Interchange Language Research Articles

How ontology can be used to achieve semantic interoperability in healthcare

Abstract Semantic interoperability allows machines to share, interpret and use data without ambiguity. Semantic Interoperability is a major concern in healthcare (c.f. the EU commission 2021 report on electronic record exchange formats). The lack of interoperability with regard to electronic health record (EHR) leads to fragmentation and a lower quality of cross-institution and cross-border healthcare. The simple choice of an interchange language (HL7, FIHR etc.)is not sufficient to ensure interoperability. Healthcare interoperability is associated with multi-level and multi-sectoral complexity, and this cannot be addressed without consideration of a range of people and needs, from application design to knowledge sharing. Each transaction needs to be defined in unambiguous details as part of a complete, consistent, coherent, and machine-readable set of specifications for interoperability between the machines to minimize any potential error. We propose a systematic process to achieve healthcare interoperability, working with healthcare professionals starting from design level to implementation level. In our seminar we will explain with examples how ontology can be used to achieve semantic interoperability in healthcare. Technical requirements, including the choice of tools (e.g. Protégé); data base (e.g. GraphDB); data model (i.e. Web Ontology Language 2 (OWL2); formal specification (i.e. Description logics (DL)); and the right syntax (RDF/XML). Will be introduced.

Geological map fusion: OneGeology-Europe and INSPIRE

Abstract Geological maps can be seen as a type of model and can be implemented in digital systems as geological spatial databases. In this context, geological map fusion can be implemented at different levels: harmonization of the conceptual data model describing the map objects; the use of shared concepts to describe properties in the model to give semantic harmonization; and ensuring geometric consistency. GeoSciML has been developed as an interchange language for geosciences information, derived from a common conceptual data model, along with common vocabularies of concepts to populate the object properties. GeoSciML and the vocabularies were used in the OneGeology-Europe project where a 1:1 million scale geological map of Europe was delivered using disseminated web services from 20 different data providers. The lessons learnt from the OneGeology-Europe project informed the development of the INSPIRE Geology Data Specification. The INSPIRE data specification is used to define what information must be made available through web services under the INSPIRE legislation, so has to be kept simple. The INSPIRE data model can be extended with GeoSciML and will provide a basis for geological map fusion.

WISP: A pattern‐based approach to the interchange of scientific workflow specifications

SummaryScientific workflows are used for dealing with complex problems in different e‐science domains. These workflows are modeled and executed using Scientific Workflow Management Systems (SWfMSs). Generally, SWfMSs provide their own Workflow Specification Language, and this is a challenge considering the possibility of interchanging workflow specifications between different SWfMSs. In this paper, we propose the use of workflow patterns combined with software architecture concepts to capture the key semantics expressed in scientific workflows specified in different Workflow Specification Languages. These concepts are materialized in a novel specification interchange language (and associated tooling) called Workflow Interchange in Science with Patterns (WISP), which is the main contribution of our work. We have evaluated WISP based on real world specifications; in this paper, we present the results of such evaluation (including an assessment of the quality of the research material available), which has eventually led us to reformulate our initial proposal with more stringent assumptions on the input and output specifications. Copyright © 2016 John Wiley & Sons, Ltd.

Synchronous set relations in rewriting logic

This paper presents a mathematical foundation and a rewriting logic infrastructure for the execution and property verification of synchronous set relations. The mathematical foundation is given in the language of abstract set relations. The infrastructure, which is written in the Maude system, enables the synchronous execution of a set relation provided by the user. By using the infrastructure, algorithm verification techniques such as reachability analysis and model checking, already available in Maude for traditional asynchronous rewriting, are automatically available to synchronous set rewriting. In this way, set-based synchronous languages and systems such as those built from agents, components, or objects can be naturally specified and simulated, and are also amenable to formal verification in the Maude system. The use of the infrastructure and some of its Maude-based verification capabilities are illustrated with an executable operational semantics of the Plan Execution Interchange Language (PLEXIL), a synchronous language developed by NASA to support autonomous spacecraft operations.

