Automatically exposing OpenLifeData via SADI semantic Web Services

Background: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

TOWARD SEMANTIC WEB SERVICES AS MVC APPLICATIONS: FROM OWL-S VIA UML

OWL-S is an application of OWL, the Web Ontology Language, that describes the semantics of Web Services so that their discovery, selection, invocation and composition can be automated. The research literature reports the use of UML diagrams for the automatic generation of Semantic Web Service descriptions in OWL-S. This paper demonstrates a higher level of automation by generating complete complete Web applications from OWL-S descriptions that have themselves been generated from UML. Previously, we proposed an approach for processing OWL-S descriptions in order to produce MVC-based skeletons for Web applications. The OWL-S ontology undergoes a series of transformations in order to generate a Model-View-Controller application implemented by a combination of Java Beans, JSP, and Servlets code, respectively. In this paper, we show in detail the documents produced at each processing step. We highlight the connections between OWL-S specifications and executable code in the various Java dialects and show the Web interfaces that result from this process.

INFRAWEBS BPEL-Based Editor for Creating the Semantic Web Services Description

INFRAWEBS project [INFRAWEBS] considers usage of semantics for the complete lifecycle of Semantic Web processes, which represent complex interactions between Semantic Web Services. One of the main initiatives in the Semantic Web is WSMO framework, aiming at describing the various aspects related to Semantic Web Services in order to enable the automation of Web Service discovery, composition, interoperation and invocation. In the paper the conceptual architecture for BPEL-based INFRAWEBS editor is proposed that is intended to construct a part of WSMO descriptions of the Semantic Web Services. The semantic description of Web Services has to cover Data, Functional, Execution and QoS semantics. The representation of Functional semantics can be achieved by adding the service functionality to the process description. The architecture relies on a functional (operational) semantics of the Business Process Execution Language for Web Services (BPEL4WS) and uses abstract state machine (ASM) paradigm. This allows describing the dynamic properties of the process descriptions in terms of partially ordered transition rules and transforming them to WSMO framework.

A survey of semantic web services formalisms

The field of Semantic Web Services (SWS) has been recognized as one of the most promising areas of emergent research within the Semantic Web initiative, exhibiting an extensive commercial potential and attracting significant attention from both industry and the research community. Currently, there exist several different frameworks and languages for formally describing a Web Service: Web Ontology Language for Services (OWL-S), Web Service Modelling Ontology (WSMO) and Semantic Annotations for the Web Services Description Language (SAWSDL) are the most important approaches. To the inexperienced user, choosing the appropriate platform for a specific SWS application may prove to be challenging, given a lack of clear separation between the ideas promoted by the associated research communities. In this paper, we systematically compare OWL-S, WSMO and SAWSDL from various standpoints, namely, that of the service requester and provider as well as the broker-based view. The comparison is meant to help users to better understand the strengths and limitations of these different approaches to formalizing SWS, and to choose the most suitable solution for a given application. Copyright © 2015 John Wiley & Sons, Ltd.

A survey of semantic web services formalisms

The field of Semantic Web Services (SWS) has been recognized as one of the most promising areas of emergent research within the Semantic Web (SW) initiative, exhibiting an extensive commercial potential, and attracting significant attention from both industry and the research community. Currently, there exist several different frameworks and languages for formally describing a Web Service: OWL-S (Web Ontology Language for Services), WSMO (Web Service Modeling Ontology) and SAWSDL (Semantic Annotations for the Web Services Description Language) are the most important approaches. To the inexperienced user, choosing the appropriate paradigm for a specific SWS application may prove to be challenging, given a lack of clear separation between the ideas promoted by the associated research communities. In this paper, we systematically compare OWL-S, WSMO and SAWSDL from various standpoints, namely that of the service requester and provider as well as the broker based view. The comparison is meant to help users to better understand the strengths and limitations of these different approaches to formalising SWS, and to choose the most suitable solution for a given use case. © 2013 IEEE.

