BACKGROUND: Now that patients increasingly get access to their healthcare records, its contents require clarification. The use of patient-friendly terms and definitions can help patients and their significant others understand their medical data. However, it is costly to make patient-friendly descriptions for the myriad of terms used in the medical domain. Furthermore, a description in more general terms, leaving out some of the details, might already be sufficient for a layperson. We developed an algorithm that employs the SNOMED CT hierarchy to generalize diagnoses to a limited set of concepts with patient-friendly terms for this purpose. However, generalization essentially implies loss of detail and might result in errors, hence these generalizations remain to be validated by clinicians. We aim to assess the medical validity of diagnosis clarification by generalization to concepts with patient-friendly terms and definitions in SNOMED CT. Furthermore, we aim to identify the characteristics that render clarifications invalid. RESULTS: Two raters identified errors in 12.7% (95% confidence interval - CI: 10.7-14.6%) of a random sample of 1,131 clarifications and they considered 14.3% (CI: 12.3-16.4%) of clarifications to be unacceptable to show to a patient. The intraclass correlation coefficient of the interrater reliability was 0.34 for correctness and 0.43 for acceptability. Errors were mostly related to the patient-friendly terms and definitions used in the clarifications themselves, but also to terminology mappings, terminology modelling, and the clarification algorithm. Clarifications considered to be most unacceptable were those that provide wrong information and might cause unnecessary worry. CONCLUSIONS: We have identified problems in generalizing diagnoses to concepts with patient-friendly terms. Diagnosis generalization can be used to create a large amount of correct and acceptable clarifications, reusing patient-friendly terms and definitions across many medical concepts. However, the correctness and acceptability have a strong dependency on terminology mappings and modelling quality, as well as the quality of the terms and definitions themselves. Therefore, validation and quality improvement are required to prevent incorrect and unacceptable clarifications, before using the generalizations in practice.

The International Society for the Study of Vascular Anomalies (ISSVA) provides a classification for vascular anomalies that enables specialists to unambiguously classify diagnoses. This classification is only available in PDF format and is not machine-readable, nor does it provide unique identifiers that allow for structured registration. In this paper, we describe the process of transforming the ISSVA classification into an ontology. We also describe the structure of this ontology, as well as two applications of the ontology using examples from the domain of rare disease research. We used the expertise of an ontology expert and clinician during the development process. We semi-automatically added mappings to relevant external ontologies using automated ontology matching systems and manual assessment by experts. The ISSVA ontology should contribute to making data for vascular anomaly research more Findable, Accessible, Interoperable, and Reusable (FAIR). The ontology is available at https://bioportal.bioontology.org/ontologies/ISSVA.

INTRODUCTION: Thanks to improvement of care, cancer has become a chronic condition. But due to the toxicity of treatment, the importance of supporting the quality of life (QoL) of cancer patients increases. Monitoring and managing QoL relies on data collected by the patient in his/her home environment, its integration, and its analysis, which supports personalization of cancer management recommendations. We review the state-of-the-art of computerized systems that employ AI and Data Science methods to monitor the health status and provide support to cancer patients managed at home. OBJECTIVE: Our main objective is to analyze the literature to identify open research challenges that a novel decision support system for cancer patients and clinicians will need to address, point to potential solutions, and provide a list of established best-practices to adopt. METHODS: We designed a review study, in compliance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, analyzing studies retrieved from PubMed related to monitoring cancer patients in their home environments via sensors and self-reporting: what data is collected, what are the techniques used to collect data, semantically integrate it, infer the patient's state from it and deliver coaching/behavior change interventions. RESULTS: Starting from an initial corpus of 819 unique articles, a total of 180 papers were considered in the full-text analysis and 109 were finally included in the review. Our findings are organized and presented in four main sub-topics consisting of data collection, data integration, predictive modeling and patient coaching. CONCLUSION: Development of modern decision support systems for cancer needs to utilize best practices like the use of validated electronic questionnaires for quality-of-life assessment, adoption of appropriate information modeling standards supplemented by terminologies/ontologies, adherence to FAIR data principles, external validation, stratification of patients in subgroups for better predictive modeling, and adoption of formal behavior change theories. Open research challenges include supporting emotional and social dimensions of well-being, including PROs in predictive modeling, and providing better customization of behavioral interventions for the specific population of cancer patients.

