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Objective To explore the feasibility of validating Dutch concept extraction tools using annotated corpora translated from English, focusing on preserving annotations during translation and addressing the scarcity of non-English annotated clinical corpora. Materials and Methods Three annotated corpora were standardized and translated from English to Dutch using 2 machine translation services, Google Translate and OpenAI GPT-4, with annotations preserved through a proposed method of embedding annotations in the text before translation. The performance of 2 concept extraction tools, MedSpaCy and MedCAT, was assessed across the corpora in both Dutch and English. Results The translation process effectively generated Dutch annotated corpora and the concept extraction tools performed similarly in both English and Dutch. Although there were some differences in how annotations were preserved across translations, these did not affect extraction accuracy. Supervised MedCAT models consistently outperformed unsupervised models, whereas MedSpaCy demonstrated high recall but lower precision. Discussion Our validation of Dutch concept extraction tools on corpora translated from English was successful, highlighting the efficacy of our annotation preservation method and the potential for efficiently creating multilingual corpora. Further improvements and comparisons of annotation preservation techniques and strategies for corpus synthesis could lead to more efficient development of multilingual corpora and accurate non-English concept extraction tools.Conclusion This study has demonstrated that translated English corpora can be used to validate non-English concept extraction tools. The annotation preservation method used during translation proved effective, and future research can apply this corpus translation method to additional languages and clinical settings.

Objective: Observational studies using electronic health record (EHR) databases often face challenges due to unspecific clinical codes that can obscure detailed medical information, hindering precise data analysis. In this study, we aimed to assess the feasibility of refining these unspecific condition codes into more specific codes in a Dutch general practitioner (GP) EHR database by leveraging the available clinical free text. Methods: We utilized three approaches for text classification—search queries, semi-supervised learning, and supervised learning—to improve the specificity of ten unspecific International Classification of Primary Care (ICPC-1) codes. Two text representations and three machine learning algorithms were evaluated for the (semi-)supervised models. Additionally, we measured the improvement achieved by the refinement process on all code occurrences in the database. Results: The classification models performed well for most codes. In general, no single classification approach consistently outperformed the others. However, there were variations in the relative performance of the classification approaches within each code and in the use of different text representations and machine learning algorithms. Class imbalance and limited training data affected the performance of the (semi-)supervised models, yet the simple search queries remained particularly effective. Ultimately, the developed models improved the specificity of over half of all the unspecific code occurrences in the database. Conclusions: Our findings show the feasibility of using information from clinical text to improve the specificity of unspecific condition codes in observational healthcare databases, even with a limited range of machine-learning techniques and modest annotated training sets. Future work could investigate transfer learning, integration of structured data, alternative semi-supervised methods, and validation of models across healthcare settings. The improved level of

Background:: Patients with cancer often have to make complex decisions about treatment, with the options varying in risk profiles and effects on survival and quality of life. Moreover, inefficient care paths make it hard for patients to participate in shared decision-making. Data-driven decision-support tools have the potential to empower patients, support personalized care, improve health outcomes and promote health equity. However, decision-support tools currently seldom consider quality of life or individual preferences, and their use in clinical practice remains limited, partly because they are not well integrated in patients’ care paths. Aim and objectives:: The central aim of the 4D PICTURE project is to redesign patients’ care paths and develop and integrate evidence-based decision-support tools to improve decision-making processes in cancer care delivery. This article presents an overview of this international, interdisciplinary project. Design, methods and analysis:: In co-creation with patients and other stakeholders, we will develop data-driven decision-support tools for patients with breast cancer, prostate cancer and melanoma. We will support treatment decisions by using large, high-quality datasets with state-of-the-art prognostic algorithms. We will further develop a conversation tool, the Metaphor Menu, using text mining combined with citizen science techniques and linguistics, incorporating large datasets of patient experiences, values and preferences. We will further develop a promising methodology, MetroMapping, to redesign care paths. We will evaluate MetroMapping and these integrated decision-support tools, and ensure their sustainability using the Nonadoption, Abandonment, Scale-Up, Spread, and Sustainability (NASSS) framework. We will explore the generalizability of MetroMapping and the decision-support tools for other types of cancer and across other EU member states. Ethics:: Through an embedded ethics approach, we will address social and et

Background Medication errors (MEs) are a major public health concern which can cause harm and financial burden within the healthcare system. Characterizing MEs is crucial to develop strategies to mitigate MEs in the future. Objectives To characterize ME-associated reports, and investigate signals of disproportionate reporting (SDRs) on MEs in the Food and Drug Administration's Adverse Event Reporting System (FAERS). Methods FAERS data from 2004 to 2020 was used. ME reports were identified with the narrow Standardised Medical Dictionary for Regulatory Activities® (MedDRA®) Query (SMQ) for MEs. Drug names were converted to the Anatomical Therapeutic Chemical (ATC) classification. SDRs were investigated using the reporting odds ratio (ROR). Results In total 488 470 ME reports were identified, mostly (59%) submitted by consumers and mainly (55%) associated with females. Median age at time of ME was 57 years (interquartile range: 37–70 years). Approximately 1 out of 3 reports stated a serious health outcome. The most prevalent reported drug class was “antineoplastic and immunomodulating agents” (25%). The most common ME type was “incorrect dose administered” (9%). Of the 1659 SDRs obtained, adalimumab was the most common drug associated with MEs, noting a ROR of 1.22 (95% confidence interval: 1.21–1.24). Conclusion This study offers a first of its kind characterization of MEs as reported to FAERS. Reported MEs are frequent and may be associated with serious health outcomes. This FAERS data provides insights on ME prevention and offers possibilities for additional in-depth analyses.

