Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Background: Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time. Results: In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator. Availability: Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/

A semantic web services-based infrastructure for context-adaptive process support

Current technologies aimed at supporting processes whether it is a business or learning process - primarily follow a metadata- and data-centric paradigm. Whereas process metadata is usually based on a specific standard specification - such as the Business Process Modeling Notation (BPMN) or the IMS Learning Design Standard - the allocation of resources is done manually at design-time, and the used data is often specific to one process context only. These facts limit the reusability of process models across different standards and contexts. To overcome these issues, we introduce an innovative Semantic Web Service-based framework aimed at changing the current paradigm to a context-adaptive service-oriented approach. Following the idea of layered semantic abstractions, our approach supports the development of abstract semantic process model - reusable across different contexts and standards - that enables a dynamic adaptation to specific actor needs and objectives. To illustrate the application of our framework and establish its feasibility, we describe a prototypical application in the E-Learning domain

A Process Framework for Semantics-aware Tourism Information Systems

The growing sophistication of user requirements in tourism due to the advent of new technologies such as the Semantic Web and mobile computing has imposed new possibilities for improved intelligence in Tourism Information Systems (TIS). Traditional software engineering and web engineering approaches cannot suffice, hence the need to find new product development approaches that would sufficiently enable the next generation of TIS. The next generation of TIS are expected among other things to: enable semantics-based information processing, exhibit natural language capabilities, facilitate inter-organization exchange of information in a seamless way, and evolve proactively in tandem with dynamic user requirements. In this paper, a product development approach called Product Line for Ontology-based Semantics-Aware Tourism Information Systems (PLOSATIS) which is a novel hybridization of software product line engineering, and Semantic Web engineering concepts is proposed. PLOSATIS is presented as potentially effective, predictable and amenable to software process improvement initiatives

Improving sustainability through intelligent cargo and adaptive decision making

In the current society, logistics is faced with the challenge to meet more stringent sustainability goals. Shippers and transport service providers both aim to reduce the carbon footprint of their logistic operations. To do so, optimal use of logistics resources and physical infrastructure should be aimed for. An adaptive decision making process for the selection of a specific transport modality, transport provider and timeslot (aimed at minimisation of the carbon footprint) enables shippers to achieve this. This requires shippers to have access to up-to-date capacity information from transport providers (e.g. current and scheduled loading status of the various transport means and information on carbon footprint) and traffic information (e.g. city logistics and current traffic information). A prerequisite is an adequate infrastructure for collaboration and open exchange of information between the various stakeholders in the logistics value chain to obtain the up-to-date information. This paper gives a view on how such an advanced information infrastructure can be realised, currently being developed within the EU iCargo project. The paper describes a reference logistics value chain, including business benefits for each of the roles in the logistics value chain of aiming for sustainability. A case analysis is presented that reflects a practical situation in which the various roles collaborate and exchange information for realizing sustainability goals, using adaptive decision making for selecting a transport modality, transport provider, and timeslot. A high-level overview is provided of the requirements on and technical implementation of the supporting advanced infrastructure for collaboration and open information exchange.In the current society, logistics is faced with the challenge to meet more stringent sustainability goals. Shippers and transport service providers both aim to reduce the carbon footprint of their logistic operations. To do so, optimal use of logistics resources and physical infrastructure should be aimed for. An adaptive decision making process for the selection of a specific transport modality, transport provider and timeslot (aimed at minimisation of the carbon footprint) enables shippers to achieve this. This requires shippers to have access to up-to-date capacity information from transport providers (e.g. current and scheduled loading status of the various transport means and information on carbon footprint) and traffic information (e.g. city logistics and current traffic information). A prerequisite is an adequate infrastructure for collaboration and open exchange of information between the various stakeholders in the logistics value chain to obtain the up-to-date information. This paper gives a view on how such an advanced information infrastructure can be realised, currently being developed within the EU iCargo project. The paper describes a reference logistics value chain, including business benefits for each of the roles in the logistics value chain of aiming for sustainability. A case analysis is presented that reflects a practical situation in which the various roles collaborate and exchange information for realizing sustainability goals, using adaptive decision making for selecting a transport modality, transport provider, and timeslot. A high-level overview is provided of the requirements on and technical implementation of the supporting advanced infrastructure for collaboration and open information exchange.In the current society, logistics is faced with the challenge to meet more stringent sustainability goals. Shippers and transport service providers both aim to reduce the carbon footprint of their logistic operations. To do so, optimal use of logistics resources and physical infrastructure should be aimed for. An adaptive decision making process for the selection of a specific transport modality, transport provider and timeslot (aimed at minimisation of the carbon footprint) enables shippers to achieve this. This requires shippers to have access to up-to-date capacity information from transport providers (e.g. current and scheduled loading status of the various transport means and information on carbon footprint) and traffic information (e.g. city logistics and current traffic information). A prerequisite is an adequate infrastructure for collaboration and open exchange of information between the various stakeholders in the logistics value chain to obtain the up-to-date information. This paper gives a view on how such an advanced information infrastructure can be realised, currently being developed within the EU iCargo project. The paper describes a reference logistics value chain, including business benefits for each of the roles in the logistics value chain of aiming for sustainability. A case analysis is presented that reflects a practical situation in which the various roles collaborate and exchange information for realizing sustainability goals, using adaptive decision making for selecting a transport modality, transport provider, and timeslot. A high-level overview is provided of the requirements on and technical implementation of the supporting advanced infrastructure for collaboration and open information exchange

