| 1. |
- Burger, Gerard, et al.
(författare)
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Natural language processing in pathology: a scoping review
- 2016
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Ingår i: Journal of Clinical Pathology. - : BMJ PUBLISHING GROUP. - 0021-9746 .- 1472-4146. ; 69:11, s. 949-955
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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.
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| 2. |
- Cornet, Ronald, et al.
(författare)
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Comparison of Three English-to-Dutch Machine Translations of SNOMED CT Procedures
- 2017
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Ingår i: MEDINFO 2017: PRECISION HEALTHCARE THROUGH INFORMATICS. - : IOS PRESS. - 9781614998303 - 9781614998297 ; , s. 848-852
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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.
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| 3. |
- Cornet, Ronald
(författare)
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Infrastructure and Capacity Building for Semantic Interoperability in Healthcare in the Netherlands
- 2017
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Ingår i: BUILDING CAPACITY FOR HEALTH INFORMATICS IN THE FUTURE. - : IOS PRESS. - 9781614997429 - 9781614997412 ; , s. 70-74
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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.
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| 4. |
- Dentler, Kathrin, et al.
(författare)
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Intra-axiom redundancies in SNOMED CT
- 2015
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Ingår i: Artificial Intelligence in Medicine. - : ELSEVIER SCIENCE BV. - 0933-3657 .- 1873-2860. ; 65:1, s. 29-34
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Tidskriftsartikel (refereegranskat)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.
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| 5. |
- Joukes, Erik, et al.
(författare)
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Collect Once, Use Many Times: End-Users Dont Practice What They Preach
- 2016
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Ingår i: EXPLORING COMPLEXITY IN HEALTH: AN INTERDISCIPLINARY SYSTEMS APPROACH. - : IOS PRESS. - 9781614996781 - 9781614996774 ; , s. 252-256
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Konferensbidrag (refereegranskat)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.
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| 6. |
- Joukes, Erik, et al.
(författare)
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Eliciting end-user expectations to guide the implementation process of a new electronic health record: A case study using concept mapping
- 2016
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Ingår i: International Journal of Medical Informatics. - : ELSEVIER IRELAND LTD. - 1386-5056 .- 1872-8243. ; 87, s. 111-117
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Tidskriftsartikel (refereegranskat)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.
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| 7. |
- Joukes, Erik, et al.
(författare)
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Time Spent on Dedicated Patient Care and Documentation Tasks Before and After the Introduction of a Structured and Standardized Electronic Health Record
- 2018
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Ingår i: Applied Clinical Informatics. - : GEORG THIEME VERLAG KG. - 1869-0327. ; 9:1
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Tidskriftsartikel (refereegranskat)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.
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| 8. |
- Kabukye, Johnblack K, et al.
(författare)
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User Requirements for an Electronic Medical Records System for Oncology in Developing Countries : A Case Study of Uganda.
- 2017
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Ingår i: AMIA ... Annual Symposium proceedings. AMIA Symposium. - 1942-597X. ; 2017, s. 1004-1013
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Konferensbidrag (refereegranskat)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.
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| 9. |
- Kodra, Yllka, et al.
(författare)
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Recommendations for Improving the Quality of Rare Disease Registries
- 2018
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 15:8
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Forskningsöversikt (refereegranskat)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.
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| 10. |
- Martinez-Costa, Catalina, et al.
(författare)
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Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case
- 2015
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Ingår i: 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
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Tidskriftsartikel (refereegranskat)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.
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