SwePub - search: WFRF:(Cornet Ronald)

Enumeration	Reference	Cover	Find
1.	Balkanyi, Laszlo, et al. (author) Medical concept representation : the years beyond 2000. 2013 In: Proceedings of Studies in Health Technology & Informatics, vol. 192. - : IOS Press. - 9781614992882 - 9781614992899 ; , s. 1011-1011 Conference paper (peer-reviewed)abstract This work aims at understanding the state of the art in the broad contextual research area of "medical concept representation". Our data support the general understanding that the focus of research has moved toward medical ontologies, which we interpret as a paradigm shift. Both the opinion of socially active groups of researchers and changes in bibliometric data since 1988 support this opinion. Socially active researchers mention the OBO foundry, SNOMED CT, and the UMLS as anchor activities.
2.	Burger, Gerard, et al. (author) Natural language processing in pathology: a scoping review 2016 In: Journal of Clinical Pathology. - : BMJ PUBLISHING GROUP. - 0021-9746 .- 1472-4146. ; 69:11, s. 949-955 Research review (peer-reviewed)abstract Background Encoded pathology data are key for medical registries and analyses, but pathology information is often expressed as free text. Objective We reviewed and assessed the use of NLP (natural language processing) for encoding pathology documents. Materials and methods Papers addressing NLP in pathology were retrieved from PubMed, Association for Computing Machinery (ACM) Digital Library and Association for Computational Linguistics (ACL) Anthology. We reviewed and summarised the study objectives; NLP methods used and their validation; software implementations; the performance on the dataset used and any reported use in practice. Results The main objectives of the 38 included papers were encoding and extraction of clinically relevant information from pathology reports. Common approaches were word/phrase matching, probabilistic machine learning and rule-based systems. Five papers (13%) compared different methods on the same dataset. Four papers did not specify the method(s) used. 18 of the 26 studies that reported F-measure, recall or precision reported values of over 0.9. Proprietary software was the most frequently mentioned category (14 studies); General Architecture for Text Engineering (GATE) was the most applied architecture overall. Practical system use was reported in four papers. Most papers used expert annotation validation. Conclusions Different methods are used in NLP research in pathology, and good performances, that is, high precision and recall, high retrieval/removal rates, are reported for all of these. Lack of validation and of shared datasets precludes performance comparison. More comparative analysis and validation are needed to provide better insight into the performance and merits of these methods.
3.	Cijvat, Charlotte D., et al. (author) Factors Influencing Development and Implementation of Patients' Access to Electronic Health Records : A Comparative Study of Sweden and the Netherlands 2021 In: Frontiers In Public Health. - : Frontiers Media S.A.. - 2296-2565. ; 9 Journal article (peer-reviewed)abstract Background: Patient-accessible electronic health records (PAEHRs) and associated national policies have increasingly been set up over the past two decades. Still little is known about the most effective strategy for developing and implementing PAEHRs. There are many stakeholders to take into account, and previous research focuses on the viewpoints of patients and healthcare professionals. Many known barriers and challenges could be solved by involving end-users in the development and implementation process. This study therefore compares barriers and facilitators for PAEHR development and implementation, both general and specific for patient involvement, that were present in Sweden and the Netherlands.Methods: There were a total of 14 semi-structured interviews with 16 key informants from both countries, on which content analysis was performed. The Consolidated Framework for Implementation Research was used to guide both the construction of the interview guides and the content analysis.Outcomes: The main barriers present in both countries are resistance from healthcare professionals and technical barriers regarding electronic health record systems and vendors. Facilitators varied across the two contexts, where the national infrastructure and program management were highlighted as facilitators in Sweden and stakeholder engagement (including patients and healthcare professionals) was described as a facilitator in both contexts. Strong leadership was also described as a critical success factor, especially when faced with healthcare professional resistance.Conclusion: Most of the major barriers and facilitators from both countries are covered in existing literature. This study, however, identified factors that can be seen as more practical and that would not have arisen from interviews with patients or physicians. Recommendations for policymakers include keeping the mentioned barriers in mind from the start of development and paving the way for facilitators, mainly strict policies, learning from peer implementers, and patient involvement, when possible. Implementers should focus on strong decision-making and project management and on preparing the healthcare organization for the PAEHR.
4.	Cornet, Ronald, et al. (author) Comparison of Three English-to-Dutch Machine Translations of SNOMED CT Procedures 2017 In: MEDINFO 2017: PRECISION HEALTHCARE THROUGH INFORMATICS. - : IOS PRESS. - 9781614998303 - 9781614998297 ; , s. 848-852 Conference paper (peer-reviewed)abstract Dutch interface terminologies are needed to use SNOMED CT in the Netherlands. Machine translation may support in their creation. The aim of our study is to compare different machine translations of procedures in SNOMED CT. Procedures were translated using Google Translate, Matecat, and Thot. Google Translate and Matecat are tools with large but general translation memories. The translation memory of Thot was trained and tuned with various configurations of a Dutch translation of parts of SNOMED CT, a medical dictionary and parts of the UMLS Metathesaurus. The configuration with the highest BLEU score, representing closeness to human translation, was selected. Similarity was determined between Thot translations and those by Google and Matecat. The validity of translations was assessed through random samples. Google and Matecat translated similarly in 85.4% of the cases and generally better than Thot. Whereas the quality of translations was considered acceptable, machine translations alone are yet insufficient.
