BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.

MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at . The source code is available under the GNU GPL from

Representation and validation of domain and range restrictions in a relational database driven ontology maintenance system

An ontology can be used to represent and organize the objects, properties, events, processes, and relations that embody an area of reality [1]. These knowledge bases may be created manually (by individuals or groups), and/or automatically using software tools, such as those developed for information retrieval and data mining. Recently, the National Science Foundation funded a large collaborative development project for the semi-automated construction of an ontology of amphibian anatomy (AmphibAnat [2]). To satisfy the extensive community curation requirements of that project, a generic, Web-based, multi-user, relational database ontology management system (RDBOM [3]) was constructed, based upon a novel theoretical ontology model called an Ontology Abstract Machine (OAM [4]). The need to support concurrent data entry by multiple users with different levels of access privileges (as determined and assigned by the administrators), made it critical to ensure that the entered data were semantically correct. In particular, the ability to define and enforce restrictions on property characteristics such as the domain and range of a relation provide several advantages. It helps to identify inconsistencies in the ontology, maintain a higher level of overall integrity, and avoid erroneous conclusions that could be made by automated reasoners. In this thesis a modified OAM model is presented that includes definitions for property characteristics and the associated validation algorithms. As proof of concept, it is shown how this modified abstract model has been implemented for domain and range restrictions in RDBOM --Abstract, page iii

The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction

The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured knowledge in this manner have started to appear as well. However, there are few, if any, user studies that are aimed at understanding what users expect from such tools, what works and what doesn't. We organized the Collaborative Knowledge Construction (CKC) Challenge to assess the state of the art for the tools that support collaborative processes for creation of various forms of structured knowledge. The goal of the Challenge was to get users to try out different tools and to learn what users expect from such tools /features that users need, features that they like or dislike. The Challenge task was to construct structured knowledge for a portal that would provide information about research. The Challenge design contained several incentives for users to participate. Forty-nine users registered for the Challenge; thirty three of them participated actively by using the tools. We collected extensive feedback from the users where they discussed their thoughts on all the tools that they tried. In this paper, we present the results of the Challenge, discuss the features that users expect from tools for collaborative knowledge constructions, the features on which Challenge participants disagreed, and the lessons that we learned

A Survey of Volunteered Open Geo-Knowledge Bases in the Semantic Web

Over the past decade, rapid advances in web technologies, coupled with innovative models of spatial data collection and consumption, have generated a robust growth in geo-referenced information, resulting in spatial information overload. Increasing 'geographic intelligence' in traditional text-based information retrieval has become a prominent approach to respond to this issue and to fulfill users' spatial information needs. Numerous efforts in the Semantic Geospatial Web, Volunteered Geographic Information (VGI), and the Linking Open Data initiative have converged in a constellation of open knowledge bases, freely available online. In this article, we survey these open knowledge bases, focusing on their geospatial dimension. Particular attention is devoted to the crucial issue of the quality of geo-knowledge bases, as well as of crowdsourced data. A new knowledge base, the OpenStreetMap Semantic Network, is outlined as our contribution to this area. Research directions in information integration and Geographic Information Retrieval (GIR) are then reviewed, with a critical discussion of their current limitations and future prospects

Survey of tools for collaborative knowledge construction and sharing

The fast growth and spread of Web 2.0 environments have demonstrated the great willingness of general Web users to contribute and share various type of content and information. Many very successful web sites currently exist which thrive on the wisdom of the crowd, where web users in general are the sole data providers and curators. The Semantic Web calls for knowledge to be semantically represented using ontologies to allow for better access and sharing of data. However, constructing ontologies collaboratively is not well supported by most existing ontology and knowledge-base editing tools. This has resulted in the recent emergence of a new range of collaborative ontology construction tools with the aim of integrating some Web 2.0 features into the process of structured knowledge construction. This paper provides a survey of the start of the art of these tools, and highlights their significant features and capabilities

A community based approach for managing ontology alignments

The Semantic Web is rapidly becoming a defacto distributed repository for semantically represented data, thus leveraging on the added on value of the network effect. Various ontology mapping techniques and tools have been devised to facilitate the bridging and integration of distributed data repositories. Nevertheless, ontology mapping can benefitfrom human supervision to increase accuracy of results. The spread of Web 2.0 approaches demonstrate the possibility of using collaborative techniques for reaching consensus. While a number of prototypes for collaborative ontology construction are being developed, collaborative ontology mapping is not yet well investigated. In this paper, we describe a prototype that combines off-the-shelf ontology mapping tools with social software techniques to enable users to collaborate on mapping ontologies

IMPROVING THE DEPENDABILITY OF DESTINATION RECOMMENDATIONS USING INFORMATION ON SOCIAL ASPECTS

Prior knowledge of the social aspects of prospective destinations can be very influential in making travel destination decisions, especially in instances where social concerns do exist about specific destinations. In this paper, we describe the implementation of an ontology-enabled Hybrid Destination Recommender System (HDRS) that leverages an ontological description of five specific social attributes of major Nigerian cities, and hybrid architecture of content-based and case-based filtering techniques to generate personalised top-n destination recommendations. An empirical usability test was conducted on the system, which revealed that the dependability of recommendations from Destination Recommender Systems (DRS) could be improved if the semantic representation of social attributes information of destinations is made a factor in the destination recommendation process

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Exploiting Synergy Between Ontologies and Recommender Systems

Recommender systems learn about user preferences over time, automatically finding things of similar interest. This reduces the burden of creating explicit queries. Recommender systems do, however, suffer from cold-start problems where no initial information is available early on upon which to base recommendations. Semantic knowledge structures, such as ontologies, can provide valuable domain knowledge and user information. However, acquiring such knowledge and keeping it up to date is not a trivial task and user interests are particularly difficult to acquire and maintain. This paper investigates the synergy between a web-based research paper recommender system and an ontology containing information automatically extracted from departmental databases available on the web. The ontology is used to address the recommender systems cold-start problem. The recommender system addresses the ontology's interest-acquisition problem. An empirical evaluation of this approach is conducted and the performance of the integrated systems measured