A formal library of set relations and its application to synchronous languages

Set relations are particularly suitable for specifying the small-step operational semantics of synchronous languages. In this paper, a formal library of set relations for the definition, verification of properties, and execution of binary set relations is presented. The formal library consists of a set of theories written in the Prototype Verification System (PVS) that contains definitions and proofs of properties, such as determinism and compositionality, for synchronous relations. The paper also proposes a serialization procedure that enables the simulation of synchronous set relations via set rewriting systems. The library and the serialization procedure are illustrated with the rewriting logic semantics of the Plan Execution Interchange Language (PLEXIL), a rich synchronous plan execution language developed by NASA to support autonomous spacecraft operations.

Interoperability results for Semantic Web technologies using OWL as the interchange language

Using Semantic Web technologies in complex scenarios requires that such technologies correctly interoperate by interchanging ontologies using the RDF(S) and OWL languages. This interoperability is not straightforward because of the high heterogeneity in Semantic Web technologies and, while the number of such technologies grows, affordable mechanisms for evaluating Semantic Web technology interoperability are needed to comprehend the current and future interoperability of Semantic Web technologies. This paper presents the OWL Interoperability Benchmarking, an international benchmarking activity that involved the evaluation of the interoperability of different Semantic Web technologies using OWL as the interchange language. It describes the evaluation resources used in this benchmarking activity, the OWL Lite Import Benchmark Suite and the IBSE tool, and presents how to use them for evaluating the OWL interoperability of Semantic Web technologies. Moreover, the paper offers an overview of the OWL interoperability results of the eight tools participating in the benchmarking: one ontology-based annotation tool (GATE), three ontology frameworks (Jena, KAON2, and SWI-Prolog), and four ontology development tools (Protégé Frames, Protégé OWL, SemTalk, and WebODE).

Rewriting Logic Semantics of a Plan Execution Language

The Plan Execution Interchange Language (PLEXIL) is a synchronous language developed by NASA to support autonomous spacecraft operations. In this paper, we propose a rewriting logic semantics of PLEXIL in Maude, a high-performance logical engine. The rewriting logic semantics is by itself a formal interpreter of the language and can be used as a semantic benchmark for the implementation of PLEXIL executives. The implementation in Maude has the additional benefit of making available to PLEXIL designers and developers all the formal analysis and verification tools provided by Maude. The formalization of the PLEXIL semantics in rewriting logic poses an interesting challenge due to the synchronous nature of the language and the prioritized rules defining its semantics. To overcome this difficulty, we propose a general procedure for simulating synchronous set relations in rewriting logic that is sound and, for deterministic relations, complete. We also report on two issues at the design level of the original PLEXIL semantics that were identified with the help of the executable specification in Maude.

Interoperability Results for Semantic Web Technologies Using OWL As the Interchange Language

Using Semantic Web technologies in complex scenarios requires that such technologies correctly interoperate by interchanging ontologies using the RDF(S) and OWL languages. This interoperability is not straightforward because of the high heterogeneity in Semantic Web technologies and, while the number of such technologies grows, affordable mechanisms for evaluating Semantic Web technology interoperability are needed to comprehend the current and future interoperability of Semantic Web technologies. This paper presents the OWL Interoperability Benchmarking, an international benchmarking activity that involved the evaluation of the interoperability of different Semantic Web technologies using OWL as the interchange language. It describes the evaluation resources used in this benchmarking activity, the OWL Lite Import Benchmark Suite and the IBSE tool, and presents how to use them for evaluating the OWL interoperability of Semantic Web technologies. Moreover, the paper offers an overview of the OWL interoperability results of the eight tools participating in the benchmarking: one ontology-based annotation tool (GATE), three ontology frameworks (Jena, KAON2, and SWI-Prolog), and four ontology development tools (Protege Frames, Protege OWL, SemTalk, and WebODE).