5.	Cornet, Ronald (author) Infrastructure and Capacity Building for Semantic Interoperability in Healthcare in the Netherlands 2017 In: BUILDING CAPACITY FOR HEALTH INFORMATICS IN THE FUTURE. - : IOS PRESS. - 9781614997429 - 9781614997412 ; , s. 70-74 Conference paper (peer-reviewed)abstract Over 15 years, a broad spectrum of activities was undertaken to realize a health IT infrastructure in the Netherlands. In this paper we reflect on the history, challenges, accomplishments, changes, and the way forward. It shows that the infrastructure depends on technical, legal, and semantic aspects, which are frequently reciprocally related. It also highlights the fact that the role of health professionals and of patients is increasingly considered as a crucial element.
6.	Cornet, Ronald, et al. (author) Redundant Elements in SNOMED CT Concept Definitions 2013 In: proceedings of AIME 2013, Lecture Notes in ComputerScience 2013, Vol. 7885. - Berlin, Heidelberg : Springer. ; , s. 186-195 Conference paper (peer-reviewed)abstract While redundant elements in SNOMED CT concept definitions are harmless from a logical point of view, they unnecessarily make concept definitions of typically large ontologies such as SNOMED CT hard to construct and to maintain. In this paper, we apply a fully automated method to detect intra-axiom redundancies in SNOMED CT. We systematically analyse the completeness and soundness of the results of our method by examining the identified redundant elements. In absence of a gold standard, we check whether our method identifies concepts that are likely to contain redundant elements because they become equivalent to their stated subsumer when they are replaced by a fully defined concept with the same definition. To evaluate soundness, we remove all identified redundancies, and test whether the logical closure is preserved by comparing the concept hierarchy to the one of the official SNOMED CT distribution. We found that 35,010 of the 296,433 SNOMED CT concepts (12%) contain redundant elements in their definitions, and that the results of our method are sound and complete with respect to our partial evaluation. We recommend to free the stated form from these redundancies. In future, knowledge modellers should be supported by being pointed to newly introduced redundancies.
7.	Cornet, Ronald, et al. (author) User-Directed Coordination in SNOMED CT 2013 In: MedInfo 2013. - Amsterdam : IOS Press. - 9781614992882 ; , s. 72-76 Conference paper (peer-reviewed)abstract The possibility of post-coordination of SNOMED CT concepts, especially by clinical users, is both an asset and a challenge for SNOMED CT implementation. To get insight in the applicability of post-coordination, we analyzed scenarios for user-directed coordination that are described in the documentation of SNOMED CT. The analyses were based on experiences from previous and ongoing research and implementation work, including national mapping projects, and investigations on collection of data for multiple uses. These scenarios show various usability and representation problems: high number of relationships for refinement and qualification, improper options for refinement, incorrect formal definitions, and lack of support for applying editorial rules. Improved user-directed coordination in SNOMED CT in real practice requires advanced sanctioning, increased consistency of definitions of concepts in SNOMED CT, and real-time analysis of the post-coordinate expression.
8.	Dendooven, Amélie, et al. (author) Coding practice in national and regional kidney biopsy registries 2021 In: BMC Nephrology. - : Springer Science and Business Media LLC. - 1471-2369. ; 22:1 Journal article (peer-reviewed)abstract Background: Kidney biopsy registries all over the world benefit research, teaching and health policy. Comparison, aggregation and exchange of data is however greatly dependent on how registration and coding of kidney biopsy diagnoses are performed. This paper gives an overview over kidney biopsy registries, explores how these registries code kidney disease and identifies needs for improvement of coding practice. Methods: A literature search was undertaken to identify biopsy registries for medical kidney diseases. These data were supplemented with information from personal contacts and from registry websites. A questionnaire was sent to all identified registries, investigating age of registries, scope, method of coding, possible mapping to international terminologies as well as self-reported problems and suggestions for improvement. Results: Sixteen regional or national kidney biopsy registries were identified, of which 11 were older than 10 years. Most registries were located either in Europe (10/16) or in Asia (4/16). Registries most often use a proprietary coding system (12/16). Only a few of these coding systems were mapped to SNOMED CT (1), older SNOMED versions (2) or ERA-EDTA PRD (3). Lack of maintenance and updates of the coding system was the most commonly reported problem. Conclusions: There were large gaps in the global coverage of kidney biopsy registries. Limited use of international coding systems among existing registries hampers interoperability and exchange of data. The study underlines that the use of a common and uniform coding system is necessary to fully realize the potential of kidney biopsy registries.
9.	Dentler, Kathrin, et al. (author) Barriers to the reuse of routinely recorded clinical data : a field report 2013 In: Proceedings of Studies in Health Technology & Informatics, vol.192. - : IOS Press. - 9781614992882 - 9781614992899 ; , s. 313-317 Conference paper (peer-reviewed)abstract Today, clinical data is routinely recorded in vast amounts, but its reuse can be challenging. A secondary use that should ideally be based on previously collected clinical data is the computation of clinical quality indicators. In the present study, we attempted to retrieve all data from our hospital that is required to compute a set of quality indicators in the domain of colorectal cancer surgery. We categorised the barriers that we encountered in the scope of this project according to an existing framework, and provide recommendations on how to prevent or surmount these barriers. Assuming that our case is not unique, these recommendations might be applicable for the design, evaluation and optimisation of Electronic Health Records.
