The article deals with and discusses two main approaches in building semantic structures for electrophysiological metadata. It is the use of conventional data structures, repositories, and programming languages on one hand and the use of formal representations of ontologies, known from knowledge representation, such as description logics or semantic web languages on the other hand. Although knowledge engineering offers languages supporting richer semantic means of expression and technological advanced approaches, conventional data structures and repositories are still popular among developers, administrators and users because of their simplicity, overall intelligibility, and lower demands on technical equipment. The choice of conventional data resources and repositories, however, raises the question of how and where to add semantics that cannot be naturally expressed using them. As one of the possible solutions, this semantics can be added into the structures of the programming language that accesses and processes the underlying data. To support this idea we introduced a software prototype that enables its users to add semantically richer expressions into a Java object-oriented code. This approach does not burden users with additional demands on programming environment since reflective Java annotations were used as an entry for these expressions. Moreover, additional semantics need not to be written by the programmer directly to the code, but it can be collected from non-programmers using a graphic user interface. The mapping that allows the transformation of the semantically enriched Java code into the Semantic Web language OWL was proposed and implemented in a library named the Semantic Framework. This approach was validated by the integration of the Semantic Framework in the EEG/ERP Portal and by the subsequent registration of the EEG/ERP Portal in the Neuroscience Information Framework.

• Publikační typ
• časopisecké články MeSH

Electronic Health Record (EHR) systems currently in use are not designed for widely interoperable longitudinal health data. Therefore, EHR data cannot be properly shared, managed and analyzed. In this article, we propose two approaches to making EHR data more comprehensive and FAIR (Findable, Accessible, Interoperable, and Reusable) and thus more useful for diagnosis and clinical research. Firstly, the data modeling based on the LinkML framework makes the data interoperability more realistic in diverse environments with various experts involved. We show the first results of how diverse health data can be integrated based on an easy-to-understand data model and without loss of available clinical knowledge. Secondly, decentralizing EHRs contributes to the higher availability of comprehensive and consistent EHR data. We propose a technology stack for decentralized EHRs and the reasons behind this proposal. Moreover, the two proposed approaches empower patients because their EHR data can become more available, understandable, and usable for them, and they can share their data according to their needs and preferences. Finally, we explore how the users of the proposed solution could be involved in the process of its validation and adoption.

• MeSH
• data management MeSH
• elektronické zdravotní záznamy * MeSH
• lidé MeSH
• sémantický web * MeSH
• software MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Objectives: The purpose of this paper is to present and discuss the adoption and use of medical terminologies and coding systems in Italy, focusing on their management and integration for guaranteeing semantic interoperability among Electronic Health Records (EHRs). Semantic interoperability guarantees meaningful exchange of data between two or more healthcare information systems, ensuring that data content is not only understandable within its original context, but also in the destination one, and is capable of supporting health service management, clinical decision-making care collaboration, as well as public health reporting, and improving clinical research. Methods: The approach used for the coding systems management and integration in the Italian Fascicolo Sanitario Elettronico (FSE)a use case is presented according to the current Italian regulations on federated EHRs. Results: Results show the need to promote an advanced approach, in conformance to the literature best cases, which takes care about a better integration and maintenance of medical terminologies and coding systems through the use of standardized models of terminology services. Conclusion: The paper presents terminology interoperability issues arisen from the described approach and related requirements to propose a solution that could allow, through sophisticated terminology services framework, to achieve also in Italy semantic interoperability.

• MeSH
• klinické kódování MeSH
• Logical Observation Identifiers Names and Codes MeSH
• řízení zdravotnických informací * MeSH
• řízený slovník * MeSH
• výměna zdravotnických informací * MeSH
• Publikační typ
• práce podpořená grantem MeSH
• Geografické názvy
• Itálie MeSH

