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.

• Klíčová slova
• EEG/ERP portal, electrophysiology, object-oriented code, ontology, semantic framework, semantic web,
• 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.

• Klíčová slova
• Distributed electronic health records, FAIR principles, HL7 FHIR, bio-data management, ontology,
• MeSH
• data management MeSH
• elektronické zdravotní záznamy * MeSH
• lidé MeSH
• sémantický web * MeSH
• software MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

To improve patient outcomes after trauma, the need to decrypt the post-traumatic immune response has been identified. One prerequisite to drive advancement in understanding that domain is the implementation of surgical biobanks. This paper focuses on the outcomes of patients with one of two diagnoses: post-traumatic arthritis and osteomyelitis. In creating surgical biobanks, currently, many obstacles must be overcome. Roadblocks exist around scoping of data that is to be collected, and the semantic integration of these data. In this paper, the generic component model and the Semantic Web technology stack are used to solve issues related to data integration. The results are twofold: (a) a scoping analysis of data and the ontologies required to harmonize and integrate it, and (b) resolution of common data integration issues in integrating data relevant to trauma surgery.

• Klíčová slova
• biomedical ontologies, knowledge representation, osteomyelitis, post-traumatic arthritis, semantic data integration, surgical biobank, system theory,
• Publikační typ
• časopisecké články MeSH

The concept of Data Management Plan (DMP) has emerged as a fundamental tool to help researchers through the systematical management of data. The Research Data Alliance DMP Common Standard (DCS) working group developed a set of universal concepts characterising a DMP so it can be represented as a machine-actionable artefact, i.e., machine-actionable Data Management Plan (maDMP). The technology-agnostic approach of the current maDMP specification: (i) does not explicitly link to related data models or ontologies, (ii) has no standardised way to describe controlled vocabularies, and (iii) is extensible but has no clear mechanism to distinguish between the core specification and its extensions.This paper reports on a community effort to create the DMP Common Standard Ontology (DCSO) as a serialisation of the DCS core concepts, with a particular focus on a detailed description of the components of the ontology. Our initial result shows that the proposed DCSO can become a suitable candidate for a reference serialisation of the DMP Common Standard.

• Klíčová slova
• Data management plan, Machine-actionable data management plan, Ontology, Semantic web technologies,
• MeSH
• bio-ontologie * MeSH
• data management * MeSH
• řízený slovník MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: A growing interest in non-pharmacological approaches aimed at cognitive rehabilitation and cognitive enhancement pointed towards the application of new technologies. The complex virtual reality (VR) presented using immersive devices has been considered a promising approach. OBJECTIVE: The article provides a systematic review of studies aimed at the efficacy of VR-based rehabilitation. First, we shortly summarize literature relevant to the role of immersion in memory assessment and rehabilitation. METHODS: We searched Web of Science, ScienceDirect, and PubMed with the search terms "memory rehabilitation", "virtual reality", "memory deficit". Only original studies investigating the efficacy of complex three-dimensional VR in rehabilitation and reporting specific memory output measures were included. RESULTS: We identified 412 citations, of which 21 met our inclusion criteria. We calculated appropriate effect sizes for 10 studies including control groups and providing descriptive data. The effect sizes range from large to small, or no effect of memory rehabilitation was present, depending on the control condition applied. Summarized studies with missing control groups point out to potential positive effects of VR but do not allow any generalization. CONCLUSIONS: Even though there are some theoretical advantages of immersive VE over non-immersive technology, there is not enough evidence yet to draw any conclusions.

• Klíčová slova
• Virtual reality, immersion, memory, rehabilitation,
• MeSH
• lidé MeSH
• neurorehabilitace * metody   MeSH
• paměť MeSH
• poruchy paměti * rehabilitace   MeSH
• terapie pomocí virtuální reality * přístrojové vybavení   metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• systematický přehled MeSH