10.	Dentler, Kathrin, et al. (author) Formalization and computation of quality measures based on electronic medical records 2014 In: JAMIA Journal of the American Medical Informatics Association. - : BMJ Publishing Group / Elsevier. - 1067-5027 .- 1527-974X. ; 21:2, s. 285-291 Journal article (peer-reviewed)abstract Objective Ambiguous definitions of quality measures in natural language impede their automated computability and also the reproducibility, validity, timeliness, traceability, comparability, and interpretability of computed results. Therefore, quality measures should be formalized before their release. We have previously developed and successfully applied a method for clinical indicator formalization (CLIF). The objective of our present study is to test whether CLIF is generalizablethat is, applicable to a large set of heterogeneous measures of different types and from various domains. Materials and methods We formalized the entire set of 159 Dutch quality measures for general practice, which contains structure, process, and outcome measures and covers seven domains. We relied on a web-based tool to facilitate the application of our method. Subsequently, we computed the measures on the basis of a large database of real patient data. Results Our CLIF method enabled us to fully formalize 100% of the measures. Owing to missing functionality, the accompanying tool could support full formalization of only 86% of the quality measures into Structured Query Language (SQL) queries. The remaining 14% of the measures required manual application of our CLIF method by directly translating the respective criteria into SQL. The results obtained by computing the measures show a strong correlation with results computed independently by two other parties. Conclusions The CLIF method covers all quality measures after having been extended by an additional step. Our web tool requires further refinement for CLIF to be applied completely automatically. We therefore conclude that CLIF is sufficiently generalizable to be able to formalize the entire set of Dutch quality measures for general practice.
11.	Dentler, Kathrin, et al. (author) Influence of data quality on computed Dutch hospital quality indicators: a case study in colorectal cancer surgery 2014 In: BMC Medical Informatics and Decision Making. - : BioMed Central. - 1472-6947. ; 14:32 Journal article (peer-reviewed)abstract Background: Our study aims to assess the influence of data quality on computed Dutch hospital quality indicators, and whether colorectal cancer surgery indicators can be computed reliably based on routinely recorded data from an electronic medical record (EMR). Methods: Cross-sectional study in a department of gastrointestinal oncology in a university hospital, in which a set of 10 indicators is computed (1) based on data abstracted manually for the national quality register Dutch Surgical Colorectal Audit (DSCA) as reference standard and (2) based on routinely collected data from an EMR. All 75 patients for whom data has been submitted to the DSCA for the reporting year 2011 and all 79 patients who underwent a resection of a primary colorectal carcinoma in 2011 according to structured data in the EMR were included. Comparison of results, investigating the causes for any differences based on data quality analysis. Main outcome measures are the computability of quality indicators, absolute percentages of indicator results, data quality in terms of availability in a structured format, completeness and correctness. Results: All indicators were fully computable based on the DSCA dataset, but only three based on EMR data, two of which were percentages. For both percentages, the difference in proportions computed based on the two datasets was significant. All required data items were available in a structured format in the DSCA dataset. Their average completeness was 86%, while the average completeness of these items in the EMR was 50%. Their average correctness was 87%. Conclusions: Our study showed that data quality can significantly influence indicator results, and that our EMR data was not suitable to reliably compute quality indicators. EMRs should be designed in a way so that the data required for audits can be entered directly in a structured and coded format.
12.	Dentler, Kathrin, et al. (author) Intra-axiom redundancies in SNOMED CT 2015 In: Artificial Intelligence in Medicine. - : ELSEVIER SCIENCE BV. - 0933-3657 .- 1873-2860. ; 65:1, s. 29-34 Journal article (peer-reviewed)abstract Objective: Intra-axiom redundancies are elements of concept definitions that are redundant as they are entailed by other elements of the concept definition. While such redundancies are harmless from a logical point of view, they make concept definitions hard to maintain, and they might lead to content-related problems when concepts evolve. The objective of this study is to develop a fully automated method to detect intra-axiom redundancies in OWL 2 EL and apply it to SNOMED Clinical Terms (SNOMED CT). Materials and methods: We developed a software program in which we implemented, adapted and extended readily existing rules for redundancy elimination. With this, we analysed occurence of redundancy in 11 releases of SNOMED CT(January 2009 to January 2014). We used the ELK reasoner to classify SNOMED CT, and Pellet for explanation of equivalence. We analysed the completeness and soundness of the results by an in-depth examination of the identified redundant elements in the July 2012 release of SNOMED CT. To determine if concepts with redundant elements lead to maintenance issues, we analysed a small sample of solved redundancies. Results: Analyses showed that the amount of redundantly defined concepts in SNOMED CT is consistently around 35,000. In the July 2012 version of SNOMED CT, 35,010(12%) of the 296,433 concepts contained redundant elements in their definitions. The results of applying our method are sound and complete with respect to our evaluation. Analysis of solved redundancies suggests that redundancies in concept definitions lead to inadequate maintenance of SNOMED CT. Conclusions: Our analysis revealed that redundant elements are continuously introduced and removed, and that redundant elements may be overlooked when concept definitions are corrected. Applying our redundancy detection method to remove intra-axiom redundancies from the stated form of SNOMED CT and to point knowledge modellers to newly introduced redundancies can support creating and maintaining a redundancy-free version of SNOMED CT. (C) 2014 Elsevier B.V. All rights reserved.