Combining ontologies and workflows to design formal protocols for biological laboratories

BackgroundLaboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization.ResultsA laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology.The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://www.bmr-genomics.it/farm/cow.ConclusionsUsing COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain.

Standards and ontologies in computational systems biology

With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.

Integration von Geschäfts- und Prozessinformation im landwirtschaftlichen Produktionsablauf

Currently under development are the ISO-Standard 11783 (part 10) for data transfer between management and machines for agricultural data interchange, the ISOagriNET (planned as ISO 17532) for communication between facilities and management, and agroXML for data interchange in business processes. Although all formats are based on the data interchange language XML, they are differently structured and their contents are not sufficiently coordinated. Introducing a Web Service, as well as allowing the use of specialized data services.

An object‐oriented and OpenGIS supported hydro information system (3O‐HIS) for upper Mersey river basin management

An Object‐Oriented and OpenGIS supported hydro information system (3O‐HIS) is developed taking into consideration the fundamental Open technologies and Open Standards using Java as the core programming language; SQL as the information interchange language; the OpenGIS consortium Specifications as the standard for the GIS application integrated into the system (Open Source projects like OpenMap as Geographical Information System and PostgreSQL with PostGIS extension as relational Database) and the Internet technologies as TCP/IP (communication protocols). The 3O‐HIS acts as a platform which can facilitate standard formats for data exchange and code sharing through Object‐Orientation and XML. The additional advantages of the 3O‐HIS are web‐based application with distributed computing and as desktop application; easy integration with different modules based on open source. A validation of the 3O‐HIS is conducted against the Upper Mersey river basin with emphasis on portability, extensibility and user friendliness. It is readily available for carrying a wider range of software tools for an integrated water basin management.

A framework for XML‐based multi‐channel contact point integration

PurposeThis paper explains the concept of how XML can be used to tie together the many different communication channels into a single contact point system. The purpose is to propose a contact point framework that utilizes XML technologies to integrate multiple communication channels.Design/methodology/approachThis is a conceptual paper where two general approaches to channel integration are described and critiqued and a third one proposed.FindingsThis paper has suggested that contact point channel integration products based on XML technology can be used to lower the design, development, management and maintenance costs. The proposed framework can be an initiative in the open source community where software developers can contribute towards the modular development of such software. The use of XML as the primary data interchange language promises to add value to the contact points of a business at a relatively low cost.Research limitations/implicationsFurther research is necessary to evaluate and perfect the use of XML in this context.Practical implicationsThis research suggests a roadmap for how systems integrators can use XML technology to integrate multiple communication channels in a Customer relationship management (CRM) environment.Originality/valueThis is the first research to examine the different approaches to CRM channel integration and propose an XML‐based framework for accomplishing this.

Mémoire: A framework for semantic interoperability of case-based reasoning systems in biology and medicine

Mémoire is a framework for sharing and distributing case bases and case-based reasoning (CBR) systems in biology and medicine. This paper first introduces the semantic Web approach to build a better Web where search engines, knowledge sources and servers, applications and services can live, work, and learn in cooperation. This semantic approach is particularly well suited for biomedical domains because significant ontologies have been developed there and constitute a sound basis for the standardization effort required for the semantic Web. Case-based reasoning systems in biomedicine have also benefited from these biomedical ontologies and models. This article demonstrates for three such systems how a semantics infused approach in CBR gives better, more accurate results in CBR. From this previous work on a semantic approach in CBR in biomedicine, the Mémoire framework has evolved. Mémoire proposes a unified OWL-based representation language for cases and case-based ontologies in biomedicine, where a Web Ontology Language (OWL) is a language to represent ontologies on the Web. Mémoire provides a set of tools for building case-based reasoning systems compliant with its language. Mémoire is extensible and can be adapted to different types of biomedical application domains, tasks, and environments. Mémoire will permit bridging the gap within the multiple case-based reasoning systems dedicated to a single domain, and make available to agents and Web services the case-based competency of the CBR systems adopting its interchange language. The approach could be extended to other application domains of CBR.

