Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus (...) on business aspects and not enough on involvement of the right sorts of researchers, in particular those that are able to see how the data and information relate to the entities of concern on the side of the patient. The lack of a central focus on the patient, and the associated focus on ‘concepts’, have spawned a variety of mutually incompatible terminologies exhibiting non-resolvable overlap. The predominance of the healthcare IT industry in the writing and selection of semantic interoperability standards mitigates against the benefits that standards, when well designed, can bring about. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

This article is an exploratory study that intends to present semantic interoperability initiatives in the area of information science and computer science. It discusses these initiatives, focusing on open science and eScience, aiming at pointing out similarities and differences in the methodologies used for an intelligent retrieval of data in heterogeneous environments that do not benefit a universal language. We will illustrate seminal initiatives regarding the compatibility of languages in information science and the alignment and semantic mapping in the (...) area of computer science, emphasizing what they have in common and their differences, showing that those seminal initiatives are still relevant nowadays. In this perspective, we want to bring up discussions about methodologies that supports a kind of “intermediate language” that allows the compatibility of research resources, semantically interconnecting their contents without forcing the use of a single language, but of a switching language, such as a metalanguage that guarantees to keep the differences of each community of speech. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it has not been able to keep (...) pace with recent developments either in semantics and ontology or in computer science and engineering. HL7’s response has been to develop its “Services-Aware Interoperability Framework” (SAIF), which is intended to provide a foundation for work on all aspects of standardization in HL7 henceforth. We here summarise the major design principles that must be satisfied by a semantic interoperability framework – principles relating both to static semantics and to computational behaviour. We then assess the SAIF in light of these principles. We conclude that the SAIF is not in a position to support the needed reform of the HL7 v3 family of standards. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

In the text, I discuss the abilities and challenges of information systems interoperability. The anticipated and expected result of interoperability is to improve the provision of public utility services to citizens and companies by means of facilitating the provision of public utility services on the basis of a “single window” principle and reducing the costs incurred by public administrations, companies, and citizens, resulting from the efficiency of the provision of public utility services. In the article, the conceptual framework (...) of interoperability is elaborated upon. Moreover, information systems and public registers for entrepreneurs in Poland exemplify whether the interoperability may be applied and, if so, whether interoperability fulfils its targets to the extent of e-Government services for entrepreneurs. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models (...) such as archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

This article considers how Spatial Big Data is situated and produced through embodied spatial experiences as data processes appear and act in small moments on mobile phone applications and other digital spatial technologies. Locating Spatial Big Data in the historical and geographical contexts of Sydney and Hong Kong, it traces how situated knowledges mediate and moderate the rising potency of discourses of cartographic reason and data logics as colonial cartographic imaginations expressed in land divisions and urban planning continue on, in (...) a world that increasingly values models of calculability, interoperability and authority. It draws on ethnographic material gathered through walking interviews in both cities, and in doing so, it argues that by using ethnographic ‘moments’, it is possible to decentre the focus on data processes to consider the critical potential of a politics of everyday experiences that produce and reflect the structures of data logics. Through these ethnographic moments, this article examines how mobile technologies are complicit in the production of Spatial Big Data, and the impact this has on the increasing regimentation and surveillance of modes of being and expression via mobile media. At the same time, it will argue that while spatial calculability has expanded from cartographic reason into data logics, the epistemological universality of Spatial Big Data is constantly being resisted – in moments of experimentation, failure, intuition, memory and desire, the ghosts of the incalculable epistemes, experiences and people, forgotten by the emphasis on calculation, continue to speak. (shrink)

Wearable devices are increasingly present in the health context, as tools for biomedical research and clinical care. In this context, wearables are considered key tools for a more digital, personalised, preventive medicine. At the same time, wearables have also been associated with issues and risks, such as those connected to privacy and data sharing. Yet, discussions in the literature have mostly focused on either technical or ethical considerations, framing these as largely separate areas of discussion, and the contribution of wearables (...) to the collection, development, application of biomedical knowledge has only partially been discussed. To fill in these gaps, in this article we provide an epistemic (knowledgerelated) overview of the main functions of wearable technology for health: monitoring, screening, detection, and prediction. On this basis, we identify 4 areas of concern in the application of wearables for these functions: data quality, balanced estimations, health equity, and fairness. To move the field forward in an effective and beneficial direction, we present recommendations for the 4 areas: local standards of quality, interoperability, access, and representativity. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular (...) O/T as a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