Semantic Description of Web Services and Possibilities of BPEL4WS

The using of the upsurge of semantics web technologies gives a possibility for an increasing of the flexibility, extensibility and consistency of the existent industrial standards for modeling of web services. In the paper the types of semantic description of web services and the degree of their realization in BPEL4WS (Business Process Execution Language for Web Services) respectively on the abstract and executable level are treated. The methods for using of BPEL4WS for the purposes of semantic web services in the direction of their semi-automatic integration are suggested.

A Description Framework and Event-Driven Architecture for the Semantic Web and Semantic Grid

In this introductory chapter we put in context and give a brief outline of the work that we thoroughly present in the rest of the dissertation. We consider this work divided in two main parts. The first part is the Firenze Framework, a knowledge level description framework rich enough to express the semantics required for describing both semantic Web services and semantic Grid services. We start by defining what the Semantic Grid is and its relation with the Semantic Web; and the possibility of their convergence since both initiatives have become mainly service-oriented. We also introduce the main motivators of the creation of this framework, one is to provide a valid description framework that works at knowledge level; the other to provide a description framework that takes into account the characteristics of Grid services in order to be able to describe them properly. The other part of the dissertation is devoted to Vega, an event-driven architecture that, by means of proposed knowledge level description framework, is able to achieve high scale provisioning of knowledge-intensive services. In this introductory chapter we portrait the anatomy of a generic event-driven architecture, and we briefly enumerate their main characteristics, which are the reason that make them our choice.

A semantic web environment for component model

Component-based development (CBD) has become an important emerging topic in the software engineering field. It promises long-sought-after benefits such as increased software reuse, reduced development time to market and, hence, reduced software production cost. Despite the huge potential, the lack of reasoning support and development environment of component modeling and verification may hinder its development. Methods and tools that can support component model analysis are highly appreciated by industry. Such a tool support should be fully automated as well as efficient. At the same time, the reasoning tool should scale up well as it may need to handle hundreds or even thousands of components that a modern software system may have. Furthermore, a distributed environment that can effectively manage and compose components is also desirable. In this paper, we present an approach to the modeling and verification of a newly proposed component model using Semantic Web languages and their reasoning tools. We use the Web Ontology Language and the Semantic Web Rule Language to precisely capture the inter-relationships and constraints among the entities in a component model. Semantic Web reasoning tools are deployed to perform automated analysis support of the component models. Moreover, we also proposed a service-oriented architecture (SOA)-based semantic web environment for CBD. The adoption of Semantic Web services and SOA make our component environment more reusable, scalable, dynamic and adaptive.

INFRAWEBS Semantic Web Service Development on the Base of Knowledge Management Layer

The paper gives an overview about the ongoing FP6-IST INFRAWEBS project and describes the main layers and software components embedded in an application oriented realisation framework. An important part of INFRAWEBS is a Semantic Web Unit (SWU) – a collaboration platform and interoperable middleware for ontology-based handling and maintaining of SWS. The framework provides knowledge about a specific domain and relies on ontologies to structure and exchange this knowledge to semantic service development modules. INFRAWEBS Designer and Composer are sub-modules of SWU responsible for creating Semantic Web Services using Case-Based Reasoning approach. The Service Access Middleware (SAM) is responsible for building up the communication channels between users and various other modules. It serves as a generic middleware for deployment of Semantic Web Services. This software toolset provides a development framework for creating and maintaining the full-life-cycle of Semantic Web Services with specific application support.

Defending web services against denial of service attacks using client puzzles

The interoperable and loosely-coupled web services architecture, while beneficial, can be resource-intensive, and is thus susceptible to denial of service (DoS) attacks in which an attacker can use a relatively insignificant amount of resources to exhaust the computational resources of a web service. We investigate the effectiveness of defending web services from DoS attacks using client puzzles, a cryptographic countermeasure which provides a form of gradual authentication by requiring the client to solve some computationally difficult problems before access is granted. In particular, we describe a mechanism for integrating a hash-based puzzle into existing web services frameworks and analyze the effectiveness of the countermeasure using a variety of scenarios on a network testbed. Client puzzles are an effective defence against flooding attacks. They can also mitigate certain types of semantic-based attacks, although they may not be the optimal solution.