INTRODUCTION: Existing methods to make data Findable, Accessible, Interoperable, and Reusable (FAIR) are usually carried out in a post hoc manner: after the research project is conducted and data are collected. De-novo FAIRification, on the other hand, incorporates the FAIRification steps in the process of a research project. In medical research, data is often collected and stored via electronic Case Report Forms (eCRFs) in Electronic Data Capture (EDC) systems. By implementing a de novo FAIRification process in such a system, the reusability and, thus, scalability of FAIRification across research projects can be greatly improved. In this study, we developed and implemented a novel method for de novo FAIRification via an EDC system. We evaluated our method by applying it to the Registry of Vascular Anomalies (VASCA). METHODS: Our EDC and research project independent method ensures that eCRF data entered into an EDC system can be transformed into machine-readable, FAIR data using a semantic data model (a canonical representation of the data, based on ontology concepts and semantic web standards) and mappings from the model to questions on the eCRF. The FAIRified data are stored in a triple store and can, together with associated metadata, be accessed and queried through a FAIR Data Point. The method was implemented in Castor EDC, an EDC system, through a data transformation application. The FAIRness of the output of the method, the FAIRified data and metadata, was evaluated using the FAIR Evaluation Services. RESULTS: We successfully applied our FAIRification method to the VASCA registry. Data entered on eCRFs is automatically transformed into machine-readable data and can be accessed and queried using SPARQL queries in the FAIR Data Point. Twenty-one FAIR Evaluator tests pass and one test regarding the metadata persistence policy fails, since this policy is not in place yet. CONCLUSION: In this study, we developed a novel method for de novo FAIRification via an EDC system. Its application in the VASCA registry and the automated FAIR evaluation show that the method can be used to make clinical research data FAIR when they are entered in an eCRF without any intervention from data management and data entry personnel. Due to the generic approach and developed tooling, we believe that our method can be used in other registries and clinical trials as well.

Ontologies and terminologies have been identified as key resources for the achievement of semantic interoperability in biomedical domains. The development of ontologies is performed as a joint work by domain experts and knowledge engineers. The maintenance and auditing of these resources is also the responsibility of such experts, and this is usually a time-consuming, mostly manual task. Manual auditing is impractical and ineffective for most biomedical ontologies, especially for larger ones. An example is SNOMED CT, a key resource in many countries for codifying medical information. SNOMED CT contains more than 300000 concepts. Consequently its auditing requires the support of automatic methods. Many biomedical ontologies contain natural language content for humans and logical axioms for machines. The 'lexically suggest, logically define' principle means that there should be a relation between what is expressed in natural language and as logical axioms, and that such a relation should be useful for auditing and quality assurance. Besides, the meaning of this principle is that the natural language content for humans could be used to generate the logical axioms for the machines. In this work, we propose a method that combines lexical analysis and clustering techniques to (1) identify regularities in the natural language content of ontologies; (2) cluster, by similarity, labels exhibiting a regularity; (3) extract relevant information from those clusters; and (4) propose logical axioms for each cluster with the support of axiom templates. These logical axioms can then be evaluated with the existing axioms in the ontology to check their correctness and completeness, which are two fundamental objectives in auditing and quality assurance. In this paper, we describe the application of the method to two SNOMED CT modules, a 'congenital' module, obtained using concepts exhibiting the attribute Occurrence - Congenital, and a 'chronic' module, using concepts exhibiting the attribute Clinical course - Chronic. We obtained a precision and a recall of respectively 75% and 28% for the 'congenital' module, and 64% and 40% for the 'chronic' one. We consider these results to be promising, so our method can contribute to the support of content editors by using automatic methods for assuring the quality of biomedical ontologies and terminologies.

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.

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.

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 generalizable--that 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.

OBJECTIVE: Terminological Systems (TSs) need to be maintained in order to sustain their utility. This paper describes a study aiming at the standardization of the maintenance processes of medical TSs by capturing the criteria for the management of the maintenance processes into a framework. Furthermore, this paper describes application of the framework, which sheds light on the current practice of TS maintenance. DESIGN: Observational study. MEASUREMENTS: By means of a literature study, criteria for the maintenance of TSs were obtained and categorized into a framework. The current practice of TS maintenance was explored by a survey among organizations that maintain a TS. Results were stratified by the size of the TS being maintained. RESULTS: From Sixty-three relevant articles, criteria for the maintenance processes of TSs were extracted and organized into four components. The primary component "Execution" concerns the core activities of the maintenance process. The other three components "Process management," "Change specifications," and "Editing tools" support the core activities of the component "Execution." The survey had a response rate of 40% (37 of 93). The answers reflect the large variation in the number of criteria that are satisfied for the participating organizations. Overall, maintenance of larger TSs seems to satisfy more criteria. CONCLUSIONS: The framework is an important step towards standardization of the maintenance of medical TSs and can be used to eliminate shortcomings in this process. Surveying the current practice showed that there is ample room to improve the maintenance processes of medical TSs, especially for the smaller TSs.

In this paper we study the diagnosis and repair of incoherent terminologies. We define a number of new nonstandard reasoning services to explain incoherence through pinpointing, and we present algorithms for all of these services. For one of the core tasks of debugging, the calculation of minimal unsatisfiability preserving subterminologies, we developed two different algorithms, one implementing a bottom-up approach using support of an external description logic reasoner, the other implementing a specialized tableau-based calculus. Both algorithms have been prototypically implemented. We study the effectiveness of our algorithms in two ways: we present a realistic case study where we diagnose a terminology used in a practical application, and we perform controlled benchmark experiments to get a better understanding of the computational properties of our algorithms in particular and the debugging problem in general.