Lidé mají tendenci zobrazovat vlastnosti podnětu z různých smyslových modalit z jedné na druhou. Tento fenomén vícemodální shody byl většinou zkoumán pomocí smyslové prezentace podnětů, ale v poslední době začali badatelé používat také verbální prezentaci. To nadneslo otázku vhodnosti této formy prezentace pro výzkum vícemodálních shod a srovnatelnosti výsledků získaných užíváním těchto dvou způsobů prezentace. Pro zodpovězení této otázky v rámci tzv. hypotézy evaluativní podobnosti, která předpokládá, že vícemodální shody podnětů jsou způsobeny podobností jejich významů, byly realizovány experimenty s 96 pregraduálními studenty, ve kterých byly použity 4 úkoly. V prvních dvou úkolech byly páry podnětů patřících k různým modalitám prezentovány smyslovou (úkol 1) a verbální (úkol 2) formou a účastníci posuzovali jejich podobnost na sedmibodové škále. V úkolech 3 a 4 byly prezentovány podněty z různých modalit individuálně v jejich smyslové (úkol 3) a verbální (úkol 4) formě a účastníci je hodnotili ve třech dimenzích konotativního nebo evaluativního významu (nabuzení, afektivní a kognitivní hodnocení). Výsledky naznačují, že verbální metoda možná není vhodná pro výzkum vícemodálních shod, a že je to způsobeno problematickým statutem hodnocení podobnosti verbalizovaných podnětů. Výsledky současně poskytují podporu hypotéze evaluativní podobnosti, protože smyslově prezentované páry podnětů byly posuzovány jako tím podobnější, čím menší byla Euklidovská vzdálenost mezi nimi v prostoru definovaném třemi dimenzemi hodnotícího významu.

People show a tendency to map stimulus properties from different sensory modalities onto each other. This phenomenon of crossmodal correspondences has been mostly studied using sensory presentation of stimuli but recently researchers have started using verbal presentation as well. This raised the question of appropriateness of this presentation form for studying crossmodal correspondences and comparability of results obtained using these two presentation forms. To answer this question within the framework of the evaluative similarity hypothesis which posits that crossmodal correspondences of stimuli are due to similarity of their meanings, an experiment was conducted with 96 undergraduate students using 4 tasks.In tasks 1 and 2, pairs of stimuli belonging to different modalities were presented in their sensory (Task 1) and verbal (Task 2) form and participants rated their similarity on a 7-point scale. In Tasks 3 and 4, stimuli from different modalities were presented individually in their sensory (Task 3) and verbal (Task 4) form and participants rated them on three dimensions of connotative or evaluative meaning (arousal, affective and cognitive evaluation). The results suggest the verbal method might not be suitable for studying crossmodal correspondences and that this is due to a problematic status of similarity ratings of verbalized stimuli. Concurrently, the results lend support to the evaluative similarity hypothesis as sensory presented pairs of stimuli were judged to be more similar the smaller was the Euclidean distance between them in a space defined by the three dimensions of evaluative meaning.

• Klíčová slova
• hypotéza evaluativní podobnosti, vícemodální shoda,
• MeSH
• asociace (psychologie) MeSH
• lidé MeSH
• psychologické testy MeSH
• verbální chování * MeSH
• výzkum MeSH
• zraková percepce * MeSH
• Check Tag
• lidé MeSH

V příspěvku jsou prezentovány výsledky šetření, jehož cílem bylo zjistit, jak studenti Zdravotně sociální fakulty Jihočeské univerzity v Českých Budějovicích vnímají na základě absolvování odborné praxe na půdě Nemocnice České Budějovice, a. s., lékaře a spolupráci s lékaři. Ke sběru dat byla použita technika dotazníku, obohacena o modifikovanou techniku sémantického diferenciálu dle Osgooda. Dotazník byl distribuován studentům ZSF JU, a to studentům druhých a třetích ročníků bakalářského studijního programu Všeobecná sestra, dále posluchačům prvního a druhého ročníku navazujícího magisterského programu Ošetřovatelství. Celkem bylo rozdáno 151 dotazníků. Navráceno bylo 105 dotazníků, z tohoto počtu nemohlo být použito 7 dotazníků pro nekorektnost vyplnění. Celkem tedy bylo použito 98 (65 %) dotazníků. Zapojování studentů do týmu a pozitivní hodnocení nejen lékařů jsou důležitými aspekty pro vstup absolventů oborů Všeobecná sestra a Ošetřovatelství do budoucí profese. Výsledky šetření prokázaly především pozitivní vnímání lékařů, což signalizuje posun ve směru od tradičního podřízeného vztahu sestra (student) – lékař ke vztahu partnerskému. I když je celkové hodnocení lékařů pozitivní, přesto pětina studentů hodnotí lékaře negativně. Výsledky této práce zviditelnily také negativní faktory, které se týkají hodnocení lékařů, a daly tak prostor pro možnou další diskusi. Dále výsledky šetření ukázaly, že studenti hodnotí své zapojování do týmu jako neefektivní. Tato skutečnost dává možnost pro další analýzu a to, zda mentorky odborné praxe na všech odděleních plní svoji roli adekvátním způsobem, zda na těchto odděleních neselhává supervizní činnost, zda pozitivní hodnocení lékařů není ovlivněno právě nízkým kontaktem s nimi.

