fit’ and propose a measure to evaluate structural fit, and a probabilistic approach to identifying the best ontology.

Background and foreground knowledge in dynamic ontology construction

Ontologies have become a key component in the Semantic Web and Knowledge management. One accepted goal is to construct ontologies from a domain specific set of texts. An ontology reflects the background knowledge used in writing and reading a text. However, a text is an act of knowledge maintenance, in that it re-enforces the background assumptions, alters links and associations in the ontology, and adds new concepts. This means that background knowledge is rarely expressed in a machine interpretable manner. When it is, it is usually in the conceptual boundaries of the domain, e.g. in textbooks or when ideas are borrowed into other domains. We argue that a partial solution to this lies in searching external resources such as specialized glossaries and the internet. We show that a random selection of concept pairs from the Gene Ontology do not occur in a relevant corpus of texts from the journal Nature. In contrast, a significant proportion can be found on the internet. Thus, we conclude that sources external to the domain corpus are necessary for the automatic construction of ontologies.

User-centred ontology learning for knowledge management

Automatic ontology building is a vital issue in many fields where they are currently built manually. This paper presents a user-centred methodology for ontology construction based on the use of Machine Learning and Natural Language Processing. In our approach, the user selects a corpus of texts and sketches a preliminary ontology (or selects an existing one) for a domain with a preliminary vocabulary associated to the elements in the ontology (lexicalisations). Examples of sentences involving such lexicalisation (e.g. ISA relation) in the corpus are automatically retrieved by the system. Retrieved examples are validated by the user and used by an adaptive Information Extraction system to generate patterns that discover other lexicalisations of the same objects in the ontology, possibly identifying new concepts or relations. New instances are added to the existing ontology or used to tune it. This process is repeated until a satisfactory ontology is obtained. The methodology largely automates the ontology construction process and the output is an ontology with an associated trained leaner to be used for further ontology modifications.

The ontology: Chimaera or Pegasus

In the context of the needs of the Semantic Web and Knowledge Management, we consider what the requirements are of ontologies. The ontology as an artifact of knowledge representation is in danger of becoming a Chimera. We present a series of facts concerning the foundations on which automated ontology construction must build. We discuss a number of different functions that an ontology seeks to fulfill, and also a wish list of ideal functions. Our objective is to stimulate discussion as to the real requirements of ontology engineering and take the view that only a selective and restricted set of requirements will enable the beast to fly.

Dynamic iterative ontology learning

The fundamental failure of current approaches to ontology learning is to view it as single pipeline with one or more specific inputs and a single static output. In this paper, we present a novel approach to ontology learning which takes an iterative view of knowledge acquisition for ontologies. Our approach is founded on three open-ended resources: a set of texts, a set of learning patterns and a set of ontological triples, and the system seeks to maintain these in equilibrium. As events occur which disturb this equilibrium, actions are triggered to re-establish a balance between the resources. We present a gold standard based evaluation of the final output of the system, the intermediate output showing the iterative process and a comparison of performance using different seed input. The results are comparable to existing performance in the literature.

An incremental tri-partite approach to ontology learning

In this paper we present a new approach to ontology learning. Its basis lies in a dynamic and iterative view of knowledge acquisition for ontologies. The Abraxas approach is founded on three resources, a set of texts, a set of learning patterns and a set of ontological triples, each of which must remain in equilibrium. As events occur which disturb this equilibrium various actions are triggered to re-establish a balance between the resources. Such events include acquisition of a further text from external resources such as the Web or the addition of ontological triples to the ontology. We develop the concept of a knowledge gap between the coverage of an ontology and the corpus of texts as a measure triggering actions. We present an overview of the algorithm and its functionalities.

Influence of corneal asymmetry on the phakometric measurement of ocular surface alignment

Phakometric measurements of corneal and crystalline lens surface alignment are influenced by corneal asymmetry in which the corneal apex does not coincide with the limbal centre. The purpose of this study was to determine the horizontal separation (e) between these corneal landmarks. Measurements were made in 60 normal eyes (30 subjects) using the Orbscan Ilz corneal analysis workstation. Our results show that both corneal landmarks typically coincide, so that e = 0, but that inter-subject variations of about ±1 mm can be expected (so that the corneal apex may fall nasal or temporal to the visual axis). This suggests that no correction for corneal asymmetry is required when estimating average amounts of ocular alignment from samples of eyes but that the measurement of e is strongly recommended for measurements in individual eyes. © 2004 The College of Optometrists.

Phakometric measurement of ocular surface radii of curvature, axial separations and alignment in relaxed and accommodated human eyes

Measurements (autokeratometry, A-scan ultrasonography and video ophthalmophakometry) of ocular surface radii, axial separations and alignment were made in the horizontal meridian of nine emmetropes (aged 20-38 years) with relaxed (cycloplegia) and active accommodation (mean ± 95% confidence interval: 3.7 ± 1.1 D). The anterior chamber depth (-1.5 ± 0.3 D) and both crystalline lens surfaces (front 3.1 ± 0.8 D; rear 2.1 ± 0.6 D) contributed to dioptric vergence changes that accompany accommodation. Accommodation did not alter ocular surface alignment. Ocular misalignment in relaxed eyes is mainly because of eye rotation (5.7 ± 1.6° temporally) with small amounts of lens tilt (0.2 ± 0.8° temporally) and decentration (0.1 ± 0.1 mm nasally) but these results must be viewed with caution as we did not account for corneal asymmetry. Comparison of calculated and empirically derived coefficients (upon which ocular surface alignment calculations depend) revealed that negligible inherent errors arose from neglect of ocular surface asphericity, lens gradient refractive index properties, surface astigmatism, effects of pupil size and centration, assumed eye rotation axis position and use of linear equations for analysing Purkinje image shifts. © 2004 The College of Optometrists.

