Ontology Based Integration of Distributed and Heterogeneous Data Sources in ACGT.

In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinic-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European. This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases. A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases. The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer. The ontology is used as a common framework for semantics, modeling the domain and acting as giving support to homogenization. SPARQL has been selected as query language for the Data Access Services and the Mediator. Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases

A Two-Level Identity Model To Support Interoperability of Identity Information in Electronic Health Record Systems.

The sharing and retrieval of health information for an electronic health record (EHR) across distributed systems involves a range of identified entities that are possible subjects of documentation (e.g., specimen, clinical analyser). Contemporary EHR specifications limit the types of entities that can be the subject of a record to health professionals and patients, thus limiting the use of two level models in healthcare information systems that contribute information to the EHR. The literature describes several information modelling approaches for EHRs, including so called “two level models”. These models differ in the amount of structure imposed on the information to be recorded, but they generally require the health documentation process for the EHR to focus exclusively on the patient as the subject of care and this definition is often a fixed one. In this thesis, the author introduces a new identity modelling approach to create a generalised reference model for sharing archetype-constrained identity information between diverse identity domains, models and services, while permitting reuse of published standard-based archetypes. The author evaluates its use for expressing the major types of existing demographic reference models in an extensible way, and show its application for standards-compliant two-level modelling alongside heterogeneous demographics models. This thesis demonstrates how the two-level modelling approach that is used for EHRs could be adapted and reapplied to provide a highly-flexible and expressive means for representing subjects of information in allied health settings that support the healthcare process, such as the laboratory domain. By relying on the two level modelling approach for representing identity, the proposed design facilitates cross-referencing and disambiguation of certain demographics standards and information models. The work also demonstrates how it can also be used to represent additional clinical identified entities such as specimen and order as subjects of clinical documentation

An HL7-CDA wrapper for facilitating semantic interoperability to rule-based Clinical Decision Support Systems

The success of Clinical Decision Support Systems (CDSS) greatly depends on its capability of being integrated in Health Information Systems (HIS). Several proposals have been published up to date to permit CDSS gathering patient data from HIS. Some base the CDSS data input on the HL7 reference model, however, they are tailored to specific CDSS or clinical guidelines technologies, or do not focus on standardizing the CDSS resultant knowledge. We propose a solution for facilitating semantic interoperability to rule-based CDSS focusing on standardized input and output documents conforming an HL7-CDA wrapper. We define the HL7-CDA restrictions in a HL7-CDA implementation guide. Patient data and rule inference results are mapped respectively to and from the CDSS by means of a binding method based on an XML binding file. As an independent clinical document, the results of a CDSS can present clinical and legal validity. The proposed solution is being applied in a CDSS for providing patient-specific recommendations for the care management of outpatients with diabetes mellitus.We thank Fagor Electrodomesticos S.Coop for their support and funding in the development of this work, specially to Juan Ramon Inurria and Jorge de Antonio Prieto. We also thank the colaboration from Universidad de Mondragon in the design of the general architecture of the telemedicine system, specially, Felix Larrinaga. This work has been partially supported by the Health Institute Carlos III through the RETICS Combiomed, RD07/0067/2001.Sáez Silvestre, C.; Bresó Guardado, A.; Vicente Robledo, J.; Robles Viejo, M.; García Gómez, JM. (2013). An HL7-CDA wrapper for facilitating semantic interoperability to rule-based Clinical Decision Support Systems. Computer Methods and Programs in Biomedicine. 109(3):239-249. doi:10.1016/j.cmpb.2012.10.003S239249109

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

Interoperability of clinical decision-support systems and electronic health records using archetypes: a case study in clinical trial eligibility

Clinical decision-support systems (CDSSs) comprise systems as diverse as sophisticated platforms to store and manage clinical data, tools to alert clinicians of problematic situations, or decision-making tools to assist clinicians. Irrespective of the kind of decision-support task CDSSs should be smoothly integrated within the clinical information system, interacting with other components, in particular with the electronic health record (EHR). However, despite decades of developments, most CDSSs lack interoperability features. We deal with the interoperability problem of CDSSs and EHRs by exploiting the dual-model methodology. This methodology distinguishes a reference model and archetypes. A reference model is represented by a stable and small object-oriented model that describes the generic properties of health record information. For their part, archetypes are reusable and domain-specific definitions of clinical concepts in the form of structured and constrained combinations of the entities of the reference model. We rely on archetypes to make the CDSS compatible with EHRs from different institutions. Concretely, we use archetypes for modelling the clinical concepts that the CDSS requires, in conjunction with a series of knowledge-intensive mappings relating the archetypes to the data sources (EHR and/or other archetypes) they depend on. We introduce a comprehensive approach, including a set of tools as well as methodological guidelines, to deal with the interoperability of CDSSs and EHRs based on archetypes. Archetypes are used to build a conceptual layer of the kind of a virtual health record (VHR) over the EHR whose contents need to be integrated and used in the CDSS, associating them with structural and terminology-based semantics. Subsequently, the archetypes are mapped to the EHR by means of an expressive mapping language and specific-purpose tools. We also describe a case study where the tools and methodology have been employed in a CDSS to support patient recruitment in the framework of a clinical trial for colorectal cancer screening. The utilisation of archetypes not only has proved satisfactory to achieve interoperability between CDSSs and EHRs but also offers various advantages, in particular from a data model perspective. First, the VHR/data models we work with are of a high level of abstraction and can incorporate semantic descriptions. Second, archetypes can potentially deal with different EHR architectures, due to their deliberate independence of the reference model. Third, the archetype instances we obtain are valid instances of the underlying reference model, which would enable e.g. feeding back the EHR with data derived by abstraction mechanisms. Lastly, the medical and technical validity of archetype models would be assured, since in principle clinicians should be the main actors in their development.This research has been supported by the Spanish Ministry of Education through Grant PR2010-0279, and by Universitat Jaume I through Project P1182009-38. Additionally, this research has been supported by the Spanish Ministry of Science and Innovation under Grant TIN2010-21388-C02-01, and by the Spanish Ministry of Economy and Competitiveness under grant PTQ-11-04987.Marcos, M.; Maldonado Segura, JA.; Martinez-Salvador, B.; Boscá Tomás, D.; Robles Viejo, M. (2013). Interoperability of clinical decision-support systems and electronic health records using archetypes: a case study in clinical trial eligibility. Journal of Biomedical Informatics. 46(4):676-689. https://doi.org/10.1016/j.jbi.2013.05.004S67668946

A METHODOLOGY FOR ONTOLOGICAL KNOWLEDGE CAPTURE FROM DATABASES \ud

The successful emergence of the Information and Communication Technologies (ICT) has contributed to the efficiency improvement in a number of economic sectors. However, some strategic economic sectors, such as construction, have not been targeted enough yet. Construction-related ICT solutions lack mechanisms to permit the effective integration of the whole supply chain. Semantic Web can tackle these issues. This paper presents a methodology for acquiring knowledge from construction-related databases. A domain ontology has been developed that contains the relevant concepts regarding supply management in the construction domain. The methodology basically consists of mapping the database content onto the ontology and a further this one’s population by applying a set of mapping rules.\ud Успешное появление информационно-коммуникационных технологий (ИКТ) внесло свой вклад в повышение эффективности многих секторов экономики. Однако, некоторые стратегические экономические сектора, такие, как строительство, не были все же достаточно исследованы. Связанные со строительством решения ИКТ испытывают недостаток в механизмах, позволяющих разрешать проблемы эффективной интеграции полной цепочки поставки. Семантическая Сеть может заняться этими проблемами. Эта статья представляет методологию, позволяющую извлекать знание из баз данных, связанных со строительством . Была разработана онтология домена, содержащая релевантные понятия, касающиеся управления поставками в домене строительства. Методология в основном состоит из отображения содержания базы данных на онтологию и дальнейшего ее заполнения , применяя набор правил отображения .\u

