10,074 research outputs found
myTea: Connecting the Web to Digital Science on the Desktop
Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results
Supporting Semantically Enhanced Web Service Discovery for Enterprise Application Integration
The availability of sophisticated Web service discovery mechanisms is an essential prerequisite for increasing the levels of efficiency and automation in EAI. In this chapter, we present an approach for developing service registries building on the UDDI standard and offering semantically-enhanced publication and discovery capabilities in order to overcome some of the known limitations of conventional service registries. The approach aspires to promote efficiency in EAI in a number of ways, but primarily by automating the task of evaluating service integrability on the basis of the input and output messages that are defined in the Web service’s interface. The presented solution combines the use of three technology standards to meet its objectives: OWL-DL, for modelling service characteristics and performing fine-grained service matchmaking via DL reasoning, SAWSDL, for creating semantically annotated descriptions of service interfaces, and UDDI, for storing and retrieving syntactic and semantic information about services and service providers
Semantic business process management: a vision towards using semantic web services for business process management
Business process management (BPM) is the approach to manage the execution of IT-supported business operations from a business expert's view rather than from a technical perspective. However, the degree of mechanization in BPM is still very limited, creating inertia in the necessary evolution and dynamics of business processes, and BPM does not provide a truly unified view on the process space of an organization. We trace back the problem of mechanization of BPM to an ontological one, i.e. the lack of machine-accessible semantics, and argue that the modeling constructs of semantic Web services frameworks, especially WSMO, are a natural fit to creating such a representation. As a consequence, we propose to combine SWS and BPM and create one consolidated technology, which we call semantic business process management (SBPM
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
Enhancing Workflow with a Semantic Description of Scientific Intent
Peer reviewedPreprin
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
XML in Motion from Genome to Drug
Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted
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