13.	Fernandez-Luque, Luis, et al. (author) Evidence-Based Health Informatics as the Foundation for the COVID-19 Response : A Joint Call for Action 2022 In: Methods of Information in Medicine. - : Thieme Verlag. - 0026-1270 .- 2511-705X. ; 59:6, s. 183-192 Journal article (peer-reviewed)abstract Background As a major public health crisis, the novel coronavirus disease 2019 (COVID-19) pandemic demonstrates the urgent need for safe, effective, and evidence-based implementations of digital health. The urgency stems from the frequent tendency to focus attention on seemingly high promising digital health interventions despite being poorly validated in times of crisis. Aim In this paper, we describe a joint call for action to use and leverage evidence-based health informatics as the foundation for the COVID-19 response and public health interventions. Tangible examples are provided for how the working groups and special interest groups of the International Medical Informatics Association (IMIA) are helping to build an evidence-based response to this crisis. Methods Leaders of working and special interest groups of the IMIA, a total of 26 groups, were contacted via e-mail to provide a summary of the scientific-based efforts taken to combat COVID-19 pandemic and participate in the discussion toward the creation of this manuscript. A total of 13 groups participated in this manuscript. Results Various efforts were exerted by members of IMIA including (1) developing evidence-based guidelines for the design and deployment of digital health solutions during COVID-19; (2) surveying clinical informaticians internationally about key digital solutions deployed to combat COVID-19 and the challenges faced when implementing and using them; and (3) offering necessary resources for clinicians about the use of digital tools in clinical practice, education, and research during COVID-19. Discussion Rigor and evidence need to be taken into consideration when designing, implementing, and using digital tools to combat COVID-19 to avoid delays and unforeseen negative consequences. It is paramount to employ a multidisciplinary approach for the development and implementation of digital health tools that have been rapidly deployed in response to the pandemic bearing in mind human factors, ethics, data privacy, and the diversity of context at the local, national, and international levels. The training and capacity building of front-line workers is crucial and must be linked to a clear strategy for evaluation of ongoing experiences.
14.	Joukes, Erik, et al. (author) Collect Once, Use Many Times: End-Users Dont Practice What They Preach 2016 In: EXPLORING COMPLEXITY IN HEALTH: AN INTERDISCIPLINARY SYSTEMS APPROACH. - : IOS PRESS. - 9781614996781 - 9781614996774 ; , s. 252-256 Conference paper (peer-reviewed)abstract Data in an Electronic Health Record must be recorded once, in a standardized and structured way at the point of care to be reusable within the care process as well as for secondary purposes (collect once, use many times (COUMT) paradigm). COUMT has not yet been fully adopted by staff in every organization. Our study intends to identify concepts that underlie its adoption and describe its current status in Dutch academic hospitals. Based on literature we have constructed a model that describes these concepts and that guided the development of a questionnaire investigating COUMT adoption. The questionnaire was sent to staff working with patient data or records in seven out of eight Dutch university hospitals. Results show high willingness of end-users to comply to COUMT in the care process. End-users agree that COUMT is important, and that they want to work in a structured and standardized way. However, end-users indicate to not actually use terminology or information standards, but often register diagnoses and procedures in free text, and experience repeated recording of data. In conclusion, we found that COUMT is currently well adopted in mind, but not yet in practice.
15.	Joukes, Erik, et al. (author) Composite Quality of Care Scores, Electronic Health Record Maturity Models, and their Associations; Preliminary Literature Review Results. 2013 In: Proceedings of Studies in Health Technology & Informatics, vol. 192. - 9781614992882 - 9781614992899 ; , s. 981-981 Conference paper (peer-reviewed)abstract To accurately assess the association between the use of EHR systems and the quality of healthcare we need (composite) measures for quality of healthcare, and a model to measure the maturity of the EHR. This Medline-based literature study therefore focussed on three topics; (1) methods to compose a measure for quality of care based on individual quality indicators (QI), (2) models to measure EHR maturity, and (3) the association between the former two. Composite quality is most often measured using opportunity-based scores, maturity is measured in functionalities or levels. EHR maturity measures are not used extensively in biomedical literature. Most studies found a positive association between EHR use and the quality of care but almost none of them differentiate in maturity of EHR which hampers firm conclusions about this relation.
