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

An Analysis of Service Ontologies

Services are increasingly shaping the world’s economic activity. Service provision and consumption have been profiting from advances in ICT, but the decentralization and heterogeneity of the involved service entities still pose engineering challenges. One of these challenges is to achieve semantic interoperability among these autonomous entities. Semantic web technology aims at addressing this challenge on a large scale, and has matured over the last years. This is evident from the various efforts reported in the literature in which service knowledge is represented in terms of ontologies developed either in individual research projects or in standardization bodies. This paper aims at analyzing the most relevant service ontologies available today for their suitability to cope with the service semantic interoperability challenge. We take the vision of the Internet of Services (IoS) as our motivation to identify the requirements for service ontologies. We adopt a formal approach to ontology design and evaluation in our analysis. We start by defining informal competency questions derived from a motivating scenario, and we identify relevant concepts and properties in service ontologies that match the formal ontological representation of these questions. We analyze the service ontologies with our concepts and questions, so that each ontology is positioned and evaluated according to its utility. The gaps we identify as the result of our analysis provide an indication of open challenges and future work

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Privacy-Preserving Reengineering of Model-View-Controller Application Architectures Using Linked Data

When a legacy system’s software architecture cannot be redesigned, implementing additional privacy requirements is often complex, unreliable and costly to maintain. This paper presents a privacy-by-design approach to reengineer web applications as linked data-enabled and implement access control and privacy preservation properties. The method is based on the knowledge of the application architecture, which for the Web of data is commonly designed on the basis of a model-view-controller pattern. Whereas wrapping techniques commonly used to link data of web applications duplicate the security source code, the new approach allows for the controlled disclosure of an application’s data, while preserving non-functional properties such as privacy preservation. The solution has been implemented and compared with existing linked data frameworks in terms of reliability, maintainability and complexity

On the Foundations of Data Interoperability and Semantic Search on the Web

This dissertation studies the problem of facilitating semantic search across disparate ontologies that are developed by different organizations. There is tremendous potential in enabling users to search independent ontologies and discover knowledge in a serendipitous fashion, i.e., often completely unintended by the developers of the ontologies. The main difficulty with such search is that users generally do not have any control over the naming conventions and content of the ontologies. Thus terms must be appropriately mapped across ontologies based on their meaning. The meaning-based search of data is referred to as semantic search, and its facilitation (aka semantic interoperability) then requires mapping between ontologies. In relational databases, searching across organizational boundaries currently involves the difficult task of setting up a rigid information integration system. Linked Data representations more flexibly tackle the problem of searching across organizational boundaries on the Web. However, there exists no consensus on how ontology mapping should be performed for this scenario, and the problem is open. We lay out the foundations of semantic search on the Web of Data by comparing it to keyword search in the relational model and by providing effective mechanisms to facilitate data interoperability across organizational boundaries. We identify two sharply distinct goals for ontology mapping based on real-world use cases. These goals are: (i) ontology development, and (ii) facilitating interoperability. We systematically analyze these goals, side-by-side, and contrast them. Our analysis demonstrates the implications of the goals on how to perform ontology mapping and how to represent the mappings. We rigorously compare facilitating interoperability between ontologies to information integration in databases. Based on the comparison, class matching is emphasized as a critical part of facilitating interoperability. For class matching, various class similarity metrics are formalized and an algorithm that utilizes these metrics is designed. We also experimentally evaluate the effectiveness of the class similarity metrics on real-world ontologies. In order to encode the correspondences between ontologies for interoperability, we develop a novel W3C-compliant representation, named skeleton

Ontology Based Integration of Distributed and Heterogeneous Data Sources in ACGT.

In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinic-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European. This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases. A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases. The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer. The ontology is used as a common framework for semantics, modeling the domain and acting as giving support to homogenization. SPARQL has been selected as query language for the Data Access Services and the Mediator. Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases

Trust and Privacy Solutions Based on Holistic Service Requirements

The products and services designed for Smart Cities provide the necessary tools to improve the management of modern cities in a more efficient way. These tools need to gather citizens’ information about their activity, preferences, habits, etc. opening up the possibility of tracking them. Thus, privacy and security policies must be developed in order to satisfy and manage the legislative heterogeneity surrounding the services provided and comply with the laws of the country where they are provided. This paper presents one of the possible solutions to manage this heterogeneity, bearing in mind these types of networks, such as Wireless Sensor Networks, have important resource limitations. A knowledge and ontology management system is proposed to facilitate the collaboration between the business, legal and technological areas. This will ease the implementation of adequate specific security and privacy policies for a given service. All these security and privacy policies are based on the information provided by the deployed platforms and by expert system processing