Many states make use of personal identity numbers to govern people living in their territory and jurisdiction, but only a few rely on an all-purpose PIN used throughout the public and private sectors. This article examines the all-purpose PIN in Finland as a political technology that brings people to the sphere of public welfare services and subjects them to governance by public authorities and expert institutions. Drawing on documentary materials and interviews, it unpacks the history and uses of the PIN (...) as an elementary building block of the Nordic welfare state, and its emerging uses in the post-welfare data economy. The article suggests that, although the PIN is capable of individualizing, identifying, and addressing individuals, its most important and widely embraced feature is the extent to which it enables interoperability among public authorities, private businesses, and their data repositories. Interoperability, together with advances in computing and information technology, has made the PIN a facilitator of public administration, state knowledge production, and everyday life. More recently, in the post-welfare data economy, interoperability has rendered the PIN a national asset in all the Nordic countries, providing a great advantage to biomedical research, innovation business, and healthcare. (shrink)

Information technologies that could be potentially used for the development of register system are currently highly advanced, but their practical adaptation in terms of register management is limited due to the void in the legal regulation. Therefore this article particularly focuses on analysis of legal regulation applied for the register system, by highlighting gaps, limitations in the legal acts regulating this area and offering resolutions of the problems. Author of the article reveals content of the category “system” and provides various (...) definitions for the term “system”. This article also includes various classification criteria for registers and revealing limitations of register classification. In addition underlining register system elements as well as general features of all the registers. The article lists register system as a complex, open, managable and purposeful system. Author concludes by stressing the importance of the register system interoperability and emphasizing that without it registers would be a “collection” of registers rather than a system. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate (...) representation of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

In this paper, we draw on Foucault's and Deleuze's theorisations of discipline and control, respectively, to understand a teacher accountability system in the US state of Texas: the Texas Teacher Evaluation and Support System (hereafter, T-TESS). Specifically, we focus on the interplay of physical and virtual modes of governance – which we develop here as physical–virtual hybridity – and the techniques that make these physical and virtual domains compatible via language interoperability, with T-TESS deployed as a representative empirical case (...) to show how such technologies work to govern teacher subjectivity. First, in-person appraiser meetings and observations re-code teachers’ linguistic behaviours, so their physical bodies and practices can become legible to and interoperable with the hybrid T-TESS system. This avoids any possible syntax errors between the linguistic expression of physical teacher speech and the digital coding language of T-TESS. Second, these digital bodies of data can now be viewed as proxies for the physical teacher body in the classroom, allowing the constant modulation in physical space (teacher bodies) and digital space (bodies of data). This is the physical–virtual hybridity of T-TESS, whereby discipline and control work symbiotically to govern both the physical and the digital expressions of teachers and their teaching. In this way, the disciplining of teachers’ language has profound effects on teachers’ bodies, both corporeal and digital. (shrink)

Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient (...) exchange of data and information among those involved, which can impede the response process and slow decision making. We, therefore, hypothesize that promoting semantic interoperability across ERO information systems might improve information exchange among stakeholders and thereby allow a more coherent response to the disaster. We propose an ontology‐based messaging service on the basis of the Emergency Data Exchange Language (EDXL) standards. The parties involved will continue to use the terminologies to which they are accustomed, but the system will resolve inconsistencies and thereby enhance mutual understanding among EROs by ensuring semantic translation of the exchanged information. The evaluation of the semantic translation demonstrated the effectiveness and accuracy of the proposed service. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...) performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

All organisations must be able to answer questions from their respective constituencies. It is not an exaggeration to say that, in this respect, it is a challenge to handle the extremely broad action platform of local government administrations (municipalities). The present paper is a walk-through of questions from the citizens that are managed at Botkyrka municipality, Sweden. It is focussed on the use of an ‘intelligent’ citizen assistant.