Context constraint integration and validation in dynamic web service compositions

System architectures that cross organisational boundaries are usually implemented based on Web service technologies due to their inherent interoperability benets. With increasing exibility requirements, such as on-demand service provision, a dynamic approach to service architecture focussing on composition at runtime is needed. The possibility of technical faults, but also violations of functional and semantic constraints require a comprehensive notion of context that captures composition-relevant aspects. Context-aware techniques are consequently required to support constraint validation for dynamic service composition. We present techniques to respond to problems occurring during the execution of dynamically composed Web services implemented in WS-BPEL. A notion of context { covering physical and contractual faults and violations { is used to safeguard composed service executions dynamically. Our aim is to present an architectural framework from an application-oriented perspective, addressing practical considerations of a technical framework

Context-adaptive learning designs by using semantic web services

IMS Learning Design (IMS-LD) is a promising technology aimed at supporting learning processes. IMS-LD packages contain the learning process metadata as well as the learning resources. However, the allocation of resources - whether data or services - within the learning design is done manually at design-time on the basis of the subjective appraisals of a learning designer. Since the actual learning context is known at runtime only, IMS-LD applications cannot adapt to a specific context or learner. Therefore, the reusability is limited and high development costs have to be taken into account to support a variety of contexts. To overcome these issues, we propose a highly dynamic approach based on Semantic Web Services (SWS) technology. Our aim is moving from the current data- and metadata-based to a context-adaptive service-orientated paradigm We introduce semantic descriptions of a learning process in terms of user objectives (learning goals) to abstract from any specific metadata standards and used learning resources. At runtime, learning goals are accomplished by automatically selecting and invoking the services that fit the actual user needs and process contexts. As a result, we obtain a dynamic adaptation to different contexts at runtime. Semantic mappings from our standard-independent process models will enable the automatic development of versatile, reusable IMS-LD applications as well as the reusability across multiple metadata standards. To illustrate our approach, we describe a prototype application based on our principles

Past, present and future of information and knowledge sharing in the construction industry: Towards semantic service-based e-construction

The paper reviews product data technology initiatives in the construction sector and provides a synthesis of related ICT industry needs. A comparison between (a) the data centric characteristics of Product Data Technology (PDT) and (b) ontology with a focus on semantics, is given, highlighting the pros and cons of each approach. The paper advocates the migration from data-centric application integration to ontology-based business process support, and proposes inter-enterprise collaboration architectures and frameworks based on semantic services, underpinned by ontology-based knowledge structures. The paper discusses the main reasons behind the low industry take up of product data technology, and proposes a preliminary roadmap for the wide industry diffusion of the proposed approach. In this respect, the paper stresses the value of adopting alliance-based modes of operation