OBJECTIVE: This systematic review aims to assess how information from unstructured text is used to develop and validate clinical prognostic prediction models. We summarize the prediction problems and methodological landscape and determine whether using text data in addition to more commonly used structured data improves the prediction performance.MATERIALS AND METHODS: We searched Embase, MEDLINE, Web of Science, and Google Scholar to identify studies that developed prognostic prediction models using information extracted from unstructured text in a data-driven manner, published in the period from January 2005 to March 2021. Data items were extracted, analyzed, and a meta-analysis of the model performance was carried out to assess the added value of text to structured-data models.RESULTS: We identified 126 studies that described 145 clinical prediction problems. Combining text and structured data improved model performance, compared with using only text or only structured data. In these studies, a wide variety of dense and sparse numeric text representations were combined with both deep learning and more traditional machine learning methods. External validation, public availability, and attention for the explainability of the developed models were limited.CONCLUSION: The use of unstructured text in the development of prognostic prediction models has been found beneficial in addition to structured data in most studies. The text data are source of valuable information for prediction model development and should not be neglected. We suggest a future focus on explainability and external validation of the developed models, promoting robust and trustworthy prediction models in clinical practice.

Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) that play important roles in the genetic heritability of traits and diseases. With most of these SNPs located on the non-coding part of the genome, it is currently assumed that these SNPs influence the expression of nearby genes on the genome. However, identifying which genes are targeted by these disease-associated SNPs remains challenging. In the past, protein knowledge graphs have often been used to identify genes that are associated with disease, also referred to as “disease genes”. Here, we explore whether protein knowledge graphs can be used to identify genes that are targeted by disease-associated non-coding SNPs by testing and comparing the performance of six existing methods for a protein knowledge graph, four of which were developed for disease gene identification. We compare our performance against two baselines: (1) an existing state-of-the-art method that is based on guilt-by-association, and (2) the leading assumption that SNPs target the nearest gene on the genome. We test these methods with four reference sets, three of which were obtained by different means. Furthermore, we combine methods to investigate whether their combination improves performance. We find that protein knowledge graphs that include predicate information perform comparable to the current state of the art, achieving an area under the receiver operating characteristic curve (AUC) of 79.6% on average across all four reference sets. Protein knowledge graphs that lack predicate information perform comparable to our other baseline (genetic distance) which achieved an AUC of 75.7% across all four reference sets. Combining multiple methods improved performance to 84.9% AUC. We conclude that methods for a protein knowledge graph can be used to identify which genes are targeted by disease-associated non-coding SNPs.

eTRANSAFE is a research project funded within the Innovative Medicines Initiative (IMI), which aims at developing integrated databases and computational tools (the eTRANSAFE ToxHub) that support the translational safety assessment of new drugs by using legacy data provided by the pharmaceutical companies that participate in the project. The project objectives include the development of databases containing preclinical and clinical data, computational systems for translational analysis including tools for data query, analysis and visualization, as well as computational models to explain and predict drug safety events.

Pre-competitive data sharing can offer the pharmaceutical industry significant benefits in terms of reducing the time and costs involved in getting a new drug to market through more informed testing strategies and knowledge gained by pooling data. If sufficient data is shared and can be co-analyzed, then it can also offer the potential for reduced animal usage and improvements in the in silico prediction of toxicological effects. Data sharing benefits can be further enhanced by applying the FAIR Guiding Principles, reducing time spent curating, transforming and aggregating datasets and allowing more time for data mining and analysis. We hope to facilitate data sharing by other organizations and initiatives by describing lessons learned as part of the Enhancing TRANslational SAFEty Assessment through Integrative Knowledge Management (eTRANSAFE) project, an Innovative Medicines Initiative (IMI) partnership which aims to integrate publicly available data sources with proprietary preclinical and clinical data donated by pharmaceutical organizations. Methods to foster trust and overcome non-technical barriers to data sharing such as legal and IPR (intellectual property rights) are described, including the security requirements that pharmaceutical organizations generally expect to be met. We share the consensus achieved among pharmaceutical partners on decision criteria to be included in internal clearance procedures used to decide if data can be shared. We also report on the consensus achieved on specific data fields to be excluded from sharing for sensitive preclinical safety and pharmacology data that could otherwise not be shared.