16.	Joukes, Erik, et al. (author) Eliciting end-user expectations to guide the implementation process of a new electronic health record: A case study using concept mapping 2016 In: International Journal of Medical Informatics. - : ELSEVIER IRELAND LTD. - 1386-5056 .- 1872-8243. ; 87, s. 111-117 Journal article (peer-reviewed)abstract Objective: To evaluate the usability of concept mapping to elicit the expectations of healthcare professionals regarding the implementation of a new electronic health record (EHR). These expectations need to be taken into account during the implementation process to maximize the chance of success of the EHR. Setting: Two university hospitals in Amsterdam, The Netherlands, in the preparation phase of jointly implementing a new EHR. During this study the hospitals had different methods of documenting patient information (legacy EHR vs. paper-based records). Method: Concept mapping was used to determine and classify the expectations of healthcare professionals regarding the implementation of a new EHR. A multidisciplinary group of 46 healthcare professionals from both university hospitals participated in this study. Expectations were elicited in focus groups, their relevance and feasibility were assessed through a web-questionnaire. Nonmetric multidimensional scaling and clustering methods were used to identify clusters of expectations. Results: We found nine clusters of expectations, each covering an important topic to enable the healthcare professionals to work properly with the new EHR once implemented: usability, data use and reuse, facility conditions, data registration, support, training, internal communication, patients, and collaboration. Average importance and feasibility of each of the clusters was high. Conclusion: Concept mapping is an effective method to find topics that, according to healthcare professionals, are important to consider during the implementation of a new EHR. The method helps to combine the input of a large group of stakeholders at limited efforts. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
17.	Joukes, Erik, et al. (author) Time Spent on Dedicated Patient Care and Documentation Tasks Before and After the Introduction of a Structured and Standardized Electronic Health Record 2018 In: Applied Clinical Informatics. - : GEORG THIEME VERLAG KG. - 1869-0327. ; 9:1 Journal article (peer-reviewed)abstract Background Physicians spend around 35% of their time documenting patient data. They are concerned that adopting a structured and standardized electronic health record (EHR) will lead to more time documenting and less time for patient care, especially during consultations. Objective This study measures the effect of the introduction of a structured and standardized EHR on documentation time and time for dedicated patient care during outpatient consultations. Methods We measured physicians time spent on four task categories during outpatient consultations: documentation, patient care, peer communication, and other activities. Physicians covered various specialties from two university hospitals that jointly implemented a structured and standardized EHR. Preimplementation, one hospital used a legacy-EHR, and one primarily paper-based records. The same physicians were observed 2 to 6 months before and 6 to 8 months after implementation. We analyzed consultation duration, and percentage of time spent on each task category. Differences in time distribution before and after implementation were tested using multilevel linear regression. Results We observed 24 physicians (162 hours, 439 consultations). We found no significant difference in consultation duration or number of consultations per hour. In the legacy-EHR center, we found the implementation associated with a significant decrease in time spent on dedicated patient care (-8.5%). In contrast, in the previously paper-based center, we found a significant increase in dedicated time spent on documentation (8.3%) and decrease in time on combined patient care and documentation (-4.6%). The effect on dedicated documentation time significantly differed between centers. Conclusion Implementation of a structured and standardized EHR was associated with 8.5% decrease in time for dedicated patient care during consultations in one center and 8.3% increase in dedicated documentation time in another center. These results are in line with physicians concerns that the introduction of a structured and standardized EHR might lead to more documentation burden and less time for dedicated patient care.
18.	Kabukye, Johnblack K, et al. (author) User Requirements for an Electronic Medical Records System for Oncology in Developing Countries : A Case Study of Uganda. 2017 In: AMIA ... Annual Symposium proceedings. AMIA Symposium. - 1942-597X. ; 2017, s. 1004-1013 Conference paper (peer-reviewed)abstract Cancer is a major public health challenge in developing countries but the healthcare systems are not well prepared to deal with the epidemic. Health information technologies such as electronic medical records (EMRs) have the potential to improve cancer care yet their adoption remains low, in part due to EMR systems not meeting user requirements. This study aimed at analyzing the user requirements for an EMR for a cancer hospital in Uganda. A user-centered approach was taken, through focus group discussion and interviews with target end users to analyze workflow, challenges and wishes. Findings highlight the uniqueness of oncology in low-resource settings and the requirements including support for oncology-specific documentation, reuse of data for research and reporting, assistance with care coordination, computerized clinical decision support, and the need to meet the constraints in terms of technological infrastructure, stretched healthcare workforce and flexibility to allow variations and exceptions.
19.	Karlsson, Daniel, et al. (author) Does SNOMED CT post-coordination scale? 2014 In: e-Health – For Continuity of Care. - : IOS Press. - 9781614994312 - 9781614994329 ; , s. 1048-52 Book chapter (peer-reviewed)abstract SNOMED CT is a compositional terminology. Construction of post-coordinated expressions allows users to specify new meaning by referencing existing SNOMED CT concepts. The use of post-coordinated expressions in information systems requires special software, a reasoner, to give the exact relations between post-coordinated expressions and existing SNOMED CT content. Thus, the performance characteristics of reasoners are important for implementation of post-coordination in information systems. This study aims to test how reasoners perform when a large number of post-coordinated expressions are added to SNOMED CT. The time needed to classify an ontology consisting of SNOMED CT plus an increasing number of post-coordinated expressions is measured. The best performing reasoner in this test classifies SNOMED CT plus 1 million post-coordinated expressions in 42 seconds. The time to classify grows a little less than quadratic as the size of the ontology increases. In conclusion, classification time is not a problem using current reasoners and current SNOMED CT releases even if a large number of post-coordinated expressions are added.
