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

Semantic annotation of Web APIs with SWEET

Recently technology developments in the area of services on the Web are marked by the proliferation of Web applications and APIs. The development and evolution of applications based on Web APIs is, however, hampered by the lack of automation that can be achieved with current technologies. In this paper we present SWEET - Semantic Web sErvices Editing Tool - a lightweight Web application for creating semantic descriptions of Web APIs. SWEET directly supports the creation of mashups by enabling the semantic annotation of Web APIs, thus contributing to the automation of the discovery, composition and invocation service tasks. Furthermore, it enables the development of composite SWS based applications on top of Linked Data

Combining SAWSDL, OWL-DL and UDDI for Semantically Enhanced Web Service Discovery

UDDI registries are included as a standard offering within the product suite of any major SOA vendor, serving as the foundation for establishing design-time and run-time SOA governance. Despite the success of the UDDI specification and its rapid uptake by the industry, the capabilities of its offered service discovery facilities are rather limited. The lack of machine-understandable semantics in the technical specifications and classification schemes used for retrieving services, prevent UDDI registries from supporting fully automated and thus truly effective service discovery. This paper presents the implementation of a semantically-enhanced registry that builds on the UDDI specification and augments its service publication and discovery facilities to overcome the aforementioned limitations. The proposed solution combines the use of SAWSDL for creating semantically annotated descriptions of service interfaces and the use of OWL-DL for modelling service capabilities and for performing matchmaking via DL reasoning

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

Enhancing Workflow with a Semantic Description of Scientific Intent

Peer reviewedPreprin

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