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

Research and Development Workstation Environment: the new class of Current Research Information Systems

Against the backdrop of the development of modern technologies in the field of scientific research the new class of Current Research Information Systems (CRIS) and related intelligent information technologies has arisen. It was called - Research and Development Workstation Environment (RDWE) - the comprehensive problem-oriented information systems for scientific research and development lifecycle support. The given paper describes design and development fundamentals of the RDWE class systems. The RDWE class system's generalized information model is represented in the article as a three-tuple composite web service that include: a set of atomic web services, each of them can be designed and developed as a microservice or a desktop application, that allows them to be used as an independent software separately; a set of functions, the functional filling-up of the Research and Development Workstation Environment; a subset of atomic web services that are required to implement function of composite web service. In accordance with the fundamental information model of the RDWE class the system for supporting research in the field of ontology engineering - the automated building of applied ontology in an arbitrary domain area, scientific and technical creativity - the automated preparation of application documents for patenting inventions in Ukraine was developed. It was called - Personal Research Information System. A distinctive feature of such systems is the possibility of their problematic orientation to various types of scientific activities by combining on a variety of functional services and adding new ones within the cloud integrated environment. The main results of our work are focused on enhancing the effectiveness of the scientist's research and development lifecycle in the arbitrary domain area.Comment: In English, 13 pages, 1 figure, 1 table, added references in Russian. Published. Prepared for special issue (UkrPROG 2018 conference) of the scientific journal "Problems of programming" (Founder: National Academy of Sciences of Ukraine, Institute of Software Systems of NAS Ukraine

JeroMF: A Software Development Framework for Building Distributed Applications Based on Microservices and JeroMQ

This report describes a project involving the design, implementation, and testing of a software development framework, called JeroMF, that can help developers create scalable distributed applications based on a microservice architecture and that uses JeroMQ (a native Java implementation of ZeroMQ) for message passing. JeroMF provides an execution framework and extensible components for implementing processes, services, communication channels, messages, communication statistics, and encryption. Applications built with JeroMF do not require a message broker or any other middleware processes. However, they may include an optional Service Registry that can facilitate for service discovery and secure communications. The Service Registry itself was implemented with JeroMF and is included as part of the JeroMF distribution. Thorough unit, integration and system test cases exist for every component of JeroMF. For validation, JeroMF was used to re-design and re-implement a distributed health-care application with 13 separate types of services and very strict security requirements

Design and realization of a middleware for mobile task coordination

The trend towards interconnection of applications has long been recognized as a key challenge for information systems design. Following this trend, organi- zations have developed and introduced many distributed systems with differ- ent functionalities. Furthermore, computing becomes today increasingly mobile; performances of mobile devices (i.e. PDAs and smartphones) as well as the expansion of high-speed mobile networks allows many tasks to be performed beyond stationary workspaces. The dramatic growth of stand-alone and partly incompatible applications will negatively affect the integration, coordination and communication for entire so- lution. Contemporary solutions focus on stationary systems only; the usage of mobile devices is limited to simple scenarios (i.e. information access). In order to support the seamless integration of mobile devices, future distributed solutions should take services and service meta-information into account (e.g. variation of network bandwidth, battery power, availability, connectivity, reachability, sensors data and locations of services and service providers). In this master thesis we want to analyze how a distributed environment with va- riety of separated (mobile) service providers - implemented with different tech- nologies - can be integrated and coordinated. Finding compromises between performance, comfort and intelligent intercommunication is the main goal of this thesis. Therefore, it is concentrated on the conceptualization and design of a central middleware component that provide the coordination and communication functionalities for stationary and mobile entities. In order to prove some possible communication scenarios, the thesis provides a middleware-based scenario