The contribution presents results of examination aimed at physicians and cooperation with physicians as regarded by students of the Health and Social Faculty of the University of South Bohemia in České Budějovice. The technique of questionnaires, enriched in modified techniques of the semantic differential by Osgood, was employed for the data accumulation. The questionnaire was distributed to students of the Faculty of Health and Social Studies of the University of South Bohemia in the second and third years of the bachelor study programme “General nursing” and also to students of the first and second years of the continuing master programme “Nursing”. Total of 151 questionnaires were distributed. One hundred and five questionnaires were returned; seven of them were not useful due to incorrect completing. This means that total of 98 (65%) of questionnaires were used. The incorporation of students into the team and positive comprehension not only of physicians are important aspects for the inclusion of alumni from the branches General nursing and Nursing into their future professions. The results of examinations particularly demonstrated positive perception of physicians, which indicates a shift from the traditional dividing of roles in healthcare services to a partnership. This fact is the first assumption necessary for successful application of the holistic attitude to the client. In spite of the generally positive comprehension of physicians, 1/5 the students consider them negatively. Results of the work presented here also pointed out negative factors concerning the consideration of physicians and offered a possibility for a future discussion. Results of the examination also documented the fact that the students perceive their inclusion into the team as ineffective. This fact presents a possibility for a further analysis in this area, whether lectors of the practical education at all the departments fulfil their role in adequate manner and whether the supervision activity fails at these departments or the positive opinions concerning physicians are just affected by low level of contacts with them.

• MeSH
• dospělí MeSH
• interprofesionální vztahy MeSH
• lékaři psychologie   statistika a číselné údaje   MeSH
• lidé MeSH
• odborný výcvik metody   statistika a číselné údaje   MeSH
• ošetřovatelská fakultní praxe statistika a číselné údaje   využití   MeSH
• ošetřovatelská péče metody   MeSH
• průzkumy a dotazníky MeSH
• studium ošetřovatelství vysokoškolské pracovní síly   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH

BACKGROUND: Ubiquitin ligases (Ub-ligases) are essential intracellular enzymes responsible for the regulation of proteome homeostasis, signaling pathway crosstalk, cell differentiation and stress responses. Individual Ub-ligases exhibit their unique functions based on the nature of their substrates. They create a complex regulatory network with alternative and feedback pathways to maintain cell homeostasis, being thus important players in many physiological and pathological conditions. However, the functional classification of Ub-ligases needs to be revised and extended. METHODS: In the current study, we used a novel semantic biclustering technique for expression profiling of Ub-ligases and ubiquitination-related genes in the murine gastrointestinal tract (GIT). We accommodated a general framework of the algorithm for finding tissue-specific gene expression clusters in GIT. In order to test identified clusters in a biological system, we used a model of epithelial regeneration. For this purpose, a dextran sulfate sodium (DSS) mouse model, following with in situ hybridization, was used to expose genes with possible compensatory features. To determine cell-type specific distribution of Ub-ligases and ubiquitination-related genes, principal component analysis (PCA) and Uniform Manifold Approximation and Projection technique (UMAP) were used to analyze the Tabula Muris scRNA-seq data of murine colon followed by comparison with our clustering results. RESULTS: Our established clustering protocol, that incorporates the semantic biclustering algorithm, demonstrated the potential to reveal interesting expression patterns. In this manner, we statistically defined gene clusters consisting of the same genes involved in distinct regulatory pathways vs distinct genes playing roles in functionally similar signaling pathways. This allowed us to uncover the potentially redundant features of GIT-specific Ub-ligases and ubiquitination-related genes. Testing the statistically obtained results on the mouse model showed that genes clustered to the same ontology group simultaneously alter their expression pattern after induced epithelial damage, illustrating their complementary role during tissue regeneration. CONCLUSIONS: An optimized semantic clustering protocol demonstrates the potential to reveal a readable and unique pattern in the expression profiling of GIT-specific Ub-ligases, exposing ontologically relevant gene clusters with potentially redundant features. This extends our knowledge of ontological relationships among Ub-ligases and ubiquitination-related genes, providing an alternative and more functional gene classification. In a similar way, semantic cluster analysis could be used for studding of other enzyme families, tissues and systems.