20.	Kodra, Yllka, et al. (author) Recommendations for Improving the Quality of Rare Disease Registries 2018 In: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 15:8 Research review (peer-reviewed)abstract Rare diseases (RD) patient registries are powerful instruments that help develop clinical research, facilitate the planning of appropriate clinical trials, improve patient care, and support healthcare management. They constitute a key information system that supports the activities of European Reference Networks (ERNs) on rare diseases. A rapid proliferation of RD registries has occurred during the last years and there is a need to develop guidance for the minimum requirements, recommendations and standards necessary to maintain a high-quality registry. In response to these heterogeneities, in the framework of RD-Connect, a European platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research, we report on a list of recommendations, developed by a group of experts, including members of patient organizations, to be used as a framework for improving the quality of RD registries. This list includes aspects of governance, Findable, Accessible, Interoperable and Reusable (FAIR) data and information, infrastructure, documentation, training, and quality audit. The list is intended to be used by established as well as new RD registries. Further work includes the development of a toolkit to enable continuous assessment and improvement of their organizational and data quality.
21.	Lee, Dennis, et al. (author) Literature review of SNOMED CT use 2014 In: JAMIA Journal of the American Medical Informatics Association. - : BMJ Group. - 1067-5027 .- 1527-974X. ; 21:E1, s. E11-E19 Research review (peer-reviewed)abstract OBJECTIVE: The aim of this paper is to report on the use of the systematised nomenclature of medicine clinical terms (SNOMED CT) by providing an overview of published papers.METHODS: Published papers on SNOMED CT between 2001 and 2012 were identified using PubMed and Embase databases using the keywords 'systematised nomenclature of medicine' and 'SNOMED CT'. For each paper the following characteristics were retrieved: SNOMED CT focus category (ie, indeterminate, theoretical, pre-development/design, implementation and evaluation/commodity), usage category (eg, prospective content coverage, used to classify or code in a study), medical domain and country.RESULTS: Our search strategy identified 488 papers. A comparison between the papers published between 2001-6 and 2007-12 showed an increase in every SNOMED CT focus category. The number of papers classified as 'theoretical' increased from 46 to 78, 'pre-development/design' increased from 61 to 173 and 'implementation' increased from 10 to 34. Papers classified as 'evaluation/commodity' only started to appear from 2010.CONCLUSIONS: The majority of studies focused on 'theoretical' and 'pre-development/design'. This is still encouraging as SNOMED CT is being harmonized with other standardized terminologies and is being evaluated to determine the content coverage of local terms, which is usually one of the first steps towards adoption. Most implementations are not published in the scientific literature, requiring a look beyond the scientific literature to gain insights into SNOMED CT implementations.
22.	Martinez-Costa, Catalina, et al. (author) Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case 2015 In: JAMIA Journal of the American Medical Informatics Association. - : Oxford University Press (OUP): Policy B - Oxford Open Option B - CC-BY / Elsevier. - 1067-5027 .- 1527-974X. ; 22:3, s. 565-576 Journal article (peer-reviewed)abstract Objective To improve semantic interoperability of electronic health records (EHRs) by ontology-based mediation across syntactically heterogeneous representations of the same or similar clinical information. Materials and Methods Our approach is based on a semantic layer that consists of: (1) a set of ontologies supported by (2) a set of semantic patterns. The first aspect of the semantic layer helps standardize the clinical information modeling task and the second shields modelers from the complexity of ontology modeling. We applied this approach to heterogeneous representations of an excerpt of a heart failure summary. Results Using a set of finite top-level patterns to derive semantic patterns, we demonstrate that those patterns, or compositions thereof, can be used to represent information from clinical models. Homogeneous querying of the same or similar information, when represented according to heterogeneous clinical models, is feasible. Discussion Our approach focuses on the meaning embedded in EHRs, regardless of their structure. This complex task requires a clear ontological commitment (ie, agreement to consistently use the shared vocabulary within some context), together with formalization rules. These requirements are supported by semantic patterns. Other potential uses of this approach, such as clinical models validation, require further investigation. Conclusion We show how an ontology-based representation of a clinical summary, guided by semantic patterns, allows homogeneous querying of heterogeneous information structures. Whether there are a finite number of top-level patterns is an open question.
