Automated Syntactic Medation for Web Service Integration

Lecture Notes in Computer Science, 2007

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services.

Web Services, 2006. …, 2006

With the rising popularity of Web services, both academia and industry have invested considerably in Web service description standards, discovery, and composition techniques. The standards based approach utilized by Web services has supported interoperability at the syntax level. However, issues of structural and semantic heterogeneity between messages exchanged by Web services are far more complex and crucial to interoperability. It is for these reasons that we recognize the value that schema/data mappings bring to Web service descriptions. In this paper, we examine challenges to interoperability; classify the types of heterogeneities that can occur between interacting services and present a possible solution for data interoperability using the mapping support provided by WSDL-S. We present a data mediation architecture using the extensibility features of WSDL and the popular SOAP engine, Axis 2. Table 2 Web service interoperability -Evaluation

Lecture Notes in Computer Science, 2014

Heterogeneity of data and data formats in bioinformatics entail mismatches between inputs and outputs of different services, making it difficult to compose them into workflows. To reduce those mismatches, bioinformatics platforms propose ad'hoc converters, called shims. When shims are written by hand, they are time-consuming to develop, and cannot anticipate all needs. When shims are automatically generated, they miss transformations, for example data composition from multiple parts, or parallel conversion of list elements. This article proposes to systematically detect convertibility from output types to input types. Convertibility detection relies on a rule system based on abstract types, close to XML Schema. Types allow to abstract data while precisely accounting for their composite structure. Detection is accompanied by an automatic generation of converters between input and output XML data. We show the applicability of our approach by abstracting concrete bioinformatics types (e.g., complex biosequences) for a number of bioinformatics services (e.g., blast). We illustrate how our automatically generated converters help to resolve data mismatches when composing workflows. We conducted an experiment on bioinformatics services and datatypes, using an implementation of our approach, as well as a survey with domain experts. The detected convertibilities and produced converters were validated as relevant from a biological point of view. Furthermore the automatically produced graph of potentially compatible services exhibited a connectivity higher than with the ad'hoc approaches. Indeed, the experts discovered unknown possible connexions.

International Journal of Enterprise Information Systems, 2007

Much of the early focus in the area of Semantic Web has been on the development of representation languages for static conceptual information, while there has been less emphasis on how to make Semantic Web applications practically useful in the context of knowledge work. To achieve this, a better coupling is needed between ontology, service descriptions and workflow modeling, including both traditional production workflow and interactive workflow techniques This article reviews the basic technologies involved in this area to provide system and business interoperability, and outlines what can be achieved by merging them in the context of real world workflow descriptions.

Advances in Grid …, 2005

Interactive applications like Problem Solving Environments require on demand access to Web Services, where the services are autonomously discovered, composed, selected and invocated based on a description of requested capabilities. Semantic Web Services aim at providing semantically interpretable capabilities through the use of shared ontologies. We demonstrate how Grid Services for an interactive biomedical application are annotated with a domain ontology, and propose algorithms for automated composition and selection of workflows, where workflows are created by semantically matching service capabilities, and where workflow selection is based on a trade-off between the types of semantic matches in the workflow and the number of services. The algorithms are demonstrated on semantically annotated Grid Services in the biomedical application.

Proc. of the 9th Intl. …, 2007

Web service composition has quickly become a key area of research in the services oriented architecture community. One of the challenges in composition is the existence of heterogeneities across independently created and autonomously managed Web service requesters and Web service providers. Previous work in this area either involved significant human effort or in cases of the efforts seeking to provide largely automated approaches, overlooked the problem of data heterogeneities, resulting in partial solutions that would not support executable workflow for real-world problems. In this paper, we present a planning-based approach to solve both the process heterogeneity and data heterogeneity problems. Our system successfully outputs an executable BPEL file which correctly solves non-trivial real-world process specifications outlind in the 2006 SWS Challenge.

Service Oriented Computing and Applications, 2010

Semantic Web Services (SWS) aim at the automated discovery, selection and orchestration of Web services on the basis of comprehensive, machine-interpretable semantic descriptions. However, heterogeneities between distinct SWS representations pose strong limitations wrt interoperability and reusability. Hence, semantic-level mediation, ie mediation between concurrent semantic representations of services, is a key requirement to allow SWS matchmaking algorithms to compare capabilities of distinct SWS. Semantic- ...

Journal of Web Semantics, 2003

In this paper, we introduce a vision for Semantic Web services which combines the growing Web services architecture and the Semantic Web and we will propose DAML-S as a prototypical example of an ontology for describing Semantic Web services. Furthermore, we show that DAML-S is not just an abstract description, but it can be efficiently implemented to support capability matching and to manage interaction between Web services. Specifically, we will describe the implementation of the DAML-S/UDDI Matchmaker that expands on UDDI by providing semantic capability matching, and we will present the DAML-S Virtual Machine that uses the DAML-S Process Model to manage the interaction with Web service. We will also show that the use of DAML-S does not produce a performance penalty during the normal operation of Web services.

Lecture notes in computer science, 2004

Journal of Biomedical Semantics, 2011

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.