| 1. |
- Balkanyi, Laszlo, et al.
(författare)
-
Medical concept representation : the years beyond 2000.
- 2013
-
Ingår i: Proceedings of Studies in Health Technology & Informatics, vol. 192. - : IOS Press. - 9781614992882 - 9781614992899 ; , s. 1011-1011
-
Konferensbidrag (refereegranskat)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.
(författare)
-
Natural language processing in pathology: a scoping review
- 2016
-
Ingår i: Journal of Clinical Pathology. - : BMJ PUBLISHING GROUP. - 0021-9746 .- 1472-4146. ; 69:11, s. 949-955
-
Forskningsöversikt (refereegranskat)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.
(författare)
-
Factors Influencing Development and Implementation of Patients' Access to Electronic Health Records : A Comparative Study of Sweden and the Netherlands
- 2021
-
Ingår i: Frontiers In Public Health. - : Frontiers Media S.A.. - 2296-2565. ; 9
-
Tidskriftsartikel (refereegranskat)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.
(författare)
-
Comparison of Three English-to-Dutch Machine Translations of SNOMED CT Procedures
- 2017
-
Ingår i: MEDINFO 2017: PRECISION HEALTHCARE THROUGH INFORMATICS. - : IOS PRESS. - 9781614998303 - 9781614998297 ; , s. 848-852
-
Konferensbidrag (refereegranskat)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
(författare)
-
Infrastructure and Capacity Building for Semantic Interoperability in Healthcare in the Netherlands
- 2017
-
Ingår i: BUILDING CAPACITY FOR HEALTH INFORMATICS IN THE FUTURE. - : IOS PRESS. - 9781614997429 - 9781614997412 ; , s. 70-74
-
Konferensbidrag (refereegranskat)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.
(författare)
-
Redundant Elements in SNOMED CT Concept Definitions
- 2013
-
Ingår i: proceedings of AIME 2013, Lecture Notes in ComputerScience 2013, Vol. 7885. - Berlin, Heidelberg : Springer. ; , s. 186-195
-
Konferensbidrag (refereegranskat)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.
(författare)
-
User-Directed Coordination in SNOMED CT
- 2013
-
Ingår i: MedInfo 2013. - Amsterdam : IOS Press. - 9781614992882 ; , s. 72-76
-
Konferensbidrag (refereegranskat)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.
(författare)
-
Coding practice in national and regional kidney biopsy registries
- 2021
-
Ingår i: BMC Nephrology. - : Springer Science and Business Media LLC. - 1471-2369. ; 22:1
-
Tidskriftsartikel (refereegranskat)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.
(författare)
-
Barriers to the reuse of routinely recorded clinical data : a field report
- 2013
-
Ingår i: Proceedings of Studies in Health Technology & Informatics, vol.192. - : IOS Press. - 9781614992882 - 9781614992899 ; , s. 313-317
-
Konferensbidrag (refereegranskat)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.
(författare)
-
Formalization and computation of quality measures based on electronic medical records
- 2014
-
Ingår i: JAMIA Journal of the American Medical Informatics Association. - : BMJ Publishing Group / Elsevier. - 1067-5027 .- 1527-974X. ; 21:2, s. 285-291
-
Tidskriftsartikel (refereegranskat)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.
|
|
