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.

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.

Knowledge representation with ontologies: present challenges future possibilities

Ontologies have become the knowledge representation medium of choice in recent years for a range of computer science specialities including the Semantic Web, Agents, and Bio-informatics. There has been a great deal of research and development in this area combined with hype and reaction. This special issue is concerned with the limitations of ontologies and how these can be addressed, together with a consideration of how we can circumvent or go beyond these constraints. The introduction places the discussion in context and presents the papers included in this issue.

Knowledge representation with ontologies:the present and future

Recently, we have seen an explosion of interest in ontologies as artifacts to represent human knowledge and as critical components in knowledge management, the semantic Web, business-to-business applications, and several other application areas. Various research communities commonly assume that ontologies are the appropriate modeling structure for representing knowledge. However, little discussion has occurred regarding the actual range of knowledge an ontology can successfully represent.

Image annotation with Photocopain

Photo annotation is a resource-intensive task, yet is increasingly essential as image archives and personal photo collections grow in size. There is an inherent con?ict in the process of describing and archiving personal experiences, because casual users are generally unwilling to expend large amounts of e?ort on creating the annotations which are required to organise their collections so that they can make best use of them. This paper describes the Photocopain system, a semi-automatic image annotation system which combines information about the context in which a photograph was captured with information from other readily available sources in order to generate outline annotations for that photograph that the user may further extend or amend.

Exchanging uncertainty: interoperable geostatistics?

Traditionally, geostatistical algorithms are contained within specialist GIS and spatial statistics software. Such packages are often expensive, with relatively complex user interfaces and steep learning curves, and cannot be easily integrated into more complex process chains. In contrast, Service Oriented Architectures (SOAs) promote interoperability and loose coupling within distributed systems, typically using XML (eXtensible Markup Language) and Web services. Web services provide a mechanism for a user to discover and consume a particular process, often as part of a larger process chain, with minimal knowledge of how it works. Wrapping current geostatistical algorithms with a Web service layer would thus increase their accessibility, but raises several complex issues. This paper discusses a solution to providing interoperable, automatic geostatistical processing through the use of Web services, developed in the INTAMAP project (INTeroperability and Automated MAPping). The project builds upon Open Geospatial Consortium standards for describing observations, typically used within sensor webs, and employs Geography Markup Language (GML) to describe the spatial aspect of the problem domain. Thus the interpolation service is extremely flexible, being able to support a range of observation types, and can cope with issues such as change of support and differing error characteristics of sensors (by utilising descriptions of the observation process provided by SensorML). XML is accepted as the de facto standard for describing Web services, due to its expressive capabilities which allow automatic discovery and consumption by ‘naive’ users. Any XML schema employed must therefore be capable of describing every aspect of a service and its processes. However, no schema currently exists that can define the complex uncertainties and modelling choices that are often present within geostatistical analysis. We show a solution to this problem, developing a family of XML schemata to enable the description of a full range of uncertainty types. These types will range from simple statistics, such as the kriging mean and variances, through to a range of probability distributions and non-parametric models, such as realisations from a conditional simulation. By employing these schemata within a Web Processing Service (WPS) we show a prototype moving towards a truly interoperable geostatistical software architecture.

Spatially clustered associations in health GIS

Overlaying maps using a desktop GIS is often the first step of a multivariate spatial analysis. The potential of this operation has increased considerably as data sources and Web services to manipulate them are becoming widely available via the Internet. Standards from the OGC enable such geospatial mashups to be seamless and user driven, involving discovery of thematic data. The user is naturally inclined to look for spatial clusters and correlation of outcomes. Using classical cluster detection scan methods to identify multivariate associations can be problematic in this context, because of a lack of control on or knowledge about background populations. For public health and epidemiological mapping, this limiting factor can be critical but often the focus is on spatial identification of risk factors associated with health or clinical status. Spatial entropy index HSu for the ScankOO analysis of the hypothetical dataset using a vicinity which is fixed by the number of points without distinction between their labels. (The size of the labels is proportional to the inverse of the index) In this article we point out that this association itself can ensure some control on underlying populations, and develop an exploratory scan statistic framework for multivariate associations. Inference using statistical map methodologies can be used to test the clustered associations. The approach is illustrated with a hypothetical data example and an epidemiological study on community MRSA. Scenarios of potential use for online mashups are introduced but full implementation is left for further research.

WSRF-based modeling of clinical trial information for collaborative cancer research

The CancerGrid consortium is developing open-standards cancer informatics to address the challenges posed by modern cancer clinical trials. This paper presents the service-oriented software paradigm implemented in CancerGrid to derive clinical trial information management systems for collaborative cancer research across multiple institutions. Our proposal is founded on a combination of a clinical trial (meta)model and WSRF (Web Services Resource Framework), and is currently being evaluated for use in early phase trials. Although primarily targeted at cancer research, our approach is readily applicable to other areas for which a similar information model is available.

