Éclair—a web service for unravelling species origin of sequences sampled from mixed host interfaces

The identification of the genes that participate at the biological interface of two species remains critical to our understanding of the mechanisms of disease resistance, disease susceptibility and symbiosis. The sequencing of complementary DNA (cDNA) libraries prepared from the biological interface between two organisms provides an inexpensive way to identify the novel genes that may be expressed as a cause or consequence of compatible or incompatible interactions. Sequence classification and annotation of species origin typically use an orthology-based approach and require access to large portions of either genome, or a close relative. Novel species- or clade-specific sequences may have no counterpart within existing databases and remain ambiguous features. Here we present a web-service, Éclair, which utilizes support vector machines for the classification of the origin of expressed sequence tags stemming from mixed host cDNA libraries. In addition to providing an interface for the classification of sequences, users are presented with the opportunity to train a model to suit their preferred species pair. Éclair is freely available at

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

WSMO-lite annotations for web services

and other research output

Semantic annotation, publication, and discovery of Java software components: an integrated approach

Component-based software development has matured into standard practice in software engineering. Among the advantages of reusing software modules are lower costs, faster development, more manageable code, increased productivity, and improved software quality. As the number of available software components has grown, so has the need for effective component search and retrieval. Traditional search approaches, such as keyword matching, have proved ineffective when applied to software components. Applying a semantically- enhanced approach to component classification, publication, and discovery can greatly increase the efficiency of searching and retrieving software components. This has been already applied in the context of Web technologies, and Web services in particular, in the frame of Semantic Web Services research. This paper examines the similarities between software components and Web services and adapts an existing Semantic Web Service publication and discovery solution into a software component annotation and discovery tool which is implemented as an Eclipse plug-in

Content enrichment through dynamic annotation

This paper describes a technique for interceding between users and the information that they browse. This facility, that we term 'dynamic annotation', affords a means of editing Web page content 'on-the-fly' between the source Web server and the requesting client. Thereby, we have a generic way of modifying the content displayed to local users by addition, removal or reorganising any information sourced from the World-Wide Web, whether this derives from local or remote pages. For some time, we have been exploring the scope for this device and we believe that it affords many potential worthwhile applications. Here, we describe two varieties of use. The first variety focuses on support for individual users in two contexts (second-language support and second language learning). The second variety of use focuses on support for groups of users. These differing applications have a common goal which is content enrichment of the materials placed before the user. Dynamic annotation provides a potent and flexible means to this end

Semantic web service automation with lightweight annotations

Web services, both RESTful and WSDL-based, are an increasingly important part of the Web. With the application of semantic technologies, we can achieve automation of the use of those services. In this paper, we present WSMO-Lite and MicroWSMO, two related lightweight approaches to semantic Web service description, evolved from the WSMO framework. WSMO-Lite uses SAWSDL to annotate WSDL-based services, whereas MicroWSMO uses the hRESTS microformat to annotate RESTful APIs and services. Both frameworks share an ontology for service semantics together with most of automation algorithms

Ontology technology for the development and deployment of learning technology systems - a survey

The World-Wide Web is undergoing dramatic changes at the moment. The Semantic Web is an initiative to bring meaning to the Web. The Semantic Web is based on ontology technology – a knowledge representation framework – at its core. We illustrate the importance of this evolutionary development. We survey five scenarios demonstrating different forms of applications of ontology technologies in the development and deployment of learning technology systems. Ontology technologies are highly useful to organise, personalise, and publish learning content and to discover, generate, and compose learning objects

Authorised Translations of Electronic Documents

A concept is proposed to extend authorised translations of documents to electronically signed, digital documents. Central element of the solution is an electronic seal, embodied as an XML data structure, which attests to the correctness of the translation and the authorisation of the translator. The seal contains a digital signature binding together original and translated document, thus enabling forensic inspection and therefore legal security in the appropriation of the translation. Organisational aspects of possible implementation variants of electronic authorised translations are discussed and a realisation as a stand-alone web-service is presented.Comment: In: Peer-reviewed Proceedings of the Information Security South Africa (ISSA) 2006 From Insight to Foresight Conference, 5 to 7 July 2006, Sandton, South Afric

Conceptual Linking: Ontology-based Open Hypermedia

This paper describes the attempts of the COHSE project to define and deploy a Conceptual Open Hypermedia Service. Consisting of • an ontological reasoning service which is used to represent a sophisticated conceptual model of document terms and their relationships; • a Web-based open hypermedia link service that can offer a range of different link-providing facilities in a scalable and non-intrusive fashion; and integrated to form a conceptual hypermedia system to enable documents to be linked via metadata describing their contents and hence to improve the consistency and breadth of linking of WWW documents at retrieval time (as readers browse the documents) and authoring time (as authors create the documents)