Phakometric measurement of ocular surface radius of curvature and alignment: evaluation of method with physical model eyes

Ophthalmophakometric measurements of ocular surface radius of curvature and alignment were evaluated on physical model eyes encompassing a wide range of human ocular dimensions. The results indicated that defocus errors arising from imperfections in the ophthalmophakometer camera telecentricity and light source collimation were smaller than experimental errors. Reasonable estimates emerged for anterior lens surface radius of curvature (accuracy: 0.02–0.10 mm; precision 0.05–0.09 mm), posterior lens surface radius of curvature (accuracy: 0.10–0.55 mm; precision 0.06–0.20 mm), eye rotation (accuracy: 0.00–0.32°; precision 0.06–0.25°), lens tilt (accuracy: 0.00–0.33°; precision 0.05–0.98°) and lens decentration (accuracy: 0.00–0.07 mm; precision 0.00–0.07 mm).

Non-invasive phakometric measurement of corneal and crystalline lens alignment in human eyes

We describe a non-invasive phakometric method for determining corneal axis rotation relative to the visual axis (β) together with crystalline lens axis tilt (α) and decentration (d) relative to the corneal axis. This does not require corneal contact A-scan ultrasonography for the measurement of intraocular surface separations. Theoretical inherent errors of the method, evaluated by ray tracing through schematic eyes incorporating the full range of human ocular component variations, were found to be larger than the measurement errors (β < 0.67°, α < 0.72° and d < 0.08 mm) observed in nine human eyes with known ocular component dimensions. Intersubject variations (mean ± S.D.: β = 6.2 ± 3.4° temporal, α = 0.2 ± 1.8° temporal and d = 0.1 ± 0.1 mm temporal) and repeatability (1.96 × S.D. of difference between repeat readings: β ± 2.0°, α ± 1.8° and d ± 0.2 mm) were studied by measuring the left eyes of 45 subjects (aged 18-42 years, 29 females and 16 males, 15 Caucasians, 29 Indian Asians, one African, refractive error range -7.25 to +1.25 D mean spherical equivalent) on two occasions. © 2005 The College of Optometrists.

Axis-alignment affects perceptual grouping: evidence from simultanagnosia

We examined the effect of grouping by the alignment of implicit axes on the perception of multiple shapes, using a patient (GK) who shows simultanagnosia as part of Blint's syndrome. Five experiments demonstrated that: (1) GK was better able to judge the orientation of a global configuration if the constituent local shapes were aligned with their major axes than if they were aligned with their edges; (2) this axis information was used implicitly, since GK was unable to discriminate between configurations of axis-aligned and edge-aligned shapes; (3) GK's sensitivity to axis-alignment persisted even when the orientations of local shapes were kept constant, indicating some form of cooperative effect between the local elements; (4) axis-alignment of shapes also facilitated his ability to discriminate single-item from multi-item configurations; (5) the effect of axis-alignment could be attributed, at least partially, to the degree to which there was matching between the orientations of local shapes and the global configuration. Taken together, the results suggest that axis-based grouping can support the selection of multiple objects.

A composite framework for the strategic alignment of information systems development

Information systems are corporate resources, therefore information systems development must be aligned with corporate strategy. This thesis proposes that effective strategic alignment of information systems requires information systems development, information systems planning and strategic management to be united. Literature in these areas is examined, breaching the academic boundaries which separate these areas, to contribute a synthesised approach to the strategic alignment of information systems development. Previous work in information systems planning has extended information systems development techniques, such as data modelling, into strategic planning activities, neglecting techniques of strategic management. Examination of strategic management in this thesis, identifies parallel trends in strategic management and information systems development; the premises of the learning school of strategic management are similar to those of soft systems approaches to information systems development. It is therefore proposed that strategic management can be supported by a soft systems approach. Strategic management tools and techniques frame individual views of a strategic situation; soft systems approaches can integrate these diverse views to explore the internal and external environments of an organisation. The information derived from strategic analysis justifies the need for an information system and provides a starting point for information systems development. This is demonstrated by a composite framework which enables each information system to be justified according to its direct contribution to corporate strategy. The proposed framework was developed through action research conducted in a number of organisations of varying types. This suggests that the framework can be widely used to support the strategic alignment of information systems development, thereby contributing to organisational success.

Clinical decision support system for point of care use: ontology driven design and software implementation

OBJECTIVES: The objective of this research was to design a clinical decision support system (CDSS) that supports heterogeneous clinical decision problems and runs on multiple computing platforms. Meeting this objective required a novel design to create an extendable and easy to maintain clinical CDSS for point of care support. The proposed solution was evaluated in a proof of concept implementation. METHODS: Based on our earlier research with the design of a mobile CDSS for emergency triage we used ontology-driven design to represent essential components of a CDSS. Models of clinical decision problems were derived from the ontology and they were processed into executable applications during runtime. This allowed scaling applications' functionality to the capabilities of computing platforms. A prototype of the system was implemented using the extended client-server architecture and Web services to distribute the functions of the system and to make it operational in limited connectivity conditions. RESULTS: The proposed design provided a common framework that facilitated development of diversified clinical applications running seamlessly on a variety of computing platforms. It was prototyped for two clinical decision problems and settings (triage of acute pain in the emergency department and postoperative management of radical prostatectomy on the hospital ward) and implemented on two computing platforms-desktop and handheld computers. CONCLUSIONS: The requirement of the CDSS heterogeneity was satisfied with ontology-driven design. Processing of application models described with the help of ontological models allowed having a complex system running on multiple computing platforms with different capabilities. Finally, separation of models and runtime components contributed to improved extensibility and maintainability of the system.

Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.