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Increasingly, taxonomies are being developed and used by industry practitioners to facilitate information interoperability and retrieval. Within a single industrial domain, there exist many taxonomies that are intended for different applications. Industry specific taxonomies often represent the vocabularies that are commonly used by the practitioners. Their jobs are multi-faceted, which include checking for code and regulatory compliance. As such, it will be very desirable if industry practitioners are able to easily locate and browse regulations of interest. In practice, multiple (...) sources of government regulations exist and they are often organized and classified by the needs of the issuing agencies that enforce them rather than the needs of the communities that use them. One way to bridge these two distinct needs is to develop methods and tools that enable practitioners to browse and retrieve government regulations using their own terms and vocabularies, for example, via existing industry taxonomies. The mapping from a single taxonomy to a single regulation is a trivial keyword matching task. We examine a relatedness analysis approach for mapping a single taxonomy to multiple regulations. We then present an approach for mapping multiple taxonomies to a single regulation by measuring the relatedness of concepts. Cosine similarity, Jaccard coefficient and market basket analysis are used to measure the semantic relatedness between concepts from two different taxonomies. Preliminary evaluations of the three relatedness analysis measures are performed using examples from the civil engineering and building industry. These examples illustrate the potential benefits of regulatory usage from the mapping between various taxonomies and regulations. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...) resolves inconsistent terminologies and promotes semantic interoperability among ERs. In this work, we discuss developing POLARISCO as an extension of Basic Formal Ontology and the Common Core Ontologies. We conclude by presenting a real use-case to check the efficiency and applicability of the proposed ontology. (shrink)

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study (...) to highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end (...) of life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: (...) This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

We consider three accepted truths about iris biometrics, involving pupil dilation, contact lenses and template aging. We also consider a relatively ignored issue that may arise in system interoperability. Experimental results from our laboratory demonstrate that the three accepted truths are not entirely true, and also that interoperability can involve subtle performance degradation. All four of these problems affect primarily the stability of the match, or authentic, distribution of template comparison scores rather than the non-match, or imposter, distribution (...) of scores. In this sense, these results confirm the security of iris biometrics in an identity verification scenario. We consider how these problems affect the usability and security of iris biometrics in large-scale applications, and suggest possible remedies. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...) and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

Electronic institutional review board systems (eIRBs) have become an integral component in ensuring compliance with Human Research Protection Program (HRPP) and IRB requirements. Despite this, few of these systems are configured to administer the single IRB (sIRB) process mandated by the National Institutes of Health (NIH) for multisite research. We interviewed 103 sIRB administrators, chairs, members, and staff members about their experiences with sIRB multisite research review. We observed three main obstacles to adapting existing eIRB systems to accommodate the sIRB (...) process: (1) Existing systems are not designed for sIRBs and are not configured to administer sIRB responsibilities, (2) they are not interoperable, and (3) resources to improve existing systems are lacking. Our findings suggest that IRBs that act as an sIRB will need major changes to their electronic systems in order to accommodate sIRB processes. These difficulties threaten both the ability of IRBs to focus on ethical rather than bureaucratic problems and the efficiency of multisite trials. (shrink)

Le présent article se propose de revenir sur le projet national CoMeRe (Communication Médiée par les Réseaux) en insistant sur la complexité du corpus développé. Constitué de quatorze sous-corpus variés, le corpus CoMeRe est un corpus de référence de la communication médiée par les réseaux en français. Quatorze enseignants-chercheurs de huit laboratoires différents se sont impliqués dans le projet et ont été guidés par trois mots clés lors de leurs collaborations : variété, standards et accès ouvert.Le corpus CoMeRe a ainsi (...) été construit sur une hypothèse de variété et contient une gamme étendue d’interactions de la CMR dont nous restituons les différences et les caractéristiques principales (courriels, clavardage, SMS, forums de discussion Internet, blogs, tweets, discussions Wikipédia, interactions provenant de mondes synthétiques). Nous détaillons ensuite comme le corpus CoMeRe a été rendu interopérable : les quatorze sous-corpus ont été standardisés, suivant le modèle de l’espace d’interaction élaboré lors du projet (Chanier & Jin, 2013) d’une part et suivant les propositions de représentation standardisée des corpus de la CMR en TEI (Text Encoding Initiative, 2019) élaborées en lien avec les partenaires européens. Enfin, les collègues tenaient à diffuser le corpus en accès ouvert pour permettre son utilisation par la communauté scientifique. Nous revenons sur les retombées du projet liées à la diffusion du corpus dans la conclusion de notre article. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection (...) with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

