5,463 research outputs found
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies
Automatic annotation of bioinformatics workflows with biomedical ontologies
Legacy scientific workflows, and the services within them, often present
scarce and unstructured (i.e. textual) descriptions. This makes it difficult to
find, share and reuse them, thus dramatically reducing their value to the
community. This paper presents an approach to annotating workflows and their
subcomponents with ontology terms, in an attempt to describe these artifacts in
a structured way. Despite a dearth of even textual descriptions, we
automatically annotated 530 myExperiment bioinformatics-related workflows,
including more than 2600 workflow-associated services, with relevant
ontological terms. Quantitative evaluation of the Information Content of these
terms suggests that, in cases where annotation was possible at all, the
annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014
conference), 15 pages, 4 figure
Context Aware Computing for The Internet of Things: A Survey
As we are moving towards the Internet of Things (IoT), the number of sensors
deployed around the world is growing at a rapid pace. Market research has shown
a significant growth of sensor deployments over the past decade and has
predicted a significant increment of the growth rate in the future. These
sensors continuously generate enormous amounts of data. However, in order to
add value to raw sensor data we need to understand it. Collection, modelling,
reasoning, and distribution of context in relation to sensor data plays
critical role in this challenge. Context-aware computing has proven to be
successful in understanding sensor data. In this paper, we survey context
awareness from an IoT perspective. We present the necessary background by
introducing the IoT paradigm and context-aware fundamentals at the beginning.
Then we provide an in-depth analysis of context life cycle. We evaluate a
subset of projects (50) which represent the majority of research and commercial
solutions proposed in the field of context-aware computing conducted over the
last decade (2001-2011) based on our own taxonomy. Finally, based on our
evaluation, we highlight the lessons to be learnt from the past and some
possible directions for future research. The survey addresses a broad range of
techniques, methods, models, functionalities, systems, applications, and
middleware solutions related to context awareness and IoT. Our goal is not only
to analyse, compare and consolidate past research work but also to appreciate
their findings and discuss their applicability towards the IoT.Comment: IEEE Communications Surveys & Tutorials Journal, 201
Towards a service-oriented e-infrastructure for multidisciplinary environmental research
Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures
Towards runtime discovery, selection and composition of semantic services
Service-orientation is gaining momentum in distributed software applications, mainly because it facilitates interoperability and allows application designers to abstract from underlying implementation technologies. Service composition has been acknowledged as a promising approach to create composite services that are capable of supporting service user needs, possibly by personalising the service delivery through the use of context information or user preferences. In this paper we discuss the challenges of automatic service composition, and present DynamiCoS, which is a novel framework that aims at supporting service composition on demand and at runtime for the benefit of service end-users. We define the DynamiCoS framework based on a service composition life-cycle. Framework mechanisms are introduced to tackle each of the phases and requirements of this life-cycle. Semantic services are used in our framework to enable reasoning on the service requests issued by end users, making it possible to automate service discovery, selection and composition. We validate our framework with a prototype that we have built in order to experiment with the mechanisms we have designed. The prototype was evaluated in a testing environment using some use case scenarios. The results of our evaluation give evidences of the feasibility of our approach to support runtime service composition. We also show the benefits of semantic-based frameworks for service composition, particularly for end-users who will be able to have more control on the service composition process
Web Service Discovery in a Semantically Extended UDDI Registry: the Case of FUSION
Service-oriented computing is being adopted at an unprecedented rate, making the effectiveness of automated service discovery an increasingly important challenge. UDDI has emerged as a de facto industry standard and fundamental building block within SOA infrastructures. Nevertheless, conventional UDDI registries lack means to provide unambiguous, semantically rich representations of Web service capabilities, and the logic inference power required for facilitating automated service discovery. To overcome this important limitation, a number of approaches have been proposed towards augmenting Web service discovery with semantics. This paper discusses the benefits of semantically extending Web service descriptions and UDDI registries, and presents an overview of the approach put forward in project FUSION, towards semantically-enhanced publication and discovery of services based on SAWSDL
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