A data mining based method for discovery of web services and their compositions

Due to the availability of huge number of web services, finding an appropriate Web service according to the requirements of a service consumer is still a challenge. Moreover, sometimes a single web service is unable to fully satisfy the requirements of the service consumer. In such cases, combinations of multiple inter-related web services can be utilised. This paper proposes a method that first utilises a semantic kernel model to find related services and then models these related Web services as nodes of a graph. An all-pair shortest-path algorithm is applied to find the best compositions of Web services that are semantically related to the service consumer requirement. The recommendation of individual and composite Web services composition for a service request is finally made. Empirical evaluation confirms that the proposed method significantly improves the accuracy of service discovery in comparison to traditional keyword-based discovery methods.

Managing digital libraries using semantic web technologies

The aim of this work is to improve retrieval and navigation services on bibliographic data held in digital libraries. This paper presents the design and implementation of OntoBib¸ an ontology-based bibliographic database system that adopts ontology-driven search in its retrieval. The presented work exemplifies how a digital library of bibliographic data can be managed using Semantic Web technologies and how utilizing the domain specific knowledge improves both search efficiency and navigation of web information and document retrieval.

Intelligent wireless web services: context-aware computing in construction-logistics supply chain

The construction industry has incurred a considerable amount of waste as a result of poor logistics supply chain network management. Therefore, managing logistics in the construction industry is critical. An effective logistic system ensures delivery of the right products and services to the right players at the right time while minimising costs and rewarding all sectors based on value added to the supply chain. This paper reports on an on-going research study on the concept of context-aware services delivery in the construction project supply chain logistics. As part of the emerging wireless technologies, an Intelligent Wireless Web (IWW) using context-aware computing capability represents the next generation ICT application to construction-logistics management. This intelligent system has the potential of serving and improving the construction logistics through access to context-specific data, information and services. Existing mobile communication deployments in the construction industry rely on static modes of information delivery and do not take into account the worker’s changing context and dynamic project conditions. The major problems in these applications are lack of context-specificity in the distribution of information, services and other project resources, and lack of cohesion with the existing desktop based ICT infrastructure. The research works focus on identifying the context dimension such as user context, environmental context and project context, selection of technologies to capture context-parameters such wireless sensors and RFID, selection of supporting technologies such as wireless communication, Semantic Web, Web Services, agents, etc. The process of integration of Context-Aware Computing and Web-Services to facilitate the creation of intelligent collaboration environment for managing construction logistics will take into account all the necessary critical parameters such as storage, transportation, distribution, assembly, etc. within off and on-site project.

Algorithm for web services matching

UDDI is a standard for publishing and discovery of web services. UDDI registries provide keyword searches for web services. The search functionality is very simple and fails to account for relationships between web services. In this paper, we propose an algorithm which retrieves closely related web services. The proposed algorithm is based on singular value decomposition (SVD) in linear algebra, which reveals semantic relationships among web services. The preliminary evaluation shows the effectiveness and feasibility of the algorithm.

PGSW-OS: a novel approach for resource management in a semantic web operating system based on a P2P grid architecture

A web operating system is an operating system that users can access from any hardware at any location. A peer-to-peer (P2P) grid uses P2P communication for resource management and communication between nodes in a grid and manages resources locally in each cluster, and this provides a proper architecture for a web operating system. Use of semantic technology in web operating systems is an emerging field that improves the management and discovery of resources and services. In this paper, we propose PGSW-OS (P2P grid semantic Web OS), a model based on a P2P grid architecture and semantic technology to improve resource management in a web operating system through resource discovery with the aid of semantic features. Our approach integrates distributed hash tables (DHTs) and semantic overlay networks to enable semantic-based resource management by advertising resources in the DHT based upon their annotations to enable semantic-based resource matchmaking. Our model includes ontologies and virtual organizations. Our technique decreases the computational complexity of searching in a web operating system environment. We perform a simulation study using the Gridsim simulator, and our experiments show that our model provides enhanced utilization of resources, better search expressiveness, scalability, and precision. © 2014 Springer Science+Business Media New York.