XMILE: towards an XML interchange language for system dynamics models

AbstractWe propose that XML should be used as an interchange language for system dynamics models and we have designed and implemented a demonstration that we call XMILE. We believe that there will be many benefits for the system dynamics community in developing a full‐scale interchange language. This paper discusses the motivation factors behind the idea of developing an interchange language for system dynamics models, and explains why XML is a good candidate framework. An initial implementation of XMILE is also presented along with initial findings about its applicability to models built on various system dynamics software platforms. Copyright © 2005 John Wiley & Sons, Ltd.

A framework for analyzing exception flow in software architectures

We present Aereal, a framework for analyzing exception flow in architecture descriptions. Aereal works as a customizable architectural-level exception handling system that can be further constrained or have some of its rules relaxed. Since different architectural styles have different policies for exception flow, Aereal makes it possible to specify rules on how exceptions flow in a given style and to check for violations of these rules. As enabling technologies. Aereal uses Alloy, a first-order relational language, ACME, an interchange language for architecture description, and their associated tool sets.

Semantic network based component organization model for program mining

Based on the definition of component ontology, an effective component classification mechanism and a facet named component relationship are proposed. Then an application domain oriented, hierarchical component organization model is established. At last a hierarchical component semantic network (HCSN) described by ontology interchange language (OIL) is presented and then its function is described. Using HCSN and cooperating with other components retrieving algorithms based on component description, other components information and their assembly or composite modes related to the key component can be found. Based on HCSN, component directory library is catalogued and a prototype system is constructed. The prototype system proves that component library organization based on this model gives guarantee to the reliability of component assembly during program mining.

Designing a high-performance database engine for the ‘Db4XML’ native XML database system

eXtensible Markup Language (XML) is fast becoming the common electronic data interchange language between applications. In this paper, we describe a database engine called ‘Db4XML’, which provides storage for XML documents in native format. Db4XML is a high performance, main memory resident database engine. Db4XML is being used as a testbed for comparing various query evaluation techniques. The use of wild card (*, ?, ‘//’, etc.) in the path expressions of a query allows users to query documents whose structural information is not available. This paper lists different techniques that can be used to evaluate generalized path expressions (GPE) and presents a performance comparison of the same. A preliminary performance study of the effect of using concurrency control techniques on the various query evaluation techniques is also performed. This paper briefly discusses a suitable recovery technique for the database engine.

A probabilistic approach to solving crossword puzzles

We attacked the problem of solving crossword puzzles by computer: given a set of clues and a crossword grid, try to maximize the number of words correctly filled in. After an analysis of a large collection of puzzles, we decided to use an open architecture in which independent programs specialize in solving specific types of clues, drawing on ideas from information retrieval, database search, and machine learning. Each expert module generates a (possibly empty) candidate list for each clue, and the lists are merged together and placed into the grid by a centralized solver. We used a probabilistic representation as a common interchange language between subsystems and to drive the search for an optimal solution. Proverb, the complete system, averages 95.3% words correct and 98.1% letters correct in under 15 minutes per puzzle on a sample of 370 puzzles taken from the New York Times and several other puzzle sources. This corresponds to missing roughly 3 words or 4 letters on a daily 15×15 puzzle, making Proverb a better-than-average cruciverbalist (crossword solver).

The Semantic Web: the roles of XML and RDF

XML and RDF are the current standards for establishing semantic interoperability on the Web, but XML addresses only document structure. RDF better facilitates interoperation because it provides a data model that can be extended to address sophisticated ontology representation techniques. We explain the role of ontologies in the architecture of the Semantic Web. We then briefly summarize key elements of XML and RDF, showing why using XML as a tool for semantic interoperability will be ineffective in the long run. We argue that a further representation and inference layer is needed on top of the Web's current layers, and to establish such a layer, we propose a general method for encoding ontology representation languages into RDF/RDF schema. We illustrate the extension method by applying it to Ontology Interchange Language, an ontology representation and inference language.