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| 2. |
- Sundvall, Erik, 1973-, et al.
(author)
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Querying archetype-based Electronic Health Records using Hadoop and Dewey encoding of openEHR models
- 2017
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In: Informatics for Health. - Amsterdam, The Netherlands : IOS Press. - 9781614997528 - 9781614997535 ; , s. 406-410
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Conference paper (peer-reviewed)abstract
- Archetype-based Electronic Health Record (EHR) systems using generic reference models from e.g. openEHR, ISO 13606 or CIMI should be easy to update and reconfigure with new types (or versions) of data models or entries, ideally with very limited programming or manual database tweaking. Exploratory research (e.g. epidemiology) leading to ad-hoc querying on a population-wide scale can be a challenge in such environments. This publication describes implementation and test of an archetype-aware Dewey encoding optimization that can be used to produce such systems in environments supporting relational operations, e.g. RDBMs and distributed map-reduce frameworks like Hadoop. Initial testing was done using a nine-node 2.2 GHz quad-core Hadoop cluster querying a dataset consisting of targeted extracts from 4+ million real patient EHRs, query results with sub-minute response time were obtained.
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| 3. |
- Freire, Sergio Miranda, et al.
(author)
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Performance of XML Databases for Epidemiological Queries in Archetype-Based EHRs
- 2012
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In: Proceedings Scandinavian Conference on Health Informatics 2012. - Linköping : Linköping University Electronic Press. - 9789175197586 ; , s. 51-57
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Conference paper (peer-reviewed)abstract
- There are very few published studies regarding the performance of persistence mechanisms for systems that use the openEHR multi level modelling approach. This paper addresses the performance and size of XML databases that store openEHR compliant documents. Database size and response times to epidemiological queries are described. An anonymized relational epidemiology database and associated epidemiological queries were used to generate openEHR XML documents that were stored and queried in four opensource XML databases. The XML databases were considerably slower and required much more space than the relational database. For population-wide epidemiological queries the response times scaled in order of magnitude at the same rate as the number of records (total database size) but were orders of magnitude slower than the original relational database. For individual focused clinical queries where patient ID was specified the response times were acceptable. This study suggests that the tested XML database configurations without further optimizations are not suitable as persistence mechanisms for openEHR-based systems in production if population-wide ad hoc querying is needed.
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| 4. |
- Hägglund, Maria, Lektor, 1975-, et al.
(author)
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Världsbäst på eHälsa kräver internationellt samarbete
- 2017
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In: Svenska dagbladet. - Stockholm, Sweden : Svenska Dagbladet AB & Co.. - 1101-2412.
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Journal article (pop. science, debate, etc.)abstract
- Det är glädjande att myndigheter nu äntligen tittar mer på internationellt delade detaljerade dokumentationsmodeller för innehåll i journaler. Vi hoppas att de ger tillräckligt kraftfulla och tydliga budskap så att de upphandlande vårdgivarna också ser vikten av detta. Om vi ska bli världsbäst på eHälsa krävs internationellt samarbete, skriver flera forskare i medicinsk informatik.
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| 7. |
- Randorff Højen, Anne, et al.
(author)
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Visualizing sets of SNOMED CT concepts to support consistent terminology implementation and reuse of clinical data
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Other publication (other academic/artistic)abstract
- Inconsistent use of concepts is an obstacle when implementing SNOMED CT to improve comparability of information. Terminology implementation should be approached by common strategies for navigating and selecting proper concepts. This study aims to explore ways of illustrating common pathways and ancestors of particular sets of concepts, to support consistent use of SNOMED CT in EHR-system implementation processes. The prototype presented here is an interactive web-based reimplementation of the terminology visualization tool TermViz. The open source prototype contains terminological features that are of relevance when exploring and comparing sets of concepts in SNOMED CT. This includes interactively rearranging graphs, fetching more concept nodes, illustrating least common parents and shared pathways in merged graphs etc. Future work should focus on evaluating the developed prototype in order to assess its applicability in EHR-system-implementation contexts.
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| 8. |
- Sundvall, Erik, 1973-, et al.
