Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface

Semantic keyword search for expert witness discovery

In the last few years, there has been an increase in the amount of information stored in semantically enriched knowledge bases, represented in RDF format. These improve the accuracy of search results when the queries are semantically formal. However framing such queries is inappropriate for inexperience users because they require specialist knowledge of ontology and syntax. In this paper, we explore an approach that automates the process of converting a conventional keyword search into a semantically formal query in order to find an expert on a semantically enriched knowledge base. A case study on expert witness discovery for the resolution of a legal dispute is chosen as the domain of interest and a system named SKengine is implemented to illustrate the approach. As well as providing an easy user interface, our experiment shows that SKengine can retrieve expert witness information with higher precision and higher recall, compared with the other system, with the same interface, implemented by a vector model approach

Semantic keyword search for expert witness discovery

In the last few years, there has been an increase in the amount of information stored in semantically enriched knowledge bases, represented in RDF format. These improve the accuracy of search results when the queries are semantically formal. However framing such queries is inappropriate for inexperience users because they require specialist knowledge of ontology and syntax. In this paper, we explore an approach that automates the process of converting a conventional keyword search into a semantically formal query in order to find an expert on a semantically enriched knowledge base. A case study on expert witness discovery for the resolution of a legal dispute is chosen as the domain of interest and a system named SKengine is implemented to illustrate the approach. As well as providing an easy user interface, our experiment shows that SKengine can retrieve expert witness information with higher precision and higher recall, compared with the other system, with the same interface, implemented by a vector model approach

Improving Knowledge Retrieval in Digital Libraries Applying Intelligent Techniques

Nowadays an enormous quantity of heterogeneous and distributed information is stored in the digital University. Exploring online collections to find knowledge relevant to a user’s interests is a challenging work. The artificial intelligence and Semantic Web provide a common framework that allows knowledge to be shared and reused in an efficient way. In this work we propose a comprehensive approach for discovering E-learning objects in large digital collections based on analysis of recorded semantic metadata in those objects and the application of expert system technologies. We have used Case Based-Reasoning methodology to develop a prototype for supporting efficient retrieval knowledge from online repositories. We suggest a conceptual architecture for a semantic search engine. OntoUS is a collaborative effort that proposes a new form of interaction between users and digital libraries, where the latter are adapted to users and their surroundings

OHMI: The Ontology of Host-Microbiome Interactions

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results

Towards engineering ontologies for cognitive profiling of agents on the semantic web

Research shows that most agent-based collaborations suffer from lack of flexibility. This is due to the fact that most agent-based applications assume pre-defined knowledge of agents’ capabilities and/or neglect basic cognitive and interactional requirements in multi-agent collaboration. The highlight of this paper is that it brings cognitive models (inspired from cognitive sciences and HCI) proposing architectural and knowledge-based requirements for agents to structure ontological models for cognitive profiling in order to increase cognitive awareness between themselves, which in turn promotes flexibility, reusability and predictability of agent behavior; thus contributing towards minimizing cognitive overload incurred on humans. The semantic web is used as an action mediating space, where shared knowledge base in the form of ontological models provides affordances for improving cognitive awareness

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer

Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value. With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of meaningful annotations needed by modern biomedical science. We present E.D., the Entity Describer, a mashup of the Connotea social tagging system, an index of semantic web-accessible controlled vocabularies, and a new public RDF database for storing social semantic annotations

Constructing Ontology-Based Cancer Treatment Decision Support System with Case-Based Reasoning

Decision support is a probabilistic and quantitative method designed for modeling problems in situations with ambiguity. Computer technology can be employed to provide clinical decision support and treatment recommendations. The problem of natural language applications is that they lack formality and the interpretation is not consistent. Conversely, ontologies can capture the intended meaning and specify modeling primitives. Disease Ontology (DO) that pertains to cancer's clinical stages and their corresponding information components is utilized to improve the reasoning ability of a decision support system (DSS). The proposed DSS uses Case-Based Reasoning (CBR) to consider disease manifestations and provides physicians with treatment solutions from similar previous cases for reference. The proposed DSS supports natural language processing (NLP) queries. The DSS obtained 84.63% accuracy in disease classification with the help of the ontology