A Maximum-Entropy approach for accurate document annotation in the biomedical domain

The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the search and the quality of the results. Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information and makes one step further towards the Semantic Web. A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task. In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with terms from the Medical Subject Headings (MeSH)

Using TREC for cross-comparison between classic IR and ontology-based search models at a Web scale

The construction of standard datasets and benchmarks to evaluate ontology-based search approaches and to compare then against baseline IR models is a major open problem in the semantic technologies community. In this paper we propose a novel evaluation benchmark for ontology-based IR models based on an adaptation of the well-known Cranfield paradigm (Cleverdon, 1967) traditionally used by the IR community. The proposed benchmark comprises: 1) a text document collection, 2) a set of queries and their corresponding document relevance judgments and 3) a set of ontologies and Knowledge Bases covering the query topics. The document collection and the set of queries and judgments are taken from one of the most widely used datasets in the IR community, the TREC Web track. As a use case example we apply the proposed benchmark to compare a real ontology-based search model (Fernandez, et al., 2008) against the best IR systems of TREC 9 and TREC 2001 competitions. A deep analysis of the strengths and weaknesses of this benchmark and a discussion of how it can be used to evaluate other ontology-based search systems is also included at the end of the paper

Semantic web service architecture for simulation model reuse

COTS simulation packages (CSPs) have proved popular in an industrial setting with a number of software vendors. In contrast, options for re-using existing models seem more limited. Re-use of simulation component models by collaborating organizations is restricted by the same semantic issues however that restrict the inter-organization use of web services. The current representations of web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging semantic web. Semantic models, in the form of ontology, utilized by web service discovery and deployment architecture provide one approach to support simulation model reuse. Semantic interoperation is achieved through the use of simulation component ontology to identify required components at varying levels of granularity (including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The paper presents the development of ontology, connector software and web service discovery architecture in order to understand how such ontology are created, maintained and subsequently used for simulation model reuse. The ontology is extracted from health service simulation - comprising hospitals and the National Blood Service. The ontology engineering framework and discovery architecture provide a novel approach to inter- organization simulation, uncovering domain semantics and adopting a less intrusive interface between participants. Although specific to CSPs the work has wider implications for the simulation community

A Web Services Component Discovery and Deployment Architecture for Simulation Model Reuse

CSPs are widely used in industry, although have yet to operate across organizational boundaries. Reuse across organizations is restricted by the same semantic issues that restrict the inter-organization use of web services. The current representations of web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging semantic web. Semantic models, in the form of ontology, utilized by web service discovery and deployment architecture provide one approach to support simulation model reuse. Semantic interoperation is achieved through the use of simulation component ontology to identify required components at varying levels of granularity (including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The paper presents the development carried out within CSPI-PDG and Fluidity Group at Brunel University, of an ontology, connector software and web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organization simulation, adopting a less intrusive interface between participants. Although specific to CSPs the work has wider implications for the simulation community

Semantic web services for simulation component reuse and interoperability: An ontology approach

Commercial-off-the-shelf (COTS) Simulation Packages (CSPs) are widely used in industry primarily due to economic factors associated with developing proprietary software platforms. Regardless of their widespread use, CSPs have yet to operate across organizational boundaries. The limited reuse and interoperability of CSPs are affected by the same semantic issues that restrict the inter-organizational use of software components and web services. The current representations of Web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging Semantic Web. The authors present new research that partially alleviates the problem of limited semantic reuse and interoperability of simulation components in CSPs. Semantic models, in the form of ontologies, utilized by the authors’ Web service discovery and deployment architecture provide one approach to support simulation model reuse. Semantic interoperation is achieved through a simulation component ontology that is used to identify required components at varying levels of granularity (i.e. including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The research presented here is based on the development of an ontology, connector software, and a Web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, by adopting a less intrusive interface between participants Although specific to CSPs this work has wider implications for the simulation community. The reason being that the community as a whole stands to benefit through from an increased awareness of the state-of-the-art in Software Engineering (for example, ontology-supported component discovery and reuse, and service-oriented computing), and it is expected that this will eventually lead to the development of a unique Software Engineering-inspired methodology to build simulations in future

Ontology construction from online ontologies

One of the main hurdles towards a wide endorsement of ontologies is the high cost of constructing them. Reuse of existing ontologies offers a much cheaper alternative than building new ones from scratch, yet tools to support such reuse are still in their infancy. However, more ontologies are becoming available on the web, and online libraries for storing and indexing ontologies are increasing in number and demand. Search engines have also started to appear, to facilitate search and retrieval of online ontologies. This paper presents a fresh view on constructing ontologies automatically, by identifying, ranking, and merging fragments of online ontologies

Ontology engineering for simulation component reuse

Commercial-off-the-shelf (COTS) simulation packages (CSPs) are widely used in industry, although they have yet to operate across organizational boundaries. Reuse across organizations is restricted by the same semantic issues that restrict the inter-organizational use of web services. The current representations of web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging semantic web. Semantic models, in the form of ontology, utilized by web service discovery and deployment architectures provide one approach to support simulation model reuse. Semantic interoperation is achieved through the use of simulation component ontologies to identify required components at varying levels of granularity (including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The paper presents the development of an ontology, connector software and web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, adopting a less intrusive interface between participants. Although specific to CSPs the work has wider implications for the simulation community