• MeSH
• gastrointestinální trakt metabolismus   MeSH
• lidé MeSH
• myši MeSH
• sémantika * MeSH
• shluková analýza MeSH
• ubikvitin genetika   metabolismus   MeSH
• ubikvitinligasy * genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: Sample collections and data are hosted within different biobanks at diverse institutions across Europe. Our data integration framework aims at incorporating data about sample collections from different biobanks into a common research infrastructure, facilitating researchers' abilities to obtain high-quality samples to conduct their research. The resulting information must be locally gathered and distributed to searchable higher level information biobank directories to maximize the visibility on the national and European levels. Therefore, biobanks and sample collections must be clearly described and unambiguously identified. We describe how to tackle the challenges of integrating biobank-related data between biobank directories using heterogeneous data schemas and different technical environments. METHODS: To establish a data exchange infrastructure between all biobank directories involved, we propose the following steps: (A) identification of core entities, terminology, and semantic relationships, (B) harmonization of heterogeneous data schemas of different Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) directories, and (C) formulation of technical core principles for biobank data exchange between directories. RESULTS: (A) We identified the major core elements to describe biobanks in biobank directories. Since all directory data models were partially based on Minimum Information About BIobank Data Sharing (MIABIS) 2.0, the MIABIS 2.0 core model was used for compatibility. (B) Different projection scenarios were elaborated in collaboration with all BBMRI.at partners. A minimum set of mandatory and optional core entities and data items was defined for mapping across all directory levels. (C) Major core data exchange principles were formulated and data interfaces implemented by all biobank directories involved. DISCUSSION: We agreed on a MIABIS 2.0-based core set of harmonized biobank attributes and established a list of data exchange core principles for integrating biobank directories on different levels. This generic approach and the data exchange core principles proposed herein can also be applied in related tasks like integration and harmonization of biobank data on the individual sample and patient levels.

• MeSH
• banky biologického materiálu * MeSH
• lidé MeSH
• odběr biologického vzorku metody   MeSH
• šíření informací metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Rakousko MeSH

This paper describes the use of standards to enhance the capability of creating semantically interoperable documents and messages. Over the past few years, many information exchange formats have been created. While the health industry continues to develop new formats that attempt to simplify or modernize interoperability across healthcare, it is continually challenged by the difficulty of current applications to exchange documents that can be interpreted by the receiver of the document. Given the variety of standard formats, a framework should be developed that can bridge across multiple exchanged formats/syntax and semantics. It should reference the business content in a consistent way that represents clinical best practices and connects to the clinical workflow that triggers information exchange. This paper describes the use of model-driven development to bring balance to the art of data exchange by supporting semantic interoperability for design and runtime. The proposed model-based approach to mapping addresses the semantic challenges and allows sending systems to first specify the meaning of their data by relating it to a defined common data dictionary of business data elements thus making it independent of other datasets. The resulting architecture proposes two sets of opensource components intended to provide a clear separation of concerns throughout the development process between design and run-time. SAMHSA is using this approach in its Information Exchange Hub (IExHub), the transformation/interface engine supporting both behavioral health and physical health interoperability for health information exchange network (HIEs).

• MeSH
• elektronické zdravotní záznamy normy   MeSH
• řízení zdravotnických informací normy   MeSH
• sémantika * MeSH
• ukládání a vyhledávání informací normy   MeSH
• výměna zdravotnických informací * normy   MeSH

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. In biomedical image analysis, chosen performance metrics often do not reflect the domain interest, and thus fail to adequately measure scientific progress and hinder translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Developed by a large international consortium in a multistage Delphi process, it is based on the novel concept of a problem fingerprint-a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), dataset and algorithm output. On the basis of the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as classification tasks at image, object or pixel level, namely image-level classification, object detection, semantic segmentation and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases.

• MeSH
• algoritmy * MeSH
• počítačové zpracování obrazu * MeSH
• sémantika MeSH
• strojové učení MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH