OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

Objective: To design a new semantically interoperable clinical repository, based on ontologies, conforming to CEN/ISO 13606 standard. Materials and Methods: The approach followed is to extend OntoCRF, a framework for the development of clinical repositories based on ontologies. The meta-model of OntoCRF has been extended by incorporating an OWL model integrating CEN/ISO 13606, ISO 21090 and SNOMED CT structure. Results: This approach has demonstrated a complete evaluation cycle involving the creation of the meta-model in OWL format, the creation of a simple test application, and the communication of standardized extracts to another organization. Discussion: Using a CEN/ISO 13606 based system, an indefinite number of archetypes can be merged (and reused) to build new applications. Our approach, based on the use of ontologies, maintains data storage independent of content specification. With this approach, relational technology can be used for storage, maintaining extensibility capabilities. Conclusions: The present work demonstrates that it is possible to build a native CEN/ISO 13606 repository for the storage of clinical data. We have demonstrated semantic interoperability of clinical information using CEN/ISO 13606 extracts

Towards Interoperability in E-health Systems: a three-dimensional approach based on standards and semantics

Proceedings of: HEALTHINF 2009 (International Conference on Helath Informatics), Porto (Portugal), January 14-17, 2009, is part of BIOSTEC (Intemational Joint Conference on Biomedical Engineering Systems and Technologies)The interoperability problem in eHealth can only be addressed by mean of combining standards and technology. However, these alone do not suffice. An appropiate framework that articulates such combination is required. In this paper, we adopt a three-dimensional (information, conference and inference) approach for such framework, based on OWL as formal language for terminological and ontological health resources, SNOMED CT as lexical backbone for all such resources, and the standard CEN 13606 for representing EHRs. Based on tha framewok, we propose a novel form for creating and supporting networks of clinical terminologies. Additionally, we propose a number of software modules to semantically process and exploit EHRs, including NLP-based search and inference, wich can support medical applications in heterogeneous and distributed eHealth systems.This work has been funded as part of the Spanish nationally funded projects ISSE (FIT-350300-2007-75) and CISEP (FIT-350301-2007-18). We also acknowledge IST-2005-027595 EU project NeO

Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts

Introduction The secondary use of Electronic Healthcare Records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, Virtual Health Records, and semantic technologies, since each of them contributes to solving aspects related to the semantic interoperability of EHR data. Our main objective is to develop methods allowing for a direct use of EHR data for the identification of patient cohorts leveraging current EHR standards and semantic web technologies. Materials and Methods We propose to take advantage of the best features of working with EHR standards and ontologies. Our proposal is based on our previous results and experience working with both technological infrastructures. Our main principle is to perform each activity at the abstraction level with the most appropriate technology available. This means that part of the processing will be performed using archetypes (i.e., data level) and the rest using ontologies (i.e., knowledge level). Our approach will start working with EHR data in proprietary format, which will be first normalized and elaborated using EHR standards and then transformed into a semantic representation, which will be exploited by automated reasoning. Results We have applied our approach to protocols for colorectal cancer screening. The results comprise the archetypes, ontologies and datasets developed for the standardization and semantic analysis of EHR data. Anonymized real data has been used and the patients have been successfully classified by the risk of developing colorectal cancer. Conclusion This work provides new insights in how archetypes and ontologies can be effectively combined for EHR-driven phenotyping. The methodological approach can be applied to other problems provided that suitable archetypes, ontologies and classification rules can be designed.This work was supported by the Ministerio de Economia y Competitividad and the FEDER program through grants TIN2010-21388-C01 and TIN2010-21388-C02. MCLG was supported by the Fundacion Seneca through grant 15555/FPI/2010.Fernández-Breis, JT.; Maldonado Segura, JA.; Marcos, M.; Legaz-García, MDC.; Moner Cano, D.; Torres-Sospedra, J.; Esteban-Gil, A.... (2013). Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts. Journal of the American Medical Informatics Association. 20(E2):288-296. https://doi.org/10.1136/amiajnl-2013-001923S28829620E2Cuggia, M., Besana, P., & Glasspool, D. (2011). Comparing semi-automatic systems for recruitment of patients to clinical trials. International Journal of Medical Informatics, 80(6), 371-388. doi:10.1016/j.ijmedinf.2011.02.003Sujansky, W. (2001). Heterogeneous Database Integration in Biomedicine. Journal of Biomedical Informatics, 34(4), 285-298. doi:10.1006/jbin.2001.1024Schadow G Russler DC Mead CN . Integrating medical information and knowledge in the HL7 RIM. Proceedings of the AMIA Symposium, 2000:764–8.Johnson PD Tu SW Musen MA . A virtual medical record for guideline-based decision support. Proceedings of the AMIA 2001 Annual Symposium, 294–8.German, E., Leibowitz, A., & Shahar, Y. (2009). An architecture for linking medical decision-support applications to clinical databases and its evaluation. Journal of Biomedical Informatics, 42(2), 203-218. doi:10.1016/j.jbi.2008.10.007Peleg, M., Keren, S., & Denekamp, Y. (2008). Mapping computerized clinical guidelines to electronic medical records: Knowledge-data ontological mapper (KDOM). Journal of Biomedical Informatics, 41(1), 180-201. doi:10.1016/j.jbi.2007.05.003Maldonado, J. A., Costa, C. M., Moner, D., Menárguez-Tortosa, M., Boscá, D., Miñarro Giménez, J. A., … Robles, M. (2012). Using the ResearchEHR platform to facilitate the practical application of the EHR standards. Journal of Biomedical Informatics, 45(4), 746-762. doi:10.1016/j.jbi.2011.11.004Parker CG Rocha RA Campbell JR . Detailed clinical models for sharable, executable guidelines. Stud Health Technol Inform 2004;107:145–8.Clinical Information Modeling Initiative. http://informatics.mayo.edu/CIMI/index.php/Main_Page (accessed Jun 2013).W3C, OWL2 Web Ontology Language. http://www.w3.org/TR/owl2-overview/ (accessed Jun 2013).European Commission. Semantic interoperability for better health and safer healthcare. Deployment and research roadmap for Europe. ISBN-13: 978-92-79-11139-6, 2009.SemanticHealthNet. http://www.semantichealthnet.eu/ (accessed Jun 2013).Martínez-Costa, C., Menárguez-Tortosa, M., Fernández-Breis, J. T., & Maldonado, J. A. (2009). A model-driven approach for representing clinical archetypes for Semantic Web environments. Journal of Biomedical Informatics, 42(1), 150-164. doi:10.1016/j.jbi.2008.05.005Iqbal AM . An OWL-DL ontology for the HL7 reference information model. Toward useful services for elderly and people with disabilities Berlin: Springer, 2011:168–75.Tao, C., Jiang, G., Oniki, T. A., Freimuth, R. R., Zhu, Q., Sharma, D., … Chute, C. G. (2012). A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. Journal of the American Medical Informatics Association, 20(3), 554-562. doi:10.1136/amiajnl-2012-001326Heymans, S., McKennirey, M., & Phillips, J. (2011). Semantic validation of the use of SNOMED CT in HL7 clinical documents. Journal of Biomedical Semantics, 2(1), 2. doi:10.1186/2041-1480-2-2Menárguez-Tortosa, M., & Fernández-Breis, J. T. (2013). OWL-based reasoning methods for validating archetypes. Journal of Biomedical Informatics, 46(2), 304-317. doi:10.1016/j.jbi.2012.11.009Lezcano, L., Sicilia, M.-A., & Rodríguez-Solano, C. (2011). Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. Journal of Biomedical Informatics, 44(2), 343-353. doi:10.1016/j.jbi.2010.11.005Tao C Wongsuphasawat K Clark K . Towards event sequence representation, reasoning and visualization for EHR data. Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI'12). New York, NY, USA: ACM:801–6.Bodenreider O . Biomedical ontologies in action: role in knowledge management, data integration and decision support. IMIA Yearbook of Medical Informatics 2008;67–79.Beale T . Archetypes. 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Using the ResearchEHR platform to facilitate the practical application of the EHR standards

Possibly the most important requirement to support co-operative work among health professionals and institutions is the ability of sharing EHRs in a meaningful way, and it is widely acknowledged that standardization of data and concepts is a prerequisite to achieve semantic interoperability in any domain. Different international organizations are working on the definition of EHR architectures but the lack of tools that implement them hinders their broad adoption. In this paper we present ResearchEHR, a software platform whose objective is to facilitate the practical application of EHR standards as a way of reaching the desired semantic interoperability. This platform is not only suitable for developing new systems but also for increasing the standardization of existing ones. The work reported here describes how the platform allows for the edition, validation, and search of archetypes, converts legacy data into normalized, archetypes extracts, is able to generate applications from archetypes and finally, transforms archetypes and data extracts into other EHR standards. We also include in this paper how ResearchEHR has made possible the application of the CEN/ISO 13606 standard in a real environment and the lessons learnt with this experience. © 2011 Elsevier Inc..This work has been partially supported by the Spanish Ministry of Science and Innovation under Grants TIN2010-21388-C02-01 and TIN2010-21388-C02-02, and by the Health Institute Carlos in through the RETICS Combiomed, RD07/0067/2001. Our most sincere thanks to the Hospital of Fuenlabrada in Madrid, including its Medical Director Pablo Serrano together with Marta Terron and Luis Lechuga for their support and work during the development of the medications reconciliation project.Maldonado Segura, JA.; Martínez Costa, C.; Moner Cano, D.; Menárguez-Tortosa, M.; Boscá Tomás, D.; Miñarro Giménez, JA.; Fernández-Breis, JT.... (2012). Using the ResearchEHR platform to facilitate the practical application of the EHR standards. Journal of Biomedical Informatics. 45(4):746-762. doi:10.1016/j.jbi.2011.11.004S74676245

A Two-Level Information Modelling Translation Methodology and Framework to Achieve Semantic Interoperability in Constrained GeoObservational Sensor Systems

As geographical observational data capture, storage and sharing technologies such as in situ remote monitoring systems and spatial data infrastructures evolve, the vision of a Digital Earth, first articulated by Al Gore in 1998 is getting ever closer. However, there are still many challenges and open research questions. For example, data quality, provenance and heterogeneity remain an issue due to the complexity of geo-spatial data and information representation. Observational data are often inadequately semantically enriched by geo-observational information systems or spatial data infrastructures and so they often do not fully capture the true meaning of the associated datasets. Furthermore, data models underpinning these information systems are typically too rigid in their data representation to allow for the ever-changing and evolving nature of geo-spatial domain concepts. This impoverished approach to observational data representation reduces the ability of multi-disciplinary practitioners to share information in an interoperable and computable way. The health domain experiences similar challenges with representing complex and evolving domain information concepts. Within any complex domain (such as Earth system science or health) two categories or levels of domain concepts exist. Those concepts that remain stable over a long period of time, and those concepts that are prone to change, as the domain knowledge evolves, and new discoveries are made. Health informaticians have developed a sophisticated two-level modelling systems design approach for electronic health documentation over many years, and with the use of archetypes, have shown how data, information, and knowledge interoperability among heterogenous systems can be achieved. This research investigates whether two-level modelling can be translated from the health domain to the geo-spatial domain and applied to observing scenarios to achieve semantic interoperability within and between spatial data infrastructures, beyond what is possible with current state-of-the-art approaches. A detailed review of state-of-the-art SDIs, geo-spatial standards and the two-level modelling methodology was performed. A cross-domain translation methodology was developed, and a proof-of-concept geo-spatial two-level modelling framework was defined and implemented. The Open Geospatial Consortium’s (OGC) Observations & Measurements (O&M) standard was re-profiled to aid investigation of the two-level information modelling approach. An evaluation of the method was undertaken using II specific use-case scenarios. Information modelling was performed using the two-level modelling method to show how existing historical ocean observing datasets can be expressed semantically and harmonized using two-level modelling. Also, the flexibility of the approach was investigated by applying the method to an air quality monitoring scenario using a technologically constrained monitoring sensor system. This work has demonstrated that two-level modelling can be translated to the geospatial domain and then further developed to be used within a constrained technological sensor system; using traditional wireless sensor networks, semantic web technologies and Internet of Things based technologies. Domain specific evaluation results show that twolevel modelling presents a viable approach to achieve semantic interoperability between constrained geo-observational sensor systems and spatial data infrastructures for ocean observing and city based air quality observing scenarios. This has been demonstrated through the re-purposing of selected, existing geospatial data models and standards. However, it was found that re-using existing standards requires careful ontological analysis per domain concept and so caution is recommended in assuming the wider applicability of the approach. While the benefits of adopting a two-level information modelling approach to geospatial information modelling are potentially great, it was found that translation to a new domain is complex. The complexity of the approach was found to be a barrier to adoption, especially in commercial based projects where standards implementation is low on implementation road maps and the perceived benefits of standards adherence are low. Arising from this work, a novel set of base software components, methods and fundamental geo-archetypes have been developed. However, during this work it was not possible to form the required rich community of supporters to fully validate geoarchetypes. Therefore, the findings of this work are not exhaustive, and the archetype models produced are only indicative. The findings of this work can be used as the basis to encourage further investigation and uptake of two-level modelling within the Earth system science and geo-spatial domain. Ultimately, the outcomes of this work are to recommend further development and evaluation of the approach, building on the positive results thus far, and the base software artefacts developed to support the approach

Towards a Digital Earth: Using Archetypes to Enable Knowledge Interoperability within Geo-Observational Sensor Systems Design

Earth System Science (ESS) observational data are often inadequately semantically enriched by geo-observational information systems in order to capture the true meaning of the associated data sets. Data models underpinning these information systems are often too rigid in their data representation to allow for the ever-changing and evolving nature of ESS domain concepts. This impoverished approach to observational data representation reduces the ability of multi-disciplinary practitioners to share information in a computable way. Object oriented techniques typically employed to model data in a complex domain (with evolving domain concepts) can unnecessarily exclude domain specialists from the design process, invariably leading to a mismatch between the needs of the domain specialists, and how the concepts are modelled. In many cases, an over simplification of the domain concept is captured by the computer scientist. This paper proposes that two-level modelling methodologies developed by Health Informaticians to tackle similar problems of specific domain use-case knowledge modelling can be re-used within ESS Informatics. A proposed methodology to re-use two-level modelling within geo-observational sensor systems is described. We show how the Open Geospatial Consortium’s (OGC) Observations & Measurements (O&M) standard can act as a pragmatic solution for a stable reference-model (necessary for two-level modelling), and upon which more volatile domain specific concepts can be defined and managed using archetypes. A use-case is presented, followed by a worked example showing the implementation methodology and considerations leading to an O&M based, two-level modelling design approach, to realise semantically rich and interoperable Earth System Science based geo-observational sensor systems

Growing an information infrastructure for healthcare based on the development of large-scale Electronic Patient Records

The papers of this thesis are not available in Munin. Paper 1. Silsand, L., Ellingsen, G. (2014). Generification by Translation: Designing Generic Systems in Context of the Local. Available in: Journal of Association for Information Systems, vol. 15(4): 3. Paper 2. Christensen, B., Silsand, L., Wynn, R. and Ellingsen, G. (2014). The biography of participation. In Proceedings of the 13th Participatory Design Conference, 6-10 Oct. Windhoek, Namibia. ACM Digital Library. Paper 3. Silsand, L. and Ellingsen, G. (2016). Complex Decision-Making in Clinical Practice. In: Proceedings of the 19th ACM Conference on Computer-Supported Cooperative Work & Social Computing (CSCW '16). ACM Digital Library. ISBN: 978-1-4503-3592-8. Paper 4: Silsand, L., Ellingsen, G. (2017). Governance of openEHR-based information Infrastructures. (Manuscript). Paper 5. Silsand, L. (2017). The ‘Holy Grail’ of Interoperability of Health Information Systems: Challenges and Implications. Available in: Stigberg S., Karlsen J., Holone H., Linnes C. (eds) Nordic Contributions in IS Research. SCIS 2017. Lecture Notes in Business Information Processing, vol 294. Springer, Cham. This thesis provides empirical insights about socio-technical interdependencies affecting the making and scaling of an Information Infrastructure (II) for healthcare based on the development of large-scale Electronic Patient Records. The Ph.D. study is an interpretive case study, where the empirical data has been collected from 2012 to 2017. In most developed countries, the pressures from politicians and public in general for better IT solutions have grown enormously, not least within Electronic Patient Record (EPR) systems. Considerable attention has been given to the proposition that the exchange of health information is a critical component to reach the triple aim of (1) better patient experiences through quality and satisfaction; (2) better health outcomes of populations; and (3) reduction of per capita cost of health care. A promising strategy for dealing with the challenges of accessibility, efficiency, and effective sharing of clinical information to support the triple aim is an open health-computing platform approach, exemplified by the openEHR approach in the empirical case. An open platform approach for computing EPR systems addresses some vital differences from the traditional proprietary systems. Accordingly, the study has payed attention to the vital difference, and analyze the technology and open platform approach to understand the challenges and implications faced by the empirical process. There are two main messages coming out of this Ph.D. study. First, when choosing an open platform approach to establish a regional or national information infrastructure for healthcare, it is important to define it as a process, not a project. Because limiting the realization of a large-scale open platform based infrastructure to the strict timeline of a project may hamper infrastructure growth. Second, realizing an open platform based information infrastructure requires large structural and organizational changes, addressing the need for integrating policy design with infrastructure design

LinkEHR-Ed: A multi-reference model archetype editor based on formal semantics

Purpose To develop a powerful archetype editing framework capable of handling multiple reference models and oriented towards the semantic description and standardization of legacy data. Methods The main prerequisite for implementing tools providing enhanced support for archetypes is the clear specification of archetype semantics. We propose a formalization of the definition section of archetypes based on types over tree-structured data. It covers the specialization of archetypes, the relationship between reference models and archetypes and conformance of data instances to archetypes. Results LinkEHR-Ed, a visual archetype editor based on the former formalization with advanced processing capabilities that supports multiple reference models, the editing and semantic validation of archetypes, the specification of mappings to data sources, and the automatic generation of data transformation scripts, is developed. Conclusions LinkEHR-Ed is a useful tool for building, processing and validating archetypes based on any reference model.This work was supported in part by the Spanish Ministry of Education and Science under grant TS12007-66S7S-C02; by the Generalitat Valenciana under grant APOSTD/2007/055 and by the program PAID-06-07 de la Universidad Politecnica de Valencia.Maldonado Segura, JA.; Moner Cano, D.; Boscá Tomás, D.; Fernandez Breis, JT.; Angulo Fernández, C.; Robles Viejo, M. (2009). LinkEHR-Ed: A multi-reference model archetype editor based on formal semantics. International Journal of Medical Informatics. 78(8):559-570. https://doi.org/10.1016/j.ijmedinf.2009.03.006S55957078

Addressing Semantic Interoperability, Privacy and Security Concerns in Electronic Health Records

The use of Electronic Health Records (EHR) in healthcare has the potential of reducing medical errors, minimizing healthcare cost and significantly improving the healthcare service quality. However, there is a barrier in healthcare data and information exchange between various healthcare systems due to the lack of interoperability. Also, with the implementation of EHR system, there are security and privacy concerns in the storage and transferring data entities.  The healthcare interoperability problem remains an issue of further research and this paper proposes a semantic interoperability framework for solving  this problem by allowing healthcare stakeholders and organizations (doctors, clinics, hospitals)using various healthcare standards to exchange data and its semantics, which can be understood by both machines and humans. Moreover, the proposed framework takes into consideration the security aspects in the semantic interoperability framework by utilizing data encryption and other technologies to secure the communication for the EHR information while ensuring real time data availability.                                                                                                  Keywords:. Semantic interoperability; Interoperability standards; Electronic Health records(EHR); Artifical Intelligence Techniques. Natural Language Processing (NLP), Word2Vec, skip gram, CBO