23.	Nyström, Mikael, 1977- (author) Enrichment of Terminology Systems for Use and Reuse in Medical Information Systems 2010 Doctoral thesis (other academic/artistic)abstract Electronic health record systems (EHR) are used to store relevant heath facts about patients. The main use of the EHR is in the care of the patient, but an additional use is to reuse the EHR information to locate and evaluate clinical evidence for treatments. To efficiently use the EHR information it is essential to use appropriate methods for information compilations. This thesis deals with use of information in medical terminology systems and ontologies to be able to better use and reuse EHR information and other medical information.The first objective of the thesis is to examine if word alignment on bilingual English-Swedish rubrics from five medical terminology systems can be used to build a bilingual dictionary. A study found that it was possible to generate a dictionary with 42 000 entries containing a high proportion of medical entries using word alignment. The method worked best using sets of rubrics with many unique words that are consistently translated. The dictionary can be used as a general medical dictionary, for use in semi-automatic translation methods, for use in cross-language information retrieval systems, and for enrichment of other terminology systems.The second objective of the thesis is to explore how connections from existing terminology systems and information models to SNOMED CT and the structure in SNOMED CT can be used to reuse information. A study examined whether the primary health care diagnose terminology system KSH97-P can obtain a richer structure using category and chapter mappings from KSH97-P to SNOMED CT and the structure in SNOMED CT. The study showed that KSH97-P can be enriched with a poly-hierarchical chapter division and additional attributes. The richer structure was used to compile statistics in new manners that showed new views of the primary care diagnoses. A literature study evaluated which kinds of information compilations those are necessary to create graphical patient overviews based on information from EHRs. It was found that a third of the patient overviews can have their information needs satisfied using compilations based on SNOMED CT encodings of the information entities in the EHR and the structure in SNOMED CT. The other overviews also need access to individual values in the EHR. This can be achieved by using well-defined information models in the EHR.
24.	Oluoch, Tom, et al. (author) A structured approach to recording AIDS-defining illnesses in Kenya: A SNOMED CT based solution 2015 In: Journal of Biomedical Informatics. - : Elsevier. - 1532-0464 .- 1532-0480. ; 56, s. 387-394 Journal article (peer-reviewed)abstract Introduction: Several studies conducted in sub-Saharan Africa (SSA) have shown that routine clinical data in HIV clinics often have errors. Lack of structured and coded documentation of diagnosis of AIDS defining illnesses (ADIs) can compromise data quality and decisions made on clinical care. Methods: We used a structured framework to derive a reference set of concepts and terms used to describe ADIs. The four sources used were: (i) CDC/Accenture list of opportunistic infections, (ii) SNOMED Clinical Terms (SNOMED CT), (iii) Focus Group Discussion (FGD) among clinicians and nurses attending to patients at a referral provincial hospital in western Kenya, and (iv) chart abstraction from the Maternal Child Health (MCH) and HIV clinics at the same hospital. Using the January 2014 release of SNOMED CT, concepts were retrieved that matched terms abstracted from approach iii and iv, and the content coverage assessed. Post-coordination matching was applied when needed. Results: The final reference set had 1054 unique ADI concepts which were described by 1860 unique terms. Content coverage of SNOMED CT was high (99.9% with pre-coordinated concepts; 100% with post-coordination). The resulting reference set for ADIs was implemented as the interface terminology on OpenMRS data entry forms. Conclusion: Different sources demonstrate complementarity in the collection of concepts and terms for an interface terminology. SNOMED CT provides a high coverage in the domain of ADIs. Further work is needed to evaluate the effect of the interface terminology on data quality and quality of care.
25.	Oluoch, Tom, et al. (author) Effect of a clinical decision support system on early action on immunological treatment failure in patients with HIV in Kenya: a cluster randomised controlled trial 2016 In: LANCET HIV. - : ELSEVIER INC. - 2352-3018. ; 3:2, s. E76-E84 Journal article (peer-reviewed)abstract Background A clinical decision support system (CDSS) is a computer program that applies a set of rules to data stored in electronic health records to off er actionable recommendations. We aimed to establish whether a CDSS that supports detection of immunological treatment failure among patients with HIV taking antiretroviral therapy (ART) would improve appropriate and timely action. Methods We did this prospective, cluster randomised controlled trial in adults and children (aged >= 18 months) who were eligible for, and receiving, ART at HIV clinics in Siaya County, western Kenya. Health facilities were randomly assigned (1: 1), via block randomisation (block size of two) with a computer-generated random number sequence, to use electronic health records either alone (control) or with CDSS (intervention). Facilities were matched by type and by number of patients enrolled in HIV care. The primary outcome measure was the difference between groups in the proportion of patients who experienced immunological treatment failure and had a documented clinical action. We used generalised linear mixed models with random effects to analyse clustered data. This trial is registered with ClinicalTrials.gov, number NCT01634802. Findings Between Sept 1, 2012, and Jan 31, 2014, 13 clinics, comprising 41 062 patients, were randomly assigned to the control group (n=6) or the intervention group (n=7). Data collection at each site took 12 months. Among patients eligible for ART, 10 358 (99%) of 10 478 patients were receiving ART at control sites and 10 991 (99%) of 11 028 patients were receiving ART at intervention sites. Of these patients, 1125 (11%) in the control group and 1342 (12%) in the intervention group had immunological treatment failure, of whom 332 (30%) and 727 (54%), respectively, received appropriate action. The likelihood of clinicians taking appropriate action on treatment failure was higher with CDSS alerts than with no decision support system (adjusted odds ratio 3.18, 95% CI 1.02-9.87). Interpretation CDSS significantly improved the likelihood of appropriate and timely action on immunological treatment failure. We expect our findings will be generalisable to virological monitoring of patients with HIV receiving ART once countries implement the 2015 WHO recommendation to scale up viral load monitoring.
