Towards an ontology-based platform-independent framework for developing KBE systems in the aerospace industry

Aerospace engineering is considered to be one of the most complex and advanced branches of engineering. The use of knowledge based engineering (KBE) technologies has played a major role in automating routine design activities in view of supporting the cost-effective and timely development of a product. However, technologies employed within KBE systems are usually platform-specific. The nature of these platform-specific models has significantly limited knowledge abstraction and reusability in KBE systems. This research paper presents a novel approach that illustrates the use of platform-independent knowledge models for the development of KBE systems in the aerospace industry. The use of semantic technologies through the definition of generic-purposed ontologies has been employed to support the notion of independent knowledge models that strengthens knowledge reusability in KBE systems. This approach has been validated qualitatively through experts’ opinion and its benefit realised in the abstraction, reusability and maintainability of KBE systems

Conceptual Linking: Ontology-based Open Hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents)

Conceptual Linking: Ontology-based Open Hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents)

The Requirements for Ontologies in Medical Data Integration: A Case Study

Evidence-based medicine is critically dependent on three sources of information: a medical knowledge base, the patients medical record and knowledge of available resources, including where appropriate, clinical protocols. Patient data is often scattered in a variety of databases and may, in a distributed model, be held across several disparate repositories. Consequently addressing the needs of an evidence-based medicine community presents issues of biomedical data integration, clinical interpretation and knowledge management. This paper outlines how the Health-e-Child project has approached the challenge of requirements specification for (bio-) medical data integration, from the level of cellular data, through disease to that of patient and population. The approach is illuminated through the requirements elicitation and analysis of Juvenile Idiopathic Arthritis (JIA), one of three diseases being studied in the EC-funded Health-e-Child project.Comment: 6 pages, 1 figure. Presented at the 11th International Database Engineering & Applications Symposium (Ideas2007). Banff, Canada September 200

Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Language technologies and the evolution of the semantic web

The availability of huge amounts of semantic markup on the Web promises to enable a quantum leap in the level of support available to Web users for locating, aggregating, sharing, interpreting and customizing information. While we cannot claim that a large scale Semantic Web already exists, a number of applications have been produced, which generate and exploit semantic markup, to provide advanced search and querying functionalities, and to allow the visualization and management of heterogeneous, distributed data. While these tools provide evidence of the feasibility and tremendous potential value of the enterprise, they all suffer from major limitations, to do primarily with the limited degree of scale and heterogeneity of the semantic data they use. Nevertheless, we argue that we are at a key point in the brief history of the Semantic Web and that the very latest demonstrators already give us a glimpse of what future applications will look like. In this paper, we describe the already visible effects of these changes by analyzing the evolution of Semantic Web tools from smart databases towards applications that harness collective intelligence. We also point out that language technology plays an important role in making this evolution sustainable and we highlight the need for improved support, especially in the area of large-scale linguistic resources