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

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

The Semantic Web is an extension of the current web in which information is given well-defined meaning. The perspective of Semantic Web is to promote the quality and intelligence of the current web by changing its contents into machine understandable form. Therefore, semantic level information is one of the cornerstones of the Semantic Web. The process of adding semantic metadata to web resources is called Semantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality, scalability, and issues which are related to diversity and inconsistency in content of different web pages. Due to the wide range of domains and the dynamic environments that the Semantic Annotation systems must be performed on, the problem of automating annotation process is one of the significant challenges in this domain. To overcome this problem, different machine learning approaches such as supervised learning, unsupervised learning and more recent ones like, semi-supervised learning and active learning have been utilized. In this paper we present an inclusive layered classification of Semantic Annotation challenges and discuss the most important issues in this field. Also, we review and analyze machine learning applications for solving semantic annotation problems. For this goal, the article tries to closely study and categorize related researches for better understanding and to reach a framework that can map machine learning techniques into the Semantic Annotation challenges and requirements

Atomic: an open-source software platform for multi-level corpus annotation

This paper presents Atomic, an open-source platform-independent desktop application for multi-level corpus annotation. Atomic aims at providing the linguistic community with a user-friendly annotation tool and sustainable platform through its focus on extensibility, a generic data model, and compatibility with existing linguistic formats. It is implemented on top of the Eclipse Rich Client Platform, a pluggable Java-based framework for creating client applications. Atomic - as a set of plug-ins for this framework - integrates with the platform and allows other researchers to develop and integrate further extensions to the software as needed. The generic graph-based meta model Salt serves as Atomic’s domain model and allows for unlimited annotation levels and types. Salt is also used as an intermediate model in the Pepper framework for conversion of linguistic data, which is fully integrated into Atomic, making the latter compatible with a wide range of linguistic formats. Atomic provides tools for both less experienced and expert annotators: graphical, mouse-driven editors and a command-line data manipulation language for rapid annotation

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Supporting user-oriented analysis for multi-view domain-specific visual languages

This is the post-print version of the final paper published in Information and Software Technology. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2008 Elsevier B.V.The integration of usable and flexible analysis support in modelling environments is a key success factor in Model-Driven Development. In this paradigm, models are the core asset from which code is automatically generated, and thus ensuring model correctness is a fundamental quality control activity. For this purpose, a common approach is to transform the system models into formal semantic domains for verification. However, if the analysis results are not shown in a proper way to the end-user (e.g. in terms of the original language) they may become useless. In this paper we present a novel DSVL called BaVeL that facilitates the flexible annotation of verification results obtained in semantic domains to different formats, including the context of the original language. BaVeL is used in combination with a consistency framework, providing support for all steps in a verification process: acquisition of additional input data, transformation of the system models into semantic domains, verification, and flexible annotation of analysis results. The approach has been validated analytically by the cognitive dimensions framework, and empirically by its implementation and application to several DSVLs. Here we present a case study of a notation in the area of Digital Libraries, where the analysis is performed by transformations into Petri nets and a process algebra.Spanish Ministry of Education and Science and MODUWEB

A linked data compliant framework for dynamic and web-scale consumption of web services

The While Semantic Web Services (SWS) research aims at automating Web service tasks such as discovery, orchestration and execution, its take-up is very limited so far. This is due to several reasons, such as inherent complexity of existing SWS frameworks and the considerable costs involved in creating correct SWS descriptions. In addition, while semantics are in use to enable tasks such as discovery, interaction between service consumers, providers and brokering environments is still not supported by semantic message descriptions. On the other hand, the Linked Data approach has produced a set of established principles for sharing and describing data, such as RDF as representation language and the integral use of dereferencable URIs. In this paper we propose to apply those principles to expose Web services and Web APIs and introduce a framework in which service registries as well as services contribute to the automation of service discovery, and hence, workload is distributed more efficiently. This is achieved by developing a Linked Data compliant Web services framework with that communicate with semi-centralised registries but compute their suitability for a given request themselves. All communications among different framework components are using RDF-based message protocols including service input and output. This framework aims at optimizing load balance and performance by dynamically assembling services at run time in a massively distributed Web environment