Large-scale, interoperable biobanks are an increasingly important asset in today's life science research and, as a result, multiple types of biobanks are being established around the globe with very different financial, organizational and legal set-ups. With interdisciplinary chapters written by lawyers, sociologists, doctors and biobank practitioners, Global Genes, Local Concerns identifies and discusses the most pressing issues in contemporary biobanking.This timely book addresses pressing questions such as: how do national biobanks best contribute to translational research?; What are the opportunities and (...) challenges that current regulations present for translational use of biobanks?; How does inter-biobank coordination and collaboration occur on various levels?; and how could academic and industrial exploitation, ownership and IPR issues be addressed and facilitated? Identifying that biobanks' foundational and operational set-ups should be legally and ethically sound, while at the same time reflecting the hopes and concerns of all the involved stakeholders, this book contributes to the continued development of international biobanking by highlighting and analysing the complexities in this important area of research.Academics in the fields of law and ethics, health law and biomedical law, as well as biobank managers and policymakers will find this insightful book a stimulating and engaging read. (shrink)

The Universal Core (UCore) is a central element of the National Information Sharing Strategy that is supported by multiple U.S. Federal Government Departments, by the intelligence community, and by a number of other national and international institutions. The goal of the UCore initiative is to foster information sharing by means of an XML schema providing consensus representations for four groups of universally understood terms under the headings who, what, when, and where. We here describe a project to create an ontology-based (...) supporting layer for UCore, entitled ‘Universal Core Semantic Layer’ (UCore SL), and describe how UCore SL can be applied to further UCore’s information sharing goals. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

The growing use of interoperable electronic health records is likely to have significant effects on the physician-patient relationship. This relationship involves two-way trust: of the physician in patients, and of the patients in their providers. Interoperable records opens up this relationship to further view, with consequences that may both enhance and undermine trust. On the one hand, physicians may learn that information from their patients is — or is not — to be trusted. On the other hand, patients may learn (...) from the increased oversight made possible by electronic records that their trust in their physicians is — or is not — warranted. Release of information through new methods of surveillance may also undermine patient trust. The article concludes that because trust is fragile, attention to transparency and confidentiality in the use of interoperable electronic records is essential. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

yamato sharply distinguishes itself from other existing upper ontologies in the following respects. Most importantly, yamato is designed with both engineering and philosophical minds. yamato is based on a sophisticated theory of roles, given that the world is full of roles. yamato has a tenable theory of functions which helps to deal with artifacts effectively. Information is a ‘content-bearing’ entity and it differs significantly from the entities that philosophers have traditionally discussed. Taking into account the modern society in which a (...) flood of information occurs, yamato has a sophisticated theory of informational objects. Quality and quantity are carefully organized for the sake of greater interoperability of real-world data. The philosophical contribution of yamato includes a theory of objects, processes, and events. Those features are illustrated with several case studies. These features lead to the intensive application of yamato in some domains such as biomedicine and learning engineering. (shrink)

Metaphors for the encounter between God and humanity and a roaming theologian’s reflective journey. This article maps the theology of Christo van der Merwe as a mobilising theology which aided the Netherdutch Reformed Church in Africa in discerning its character, role and purpose. The core of Van der Merwe’s theology consists of a journey with God as encountered in the narratives about Jesus and the Spirit told in the Christian Bible. The article shows that the mobilising core of his theology (...) is due to an ‘interoperational relationship’ between ‘knowing and believing’. In the article, the metaphor ‘roaming’ is used to illustrate this biographical journey as contextual theology which equips pastors with ministerial skills to take care of people who are haunted by trauma. (shrink)