Archetype based intelligent system for healthcare interoperability

Tese doutoramento - Programa Doutoral em Engenharia BiomédicaThe healthcare arena configures an environment of both complexity and cooperation, in which numerous and distinct information systems must exchange information in a expedite and consolidated manner. Where healthcare interoperability is concerned several techniques, methodologies, architectures and standards exist. However subjects such as service distribution, fault tolerance, standards, communication flavoring and tightly-bound systems still are a major issue of concern. This work studies and researches the best methodologies to imbue intelligent behaviours combined with ontology and moral awareness into multi-agents system applied to healthcare environments. Its core objective is to propose, develop, implement and evaluate an archetype for an interoperability platform oriented towards the healthcare environment. This archetype was validated in several implementation in different major healthcare institutions. It is based in an agent framework named JADE and is adapted and oriented towards the healthcare environment. Henceforth the resulting archetype addresses the existing limitations in past and present solutions regarding healthcare interoperability. It explores the limits of intelligent behaviours in multi-agent systems applied to interoperation procedures in healthcare, towards the improvement of the reliability and quality of information exchanged.A área da saúde configura um ambiente de grande complexidade e cooperação onde inúmeros e distintos sistemas de informação têm que trocar informação entre si de uma forma expedita e consolidada. No âmbito da interoperabilidade hospitalar existem várias técnicas, metodologias, arquiteturas e standards. No entanto, temas como distribuição de serviços, tolerância à falha, standards, flavouring de comunicações e sistemas fortemente acoplados, continuam a ser um importante fonte de preocupação. Este trabalho estuda e pesquiza as melhores metodologias de embeber comportamentos inteligentes combinados com ontologias e noções morais em sistemas multi-agentes aplicados a ambientes hospitalares. O seu objectivo principal é propor, desenvolver, implementar e avaliar um arquétipo para uma plataforma de interoperabilidade orientada para o ambiente hospitalar. Este arquétipo foi validado em diferentes implementações em instituições de saúde portuguesas de grande dimensão. Esta plataforma é baseada numa framework de agentes denominada JADE e foi adaptada e orientada para o ambiente hospitalar.. Desta forma o arquétipo resultante é orientado para resolver as limitações existentes nas soluções atuais de interoperabilidade hospitalar. Este explora os limites dos comportamentos inteligentes em sistemas multi-agente quando aplicados em procedimentos de interoperabilidade na área da saúde para melhorar a fiabilidade e qualidade da informação trocada entre estes sistemas

Sharing and viewing segments of electronic patient records service (SVSEPRS) using multidimensional database model

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The concentration on healthcare information technology has never been determined than it is today. This awareness arises from the efforts to accomplish the extreme utilization of Electronic Health Record (EHR). Due to the greater mobility of the population, EHR will be constructed and continuously updated from the contribution of one or many EPRs that are created and stored at different healthcare locations such as acute Hospitals, community services, Mental Health and Social Services. The challenge is to provide healthcare professionals, remotely among heterogeneous interoperable systems, with a complete view of the selective relevant and vital EPRs fragments of each patient during their care. Obtaining extensive EPRs at the point of delivery, together with ability to search for and view vital, valuable, accurate and relevant EPRs fragments can be still challenging. It is needed to reduce redundancy, enhance the quality of medical decision making, decrease the time needed to navigate through very high number of EPRs, which consequently promote the workflow and ease the extra work needed by clinicians. These demands was evaluated through introducing a system model named SVSEPRS (Searching and Viewing Segments of Electronic Patient Records Service) to enable healthcare providers supply high quality and more efficient services, redundant clinical diagnostic tests. Also inappropriate medical decision making process should be avoided via allowing all patients‟ previous clinical tests and healthcare information to be shared between various healthcare organizations. Multidimensional data model, which lie at the core of On-Line Analytical Processing (OLAP) systems can handle the duplication of healthcare services. This is done by allowing quick search and access to vital and relevant fragments from scattered EPRs to view more comprehensive picture and promote advances in the diagnosis and treatment of illnesses. SVSEPRS is a web based system model that helps participant to search for and view virtual EPR segments, using an endowed and well structured Centralised Multidimensional Search Mapping (CMDSM). This defines different quantitative values (measures), and descriptive categories (dimensions) allows clinicians to slice and dice or drill down to more detailed levels or roll up to higher levels to meet clinicians required fragment

