Annotation of SBML Models Through Rule-Based Semantic Integration

*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.
*Results:* We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.
*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RB

SEMA4A: An ontology for emergency notification systems accessibility

This is the post-print version of the final paper published in Expert Systems with Applications. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2009 Elsevier B.V.Providing alert communication in emergency situations is vital to reduce the number of victims. Reaching this goal is challenging due to users’ diversity: people with disabilities, elderly and children, and other vulnerable groups. Notifications are critical when an emergency scenario is going to happen (e.g. a typhoon approaching) so the ability to transmit notifications to different kind of users is a crucial feature for such systems. In this work an ontology was developed by investigating different sources: accessibility guidelines, emergency response systems, communication devices and technologies, taking into account the different abilities of people to react to different alarms (e.g. mobile phone vibration as an alarm for deafblind people). We think that the proposed ontology addresses the information needs for sharing and integrating emergency notification messages over distinct emergency response information systems providing accessibility under different conditions and for different kind of users.Ministerio de Educación y Cienci

A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Issues in integrating existing multi-agent systems for power engineering applications

Multi-agent systems (MAS) have proven to be an effective platform for diagnostic and condition monitoring applications in the power industry. For example, a multi-agent system architecture, entitled condition monitoring multi-agent system (COMMAS) (McArthur et al., 2004), has been applied to the ultra high frequency (UHF) monitoring of partial discharge activity inside transformers. Additionally, a multi-agent system, entitled protection engineering diagnostic agents (PEDA) (Hossack et al., 2003), has demonstrated the use of MAS technology for automated and enhanced post-fault analysis of power systems disturbances based on SCADA and digital fault recorder (DFR) data. In this paper, the authors propose the integration of COMMAS and PEDA as a means of offering enhanced decision support to engineers tasked with managing transformer assets. By providing automatically interpreted data related to condition monitoring and power system disturbances, the proposed integrated system offer engineers a more comprehensive picture of the health of a given transformer. Defects and deterioration in performance can be correlated with the operating conditions it experiences. The integration of COMMAS and PEDA has highlighted the issues inherent to the inter-operation of existing multi-agent systems and, in particular, the issues surrounding the use of differing ontologies. The authors believe that these issues need to be addressed if there is to be widespread deployment of MAS technology within the power industry. This paper presents research undertaken to integrate the two MAS and to deal with ontology issues

An Ontology-Based Method for Semantic Integration of Business Components

Building new business information systems from reusable components is today an approach widely adopted and used. Using this approach in analysis and design phases presents a great interest and requires the use of a particular class of components called Business Components (BC). Business Components are today developed by several manufacturers and are available in many repositories. However, reusing and integrating them in a new Information System requires detection and resolution of semantic conflicts. Moreover, most of integration and semantic conflict resolution systems rely on ontology alignment methods based on domain ontology. This work is positioned at the intersection of two research areas: Integration of reusable Business Components and alignment of ontologies for semantic conflict resolution. Our contribution concerns both the proposal of a BC integration solution based on ontologies alignment and a method for enriching the domain ontology used as a support for alignment.Comment: IEEE New Technologies of Distributed Systems (NOTERE), 2011 11th Annual International Conference; ISSN: 2162-1896 Print ISBN: 978-1-4577-0729-2 INSPEC Accession Number: 12122775 201

Discovering the Impact of Knowledge in Recommender Systems: A Comparative Study

Recommender systems engage user profiles and appropriate filtering techniques to assist users in finding more relevant information over the large volume of information. User profiles play an important role in the success of recommendation process since they model and represent the actual user needs. However, a comprehensive literature review of recommender systems has demonstrated no concrete study on the role and impact of knowledge in user profiling and filtering approache. In this paper, we review the most prominent recommender systems in the literature and examine the impression of knowledge extracted from different sources. We then come up with this finding that semantic information from the user context has substantial impact on the performance of knowledge based recommender systems. Finally, some new clues for improvement the knowledge-based profiles have been proposed.Comment: 14 pages, 3 tables; International Journal of Computer Science & Engineering Survey (IJCSES) Vol.2, No.3, August 201

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

What can be done with the Semantic Web? An overview of Watson-based applications

Thanks to the huge efforts deployed in the community for creating, building and generating semantic information for the Semantic Web, large amounts of machine processable knowledge are now openly available. Watson is an infrastructure component for the Semantic Web, a gateway that provides the necessary functions to support applications in using the Semantic Web. In this paper, we describe a number of applications relying on Watson, with the purpose of demonstrating what can be achieved with the Semantic Web nowadays and what sort of new, smart and useful features can be derived from the exploitation of this large, distributed and heterogeneous base of semantic information