mSpace: improving information access to multimedia domains with multimodal exploratory search

Overview of mSpace interaction approach for presenting exploratory search particularly in the audio domain by using slices, preview cues, and user-determined organization of information from high-dimensional space

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

Requirements for Information Extraction for Knowledge Management

Knowledge Management (KM) systems inherently suffer from the knowledge acquisition bottleneck - the difficulty of modeling and formalizing knowledge relevant for specific domains. A potential solution to this problem is Information Extraction (IE) technology. However, IE was originally developed for database population and there is a mismatch between what is required to successfully perform KM and what current IE technology provides. In this paper we begin to address this issue by outlining requirements for IE based KM

Opening up Magpie via semantic services

Magpie is a suite of tools supporting a ‘zero-cost’ approach to semantic web browsing: it avoids the need for manual annotation by automatically associating an ontology-based semantic layer to web resources. An important aspect of Magpie, which differentiates it from superficially similar hypermedia systems, is that the association between items on a web page and semantic concepts is not merely a mechanism for dynamic linking, but it is the enabling condition for locating services and making them available to a user. These services can be manually activated by a user (pull services), or opportunistically triggered when the appropriate web entities are encountered during a browsing session (push services). In this paper we analyze Magpie from the perspective of building semantic web applications and we note that earlier implementations did not fulfill the criterion of “open as to services”, which is a key aspect of the emerging semantic web. For this reason, in the past twelve months we have carried out a radical redesign of Magpie, resulting in a novel architecture, which is open both with respect to ontologies and semantic web services. This new architecture goes beyond the idea of merely providing support for semantic web browsing and can be seen as a software framework for designing and implementing semantic web applications