Towards a Learning Health System: a SOA based platform for data re-use in chronic infectious diseases

Abstract Information and Communication Technology (ICT) tools can efficiently support clinical research by providing means to collect automatically huge amount of data useful for the management of clinical trials conduction. Clinical trials are indispensable tools for Evidence-Based Medicine and represent the most prevalent clinical research activity. Clinical trials cover only a restricted part of the population that respond to particular and strictly controlled requirements, offering a partial view of the overall patients\u2019 status. For instance, it is not feasible to consider patients with comorbidities employing only one kind of clinical trial. Instead, a system that have a comprehensive access to all the clinical data of a patient would have a global view of all the variables involved, reflecting real-world patients\u2019 experience. The Learning Health System is a system with a broader vision, in which data from various sources are assembled, analyzed by various means and then interpreted. The Institute of Medicine (IOM) provides this definition: \u201cIn a Learning Health System, progress in science, informatics, and care culture align to generate new knowledge as an ongoing, natural by-product of the care experience, and seamlessly refine and deliver best practices for continuous improvement in health and health care\u201d. The final goal of my project is the realization of a platform inspired by the idea of Learning Health System, which will be able to re-use data of different nature coming from widespread health facilities, providing systematic means to learn from clinicians\u2019 experience to improve both the efficiency and the quality of healthcare delivery. The first approach is the development of a SOA-based architecture to enable data collection from sparse facilities into a single repository, to allow medical institutions to share information without an increase in costs and without the direct involvement of users. Through this architecture, every single institution would potentially be able to participate and contribute to the realization of a Learning Health System, that can be seen as a closed cycle constituted by a sequential process of transforming patient-care data into knowledge and then applying this knowledge to clinical practice. Knowledge, that can be inferred by re-using the collected data to perform multi-site, practice-based clinical trials, could be concretely applied to clinical practice through Clinical Decision Support Systems (CDSS), which are instruments that aim to help physicians in making more informed decisions. With 4 this objective, the platform developed not only supports clinical trials execution, but also enables data sharing with external research databases to participate in wider clinical trials also at a national level without effort. The results of these studies, integrated with existing guidelines, can be seen as the knowledge base of a decision support system. Once designed and developed, the adoption of this system for chronical infective diseases management at a regional level helped in unifying data all over the Ligurian territory and actively monitor the situation of specific diseases (like HIV, HCV and HBV) for which the concept of retention in care assumes great importance. The use of dedicated standards is essential to grant the necessary level of interoperability among the structures involved and to allow future extensions to other fields. A sample scenario was created to support antiretroviral drugs prescription in the Ligurian HIV Network setting. It was thoroughly tested by physicians and its positive impact on clinical care was measured in terms of improvements in patients\u2019 quality of life, prescription appropriateness and therapy adherence. The benefits expected from the employment of the system developed were verified. Student\u2019s T test was used to establish if significant differences were registered between data collected before and after the introduction of the system developed. The results were really acceptable with the minimum p value in the order of 10 125 and the maximum in the order of 10 123. It is reasonable to assess that the improvements registered in the three analysis considered are ascribable to this system introduction and not to other factors, because no significant differences were found in the period before its release. Speed is a focal point in a system that provides decision support and it is highly recognized the importance of velocity optimization. Therefore, timings were monitored to evaluate the responsiveness of the system developed. Extremely acceptable results were obtained, with the waiting times of the order of 10 121 seconds. The importance of the network developed has been widely recognized by the medical staff involved, as it is also assessed by a questionnaire they compiled to evaluate their level of satisfaction