The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

Ontology-based modelling of architectural styles

The conceptual modelling of software architectures is of central importance for the quality of a software system. A rich modelling language is required to integrate the different aspects of architecture modelling, such as architectural styles, structural and behavioural modelling, into a coherent framework. Architectural styles are often neglected in software architectures. We propose an ontological approach for architectural style modelling based on description logic as an abstract, meta-level modelling instrument. We introduce a framework for style definition and style combination. The application of the ontological framework in the form of an integration into existing architectural description notations is illustrated

Ontology-based patterns for the integration of business processes and enterprise application architectures

Increasingly, enterprises are using Service-Oriented Architecture (SOA) as an approach to Enterprise Application Integration (EAI). SOA has the potential to bridge the gap between business and technology and to improve the reuse of existing applications and the interoperability with new ones. In addition to service architecture descriptions, architecture abstractions like patterns and styles capture design knowledge and allow the reuse of successfully applied designs, thus improving the quality of software. Knowledge gained from integration projects can be captured to build a repository of semantically enriched, experience-based solutions. Business patterns identify the interaction and structure between users, business processes, and data. Specific integration and composition patterns at a more technical level address enterprise application integration and capture reliable architecture solutions. We use an ontology-based approach to capture architecture and process patterns. Ontology techniques for pattern definition, extension and composition are developed and their applicability in business process-driven application integration is demonstrated

A Semantic-Agent Framework for PaaS Interoperability

Suchismita Hoare, Na Helian, and Nathan Baddoo, 'A Semantic-Agent Framework for PaaS Interoperability', in Proceedings of the The IEEE International Conference on Cloud and Big Data Computing, Toulouse, France, 18-21, July 2016. DOI: 10.1109/UIC-ATC-ScalCom-CBDCom-IoP-SmartWorld.2016.0126 © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Cloud Platform as a Service (PaaS) is poised for a wider adoption by its relevant stakeholders, especially Cloud application developers. Despite this, the service model is still plagued with several adoption inhibitors, one of which is lack of interoperability between proprietary application infrastructure services of public PaaS solutions. Although there is some progress in addressing the general PaaS interoperability issue through various devised solutions focused primarily on API compatibility and platform-agnostic application design models, interoperability specific to differentiated services provided by the existing public PaaS providers and the resultant disparity owing to the offered services’ semantics has not been addressed effectively, yet. The literature indicates that this dimension of PaaS interoperability is awaiting evolution in the state-of-the-art. This paper proposes the initial system design of a PaaS interoperability (IntPaaS) framework to be developed through the integration of semantic and agent technologies to enable transparent interoperability between incompatible PaaS services. This will involve uniform description through semantic annotation of PaaS provider services utilizing the OWL-S ontology, creating a knowledgebase that enables software agents to automatically search for suitable services to support Cloud-based Greenfield application development. The rest of the paper discusses the identified research problem along with the proposed solution to address the issue.Submitted Versio

A conceptual model for semantically-based e-government portals

Issues of semantic interoperability and service integration for e-government portals are the domain of interest of the present paper. We propose a Conceptual Model for One-Stop e-Government Portals based on the Semantic Web Service technology. We describe our research into building the three basic ontologies and their integration with standard ontologies. The result is a project-independent reusable model. At the same time, we outline a simple methodology for applying the proposed conceptual model into a specific scenario

Mediation of semantic web services in IRS-III

Business applications composed of heterogeneous distributed components or Web services need mediation to resolve data and process mismatches at runtime. This paper describes mediation in IRS-III, a framework and platform for developing WSMO-based Semantic Web Services. We present our approach to mediation within Semantic Web Services and highlight the role of WSMO mediator types when solving mismatches at the semantic level between a service requester and a service provider. We describe the components of our mediation framework and how it can handle data, goal and process mediation during the activities of selection, composition and invocation of Semantic Web Services

Past, present and future of information and knowledge sharing in the construction industry: Towards semantic service-based e-construction

The paper reviews product data technology initiatives in the construction sector and provides a synthesis of related ICT industry needs. A comparison between (a) the data centric characteristics of Product Data Technology (PDT) and (b) ontology with a focus on semantics, is given, highlighting the pros and cons of each approach. The paper advocates the migration from data-centric application integration to ontology-based business process support, and proposes inter-enterprise collaboration architectures and frameworks based on semantic services, underpinned by ontology-based knowledge structures. The paper discusses the main reasons behind the low industry take up of product data technology, and proposes a preliminary roadmap for the wide industry diffusion of the proposed approach. In this respect, the paper stresses the value of adopting alliance-based modes of operation

An ontology of agile aspect oriented software development

Both agile methods and aspect oriented programming (AOP) have emerged in recent years as new paradigms in software development. Both promise to free the process of building software systems from some of the constraints of more traditional approaches. As a software engineering approach on the one hand, and a software development tool on the other, there is the potential for them to be used in conjunction. However, thus far, there has been little interplay between the two. Nevertheless, there is some evidence that there may be untapped synergies that may be exploited, if the appropriate approach is taken to integrating AOP with agile methods. This paper takes an ontological approach to supporting this integration, proposing ontology enabled development based on an analysis of existing ontologies of aspect oriented programming, a proposed ontology of agile methods, and a derived ontology of agile aspect oriented development

Context constraint integration and validation in dynamic web service compositions

System architectures that cross organisational boundaries are usually implemented based on Web service technologies due to their inherent interoperability benets. With increasing exibility requirements, such as on-demand service provision, a dynamic approach to service architecture focussing on composition at runtime is needed. The possibility of technical faults, but also violations of functional and semantic constraints require a comprehensive notion of context that captures composition-relevant aspects. Context-aware techniques are consequently required to support constraint validation for dynamic service composition. We present techniques to respond to problems occurring during the execution of dynamically composed Web services implemented in WS-BPEL. A notion of context { covering physical and contractual faults and violations { is used to safeguard composed service executions dynamically. Our aim is to present an architectural framework from an application-oriented perspective, addressing practical considerations of a technical framework

Business integration models in the context of web services.

E-commerce development and applications have been bringing the Internet to business and marketing and reforming our current business styles and processes. The rapid development of the Web, in particular, the introduction of the semantic web and web service technologies, enables business processes, modeling and management to enter an entirely new stage. Traditional web based business data and transactions can now be analyzed, extracted and modeled to discover new business rules and to form new business strategies, let alone mining the business data in order to classify customers or products. In this paper, we investigate and analyze the business integration models in the context of web services using a micro-payment system because a micro-payment system is considered to be a service intensive activity, where many payment tasks involve different forms of services, such as payment method selection for buyers, security support software, product price comparison, etc. We will use the micro-payment case to discuss and illustrate how the web services approaches support and transform the business process and integration model.