26.	Oluoch, Tom, et al. (author) Inconsistencies between Recorded Opportunistic Infections and WHO HIV Staging in Western Kenya. 2013 In: Proceedings of Studies in Health Technology & Informatics, vol. 192. - : IOS Press. - 9781614992882 - 9781614992899 ; , s. 1139-1139 Conference paper (peer-reviewed)abstract Opportunistic infections (OIs) are the main cause of morbidity and mortality among patients with HIV in developing countries. It is therefore critical that accurate diagnoses are made and that they are correctly recorded and managed. We reviewed 200 randomly selected records of clinical encounters with HIV infected pregnant women attending the ante-natal care (ANC) clinic in July 2012 at the Jaramogi Oginga Odinga Teaching and Referral Hospital in Kenya. None of the clients in WHO stage 4 and 2.8% of those in WHO stage 3 had a new OI diagnosis recorded during the clinical encounter. This data suggests current under-recording of OIs and the inconsistency between WHO staging and OI diagnosis. Structured methods such as SNOMED CT have the potential to improve complete and accurate recording of OIs which, in turn, enable automatedand accurate WHO staging.
27.	Rosenbeck Goeg, Kirstine, et al. (author) Clustering clinical models from local electronic health records based on semantic similarity 2015 In: Journal of Biomedical Informatics. - : Elsevier. - 1532-0464 .- 1532-0480. ; 54, s. 294-304 Journal article (peer-reviewed)abstract Background: Clinical models in electronic health records are typically expressed as templates which support the multiple clinical workflows in which the system is used. The templates are often designed using local rather than standard information models and terminology, which hinders semantic interoperability. Semantic challenges can be solved by harmonizing and standardizing clinical models. However, methods supporting harmonization based on existing clinical models are lacking. One approach is to explore semantic similarity estimation as a basis of an analytical framework. Therefore, the aim of this study is to develop and apply methods for intrinsic similarity-estimation based analysis that can compare and give an overview of multiple clinical models. Method: For a similarity estimate to be intrinsic it should be based on an established ontology, for which SNOMED CT was chosen. In this study, Lin similarity estimates and Sokal and Sneath similarity estimates were used together with two aggregation techniques (average and best-match-average respectively) resulting in a total of four methods. The similarity estimations are used to hierarchically cluster templates. The test material consists of templates from Danish and Swedish EHR systems. The test material was used to evaluate how the four different methods perform. Result and discussion: The best-match-average aggregation technique performed better in terms of clustering similar templates than the average aggregation technique. No difference could be seen in terms of the choice of similarity estimate in this study, but the finding may be different for other datasets. The dendrograms resulting from the hierarchical clustering gave an overview of the templates and a basis of further analysis. Conclusion: Hierarchical clustering of templates based on SNOMED CT and semantic similarity estimation with best-match-average aggregation technique can be used for comparison and summarization of multiple templates. Consequently, it can provide a valuable tool for harmonization and standardization of clinical models.
28.	Schulz, Stefan, et al. (author) An Ontological Analysis of Reference in Health Record Statements 2014 In: Formal Ontology in Information Systems. - Amsterdam : IOS Press. - 9781614994374 - 9781614994381 ; , s. 289-302 Conference paper (peer-reviewed)abstract The relation between an information entity and its referent can be described as a second-order statement, as long as the referent is a type. This is typical for medical discourse such as diagnostic statements in electronic health records (EHRs), which often express hypotheses or probability assertions about the existence of an instance of, e.g. a disease type. This paper presents several approximations using description logics and a query language, the entailments of which are checked against a reference standard. Their pros and cons are discussed in the light of formal ontology and logic.
29.	Schulz, Stefan, et al. (author) From Concept Representations to Ontologies : A Paradigm Shift in Health Informatics? 2013 In: Healthcare informatics research. - : The Korean Society of Medical Informatics. - 2093-3681 .- 2093-369X. ; 19:4, s. 235-242 Journal article (peer-reviewed)abstract OBJECTIVES: This work aims at uncovering challenges in biomedical knowledge representation research by providing an understanding of what was historically called "medical concept representation" and used as the name for a working group of the International Medical Informatics Association.METHODS: Bibliometrics, text mining, and a social media survey compare the research done in this area between two periods, before and after 2000.RESULTS: Both the opinion of socially active groups of researchers and the interpretation of bibliometric data since 1988 suggest that the focus of research has moved from "medical concept representation" to "medical ontologies".CONCLUSIONS: It remains debatable whether the observed change amounts to a paradigm shift or whether it simply reflects changes in naming, following the natural evolution of ontology research and engineering activities in the 1990s. The availability of powerful tools to handle ontologies devoted to certain areas of biomedicine has not resulted in a large-scale breakthrough beyond advances in basic research.
30.	Scott, Philip J., et al. (author) Informatics for Health 2017: Advancing both science and practice 2017 In: Journal of Innovation in Health Informatics. - : BCS, The Chartered Institute for IT. - 2058-4563 .- 2058-4555. Conference paper (other academic/artistic)abstract The Informatics for Health congress, 24-26 April 2017, in Manchester, UK, brought together the Medical Informatics Europe (MIE) conference and the Farr Institute International Conference. This special issue of the Journal of Innovation in Health Informatics contains 113 presentation abstracts and 149 poster abstracts from the congress.

Skapa referenser, mejla, bekava och länka

Permalink

Träfflista för sökning "WFRF:(Cornet Ronald) "

Refine your search

Year