(author)
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Approaches to learning openEHR : a qualitative survey, observations, and suggestions
- 2016
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In: Proceedings from the 14th Scandinavian Conference on Health Informatics 2016. - Linköping : Linköping University Electronic Press. - 9789176857762 ; , s. 29-36
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Conference paper (peer-reviewed)abstract
- Approaches such as ISO 13606 and openEHR aim to address data reusability by defining clinical data structures called archetypes and templates, based on a reference model. A problem with these approaches is that parts of them currently are rather difficult to learn. It can be hard to imagine what an archetype-based clinical system combined with modern terminology systems will look like and what consequences different modeling choices have, without seeing and experimenting with an operational system. This paper reports findings from a survey among openEHR learners and educators combined with observations of related openEHR mailing list discussions. The paper ends with an opinion piece, where we discuss potentially fruitful ways to learn, explore, and extend archetype-based EHR systems using visualization and examples.The findings highlight potential stumble blocks and solutions and should be of interest for both educators and self-learners.
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| 9. |
- Sundvall, Erik, 1973-, et al.
(author)
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Graphical Overview and Navigation of Electronic Health Records in a prototyping environment using Google Earth and openEHR Archetypes
- 2007
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In: MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics – Building Sustainable Health Systems. - : IOS Press. - 9781586037741 ; 129:Pt 2, s. 1043-7
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Conference paper (peer-reviewed)abstract
- This paper describes selected earlier approaches to graphically relating events to each other and to time; some new combinations are also suggested. These are then combined into a unified prototyping environment for visualization and navigation of electronic health records. Google Earth (GE) is used for handling display and interaction of clinical information stored using openEHR data structures and ‘archetypes’. The strength of the approach comes from GE's sophisticated handling of detail levels, from coarse overviews to fine-grained details that has been combined with linear, polar and region-based views of clinical events related to time. The system should be easy to learn since all the visualization styles can use the same navigation.The structured and multifaceted approach to handling time that is possible with archetyped openEHR data lends itself well to visualizing and integration with openEHR components is provided in the environment.
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| 10. |
- Sundvall, Erik, 1973-, et al.
(author)
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Integration of Tools for Binding Archetypes to SNOMED CT
- 2008
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In: BMC Medical Informatics and Decision Making. - : Springer. - 1472-6947. ; 8:S7
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Journal article (peer-reviewed)abstract
- BackgroundThe Archetype formalism and the associated Archetype Definition Language have been proposed as an ISO standard for specifying models of components of electronic healthcare records as a means of achieving interoperability between clinical systems. This paper presents an archetype editor with support for manual or semi-automatic creation of bindings between archetypes and terminology systems.MethodsLexical and semantic methods are applied in order to obtain automatic mapping suggestions. Information visualisation methods are also used to assist the user in exploration and selection of mappings.ResultsAn integrated tool for archetype authoring, semi-automatic SNOMED CT terminology binding assistance and terminology visualization was created and released as open source.ConclusionFinding the right terms to bind is a difficult task but the effort to achieve terminology bindings may be reduced with the help of the described approach. The methods and tools presented are general, but here only bindings between SNOMED CT and archetypes based on the openEHR reference model are presented in detail.BackgroundThe Archetype formalism and the associated Archetype Definition Language have been proposed as an ISO standard for specifying models of components of electronic healthcare records as a means of achieving interoperability between clinical systems. This paper presents an archetype editor with support for manual or semi-automatic creation of bindings between archetypes and terminology systems.MethodsLexical and semantic methods are applied in order to obtain automatic mapping suggestions. Information visualisation methods are also used to assist the user in exploration and selection of mappings.ResultsAn integrated tool for archetype authoring, semi-automatic SNOMED CT terminology binding assistance and terminology visualization was created and released as open source.ConclusionFinding the right terms to bind is a difficult task but the effort to achieve terminology bindings may be reduced with the help of the described approach. The methods and tools presented are general, but here only bindings between SNOMED CT and archetypes based on the openEHR reference model are presented in detail.
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| 11. |
- Sundvall, Erik, 1973-, et al.