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.

Automatic identification of best answers in online enquiry communities

Online communities are prime sources of information. The Web is rich with forums and Question Answering (Q&A) communities where people go to seek answers to all kinds of questions. Most systems employ manual answer-rating procedures to encourage people to provide quality answers and to help users locate the best answers in a given thread. However, in the datasets we collected from three online communities, we found that half their threads lacked best answer markings. This stresses the need for methods to assess the quality of available answers to: 1) provide automated ratings to fill in for, or support, manually assigned ones, and; 2) to assist users when browsing such answers by filtering in potential best answers. In this paper, we collected data from three online communities and converted it to RDF based on the SIOC ontology. We then explored an approach for predicting best answers using a combination of content, user, and thread features. We show how the influence of such features on predicting best answers differs across communities. Further we demonstrate how certain features unique to some of our community systems can boost predictability of best answers.

Ontology-based knowledge capture and sharing in enterprise organisations

Despite years of effort in building organisational taxonomies, the potential of ontologies to support knowledge management in complex technical domains is under-exploited. The authors of this chapter present an approach to using rich domain ontologies to support sense-making tasks associated with resolving mechanical issues. Using Semantic Web technologies, the authors have built a framework and a suite of tools which support the whole semantic knowledge lifecycle. These are presented by describing the process of issue resolution for a simulated investigation concerning failure of bicycle brakes. Foci of the work have included ensuring that semantic tasks fit in with users’ everyday tasks, to achieve user acceptability and support the flexibility required by communities of practice with differing local sub-domains, tasks, and terminology.

Scaling up question-answering to linked data

Linked Data semantic sources, in particular DBpedia, can be used to answer many user queries. PowerAqua is an open multi-ontology Question Answering (QA) system for the Semantic Web (SW). However, the emergence of Linked Data, characterized by its openness, heterogeneity and scale, introduces a new dimension to the Semantic Web scenario, in which exploiting the relevant information to extract answers for Natural Language (NL) user queries is a major challenge. In this paper we discuss the issues and lessons learned from our experience of integrating PowerAqua as a front-end for DBpedia and a subset of Linked Data sources. As such, we go one step beyond the state of the art on end-users interfaces for Linked Data by introducing mapping and fusion techniques needed to translate a user query by means of multiple sources. Our first informal experiments probe whether, in fact, it is feasible to obtain answers to user queries by composing information across semantic sources and Linked Data, even in its current form, where the strength of Linked Data is more a by-product of its size than its quality. We believe our experiences can be extrapolated to a variety of end-user applications that wish to scale, open up, exploit and re-use what possibly is the greatest wealth of data about everything in the history of Artificial Intelligence. © 2010 Springer-Verlag.

Integration of semantically annotated data by the KnoFuss architecture

Most of the existing work on information integration in the Semantic Web concentrates on resolving schema-level problems. Specific issues of data-level integration (instance coreferencing, conflict resolution, handling uncertainty) are usually tackled by applying the same techniques as for ontology schema matching or by reusing the solutions produced in the database domain. However, data structured according to OWL ontologies has its specific features: e.g., the classes are organized into a hierarchy, the properties are inherited, data constraints differ from those defined by database schema. This paper describes how these features are exploited in our architecture KnoFuss, designed to support data-level integration of semantic annotations.

Using the Dempster-Shafer theory of evidence to resolve ABox inconsistencies

Automated ontology population using information extraction algorithms can produce inconsistent knowledge bases. Confidence values assigned by the extraction algorithms may serve as evidence in helping to repair inconsistencies. The Dempster-Shafer theory of evidence is a formalism, which allows appropriate interpretation of extractors’ confidence values. This chapter presents an algorithm for translating the subontologies containing conflicts into belief propagation networks and repairing conflicts based on the Dempster-Shafer plausibility.

Browsing for information by highlighting automatically generated annotations:a user study and evaluation

The realization of the Semantic Web is constrained by a knowledge acquisition bottleneck, i.e. the problem of how to add RDF mark-up to the millions of ordinary web pages that already exist. Information Extraction (IE) has been proposed as a solution to the annotation bottleneck. In the task based evaluation reported here, we compared the performance of users without access to annotation, users working with annotations which had been produced from manually constructed knowledge bases, and users working with annotations augmented using IE. We looked at retrieval performance, overlap between retrieved items and the two sets of annotations, and usage of annotation options. Automatically generated annotations were found to add value to the browsing experience in the scenario investigated. Copyright 2005 ACM.