DESIGNING A FRAMEWORK FOR RESTFUL MULTI-AGENT SYSTEMS

Nowadays there are many systems that require some degree of automation. To attain this automation, agent technology has generally been found to be a promising approach. An agent is a piece of software that does activities on behalf of a user or another program. However, designing and deploying an agent infrastructure that achieves scalability is still a major challenge. In this thesis, a pattern for designing agents following RESTful principles is proposed in an effort to address the aforementioned challenges. In addition, the pattern will follow the FIPA Abstract Architecture; which is aimed at developing intelligent agents and supporting interoperability among agents and agent-based systems. Furthermore, an evaluation is done to investigate the scalability of the deployment of a RESTful multi-agent system

Comparative study of healthcare messaging standards for interoperability in ehealth systems

Advances in the information and communication technology have created the field of "health informatics," which amalgamates healthcare, information technology and business. The use of information systems in healthcare organisations dates back to 1960s, however the use of technology for healthcare records, referred to as Electronic Medical Records (EMR), management has surged since 1990’s (Net-Health, 2017) due to advancements the internet and web technologies. Electronic Medical Records (EMR) and sometimes referred to as Personal Health Record (PHR) contains the patient’s medical history, allergy information, immunisation status, medication, radiology images and other medically related billing information that is relevant. There are a number of benefits for healthcare industry when sharing these data recorded in EMR and PHR systems between medical institutions (AbuKhousa et al., 2012). These benefits include convenience for patients and clinicians, cost-effective healthcare solutions, high quality of care, resolving the resource shortage and collecting a large volume of data for research and educational needs. My Health Record (MyHR) is a major project funded by the Australian government, which aims to have all data relating to health of the Australian population stored in digital format, allowing clinicians to have access to patient data at the point of care. Prior to 2015, MyHR was known as Personally Controlled Electronic Health Record (PCEHR). Though the Australian government took consistent initiatives there is a significant delay (Pearce and Haikerwal, 2010) in implementing eHealth projects and related services. While this delay is caused by many factors, interoperability is identified as the main problem (Benson and Grieve, 2016c) which is resisting this project delivery. To discover the current interoperability challenges in the Australian healthcare industry, this comparative study is conducted on Health Level 7 (HL7) messaging models such as HL7 V2, V3 and FHIR (Fast Healthcare Interoperability Resources). In this study, interoperability, security and privacy are main elements compared. In addition, a case study conducted in the NSW Hospitals to understand the popularity in usage of health messaging standards was utilised to understand the extent of use of messaging standards in healthcare sector. Predominantly, the project used the comparative study method on different HL7 (Health Level Seven) messages and derived the right messaging standard which is suitable to cover the interoperability, security and privacy requirements of electronic health record. The issues related to practical implementations, change over and training requirements for healthcare professionals are also discussed

Migrating Integration from SOAP to REST : Can the Advantages of Migration Justify the Project?

This thesis investigates the functional and conceptual differences between SOAP-based and RESTful web services and their implications in the context of a real-world migration project. The primary research questions addressed are: • What are the key functional and conceptual differences between SOAP-based and RESTful web services? • How can SOAP-based and RESTful service clients be implemented into a general client? • Can developing a client to work with REST and SOAP be justified based on differences in performance and maintainability? The thesis begins with a literature review of the core principles and features of SOAP and REST, highlighting their strengths, weaknesses, and suitability for different use cases. A detailed comparison table is provided to summarize the key differences between the two web services. The thesis presents a case study of a migration project from Lemonsoft's web team, which involved adapting an existing integration to support SOAP-based and RESTful services. The project utilized design patterns and a general client implementation to achieve a unified solution compatible with both protocols. In terms of performance, the evaluation showed that the general client led to faster execution times and reduced memory usage, enhancing the overall system efficiency. Additionally, improvements in maintainability were achieved by simplifying the codebase, using design patterns and object factories, adopting an interface-driven design, and promoting collaborative code reviews. These enhancements have not only resulted in a better user experience but also minimized future resource demands and maintenance costs. In conclusion, this thesis provides valuable insights into the functional and conceptual differences between SOAP-based and RESTful web services, the challenges and best practices for implementing a general client, and the justification for resource usage in such a solution based on performance and maintainability improvements