(author)
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Interactive Visualization and Navigation of Complex Terminology Systems, Exemplified by SNOMED CT
- 2006
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In: Ubiquity. - : IOS Press. - 9781586036478 ; , s. 851-856
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Conference paper (peer-reviewed)abstract
- Free-text queries are natural entries into the exploration of complex terminology systems. The way search results are presented has impact on the users ability to grasp the overall structure of the system. Complex hierarchies like the one used in SNOMED CT, where nodes have multiple parents (IS-A) and several other relationship types, makes visualization challenging. This paper presents a prototype, Term Viz, applying well known methods like "focus+context" and self-organizing layouts from the fields of Information Visualization and Graph Drawing to terminologies like SNOMED CT and ICD-10. The user can simultaneously focus on several nodes in the terminologies and then use interactive animated graph navigation and semantic zooming to further explore the terminology systems without loosing context. The prototype, based on Open Source Java components, demonstrates how a number of Information Visualisation methods can aid the exploration of medical terminologies with millions of elements and can serve as a base for further development.
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| 12. |
- Sundvall, Erik, 1973-
(author)
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Scalability and Semantic Sustainability in Electronic Health Record Systems
- 2013
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Doctoral thesis (other academic/artistic)abstract
- This work is a small contribution to the greater goal of making software systems used in healthcare more useful and sustainable. To come closer to that goal, health record data will need to be more computable and easier to exchange between systems.Interoperability refers to getting systems to work together and semantics concerns the study of meanings. If Semantic interoperability is achieved then information entered in one information system is usable in other systems and reusable for many purposes. Scalability refers to the extent to which a system can gracefully grow by adding more resources. Sustainability refers more to how to best use available limited resources. Both aspects are important.The main focus and aim of the thesis is to increase knowledge about how to support scalability and semantic sustainability. It reports explorations of how to apply aspects of the above to Electronic Health Record (EHR) systems, associated infrastructure, data structures, terminology systems, user interfaces and their mutual boundaries.Using terminology systems is one way to improve computability and comparability of data. Modern complex ontologies and terminology systems can contain hundreds of thousands of concepts that can have many kinds of relationships to multiple other concepts. This makes visualization challenging. Many visualization approaches designed to show the local neighbourhood of a single concept node do not scale well to larger sets of nodes. The interactive TermViz approach described in this thesis, is designed to aid users to navigate and comprehend the context of several nodes simultaneously. Two applications are presented where TermViz aids management of the boundary between EHR data structures and the terminology system SNOMED CT.The amount of available time from people skilled in health informatics is limited. Adequate methods and tools are required to develop, maintain and reuse health-IT solutions in a sustainable way. Multiple levels of modelling including a fixed reference model and another layer of flexible reusable ‘archetypes’ for domain specific data structures, is an approach with that aim used in openEHR and the ISO 13606 standard. This approach, including learning, implementing and managing it, is explored from different angles in this thesis. An architecture applying Representational State Transfer (REST) to archetype-based EHR systems, in order to address scalability, is presented. Combined with archetyping this architecture also aims at enabling a sustainable way of continuously evolving multi-vendor EHR solutions. An experimental open source implementation of it, aimed for learning and prototyping, is also presented.Manually changing database structures used for storage every time new versions of archetypes and associated data structures are needed is likely not a sustainable activity. Thus storage systems that can handle change with minimal manual interventions are desirable. Initial explorations of performance and scalability in such systems are also reportedGraphical user interfaces focused on EHR navigation, time-perspectives and highlighting of EHR content are also presented – illustrating what can be done with computable health record data and the presented approaches.Desirable aspects of semantic sustainability have been discussed, including: sustainable use of limited resources (such as available time of skilled people), and reduction of unnecessary risks. A semantic sustainability perspective should be inspired and informed by research in complex systems theory, and should also include striving to be highly aware of when and where technical debt is being built up. Semantic sustainability is a shared responsibility.The combined results presented contribute to increasing knowledge about ways to support scalability and semantic sustainability in the context of electronic health record systems. Supporting tools, architectures and approaches are additional contributions.
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