OBJECTIVES: This study aims to describe the data structure and harmonisation process, explore data quality and define characteristics, treatment, and outcomes of patients across six federated antineutrophil cytoplasmic antibody-associated vasculitis (AAV) registries. METHODS: Through creation of the vasculitis-specific Findable, Accessible, Interoperable, Reusable, VASCulitis ontology, we harmonised the registries and enabled semantic interoperability. We assessed data quality across the domains of uniqueness, consistency, completeness and correctness. Aggregated data were retrieved using the semantic query language SPARQL Protocol and Resource Description Framework Query Language (SPARQL) and outcome rates were assessed through random effects meta-analysis. RESULTS: A total of 5282 cases of AAV were identified. Uniqueness and data-type consistency were 100% across all assessed variables. Completeness and correctness varied from 49%-100% to 60%-100%, respectively. There were 2754 (52.1%) cases classified as granulomatosis with polyangiitis (GPA), 1580 (29.9%) as microscopic polyangiitis and 937 (17.7%) as eosinophilic GPA. The pattern of organ involvement included: lung in 3281 (65.1%), ear-nose-throat in 2860 (56.7%) and kidney in 2534 (50.2%). Intravenous cyclophosphamide was used as remission induction therapy in 982 (50.7%), rituximab in 505 (17.7%) and pulsed intravenous glucocorticoid use was highly variable (11%-91%). Overall mortality and incidence rates of end-stage kidney disease were 28.8 (95% CI 19.7 to 42.2) and 24.8 (95% CI 19.7 to 31.1) per 1000 patient-years, respectively. CONCLUSIONS: In the largest reported AAV cohort-study, we federated patient registries using semantic web technologies and highlighted concerns about data quality. The comparison of patient characteristics, treatment and outcomes was hampered by heterogeneous recruitment settings.

• Klíčová slova
• epidemiology, granulomatosis with polyangiitis, quality indicators, health care, systemic vasculitis,
• MeSH
• ANCA-asociované vaskulitidy * farmakoterapie   epidemiologie   komplikace   MeSH
• granulomatóza s polyangiitidou * farmakoterapie   epidemiologie   komplikace   MeSH
• lidé MeSH
• mikroskopická polyangiitida * farmakoterapie   epidemiologie   MeSH
• protilátky proti cytoplazmě neutrofilů MeSH
• registrace MeSH
• správnost dat MeSH
• ukládání a vyhledávání informací MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• metaanalýza MeSH
• Názvy látek
• protilátky proti cytoplazmě neutrofilů MeSH

As in other areas of experimental science, operation of electrophysiological laboratory, design and performance of electrophysiological experiments, collection, storage and sharing of experimental data and metadata, analysis and interpretation of these data, and publication of results are time consuming activities. If these activities are well organized and supported by a suitable infrastructure, work efficiency of researchers increases significantly. This article deals with the main concepts, design, and development of software and hardware infrastructure for research in electrophysiology. The described infrastructure has been primarily developed for the needs of neuroinformatics laboratory at the University of West Bohemia, the Czech Republic. However, from the beginning it has been also designed and developed to be open and applicable in laboratories that do similar research. After introducing the laboratory and the whole architectural concept the individual parts of the infrastructure are described. The central element of the software infrastructure is a web-based portal that enables community researchers to store, share, download and search data and metadata from electrophysiological experiments. The data model, domain ontology and usage of semantic web languages and technologies are described. Current data publication policy used in the portal is briefly introduced. The registration of the portal within Neuroscience Information Framework is described. Then the methods used for processing of electrophysiological signals are presented. The specific modifications of these methods introduced by laboratory researches are summarized; the methods are organized into a laboratory workflow. Other parts of the software infrastructure include mobile and offline solutions for data/metadata storing and a hardware stimulator communicating with an EEG amplifier and recording software.

• Klíčová slova
• electrophysiology, event related potentials, infrastructure, neuroinformatics, portal, signal processing methods, stimulator, workflow,
• Publikační typ
• časopisecké články MeSH

Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database systems and databases stored in them to be interoperable with each other. One of the possible solutions to address this issue is to use systems based on Semantic Web technologies, namely on the Resource Description Framework (RDF) to express data and on the SPARQL query language to retrieve the data. Many existing biological and chemical databases are stored in the form of a relational database (RDB). Converting a relational database into the RDF form and storing it in a native RDF database system may not be desirable in many cases. It may be necessary to preserve the original database form, and having two versions of the same data may not be convenient. A solution may be to use a system mapping the relational database to the RDF form. Such a system keeps data in their original relational form and translates incoming SPARQL queries to equivalent SQL queries, which are evaluated by a relational-database system. This review compares different RDB-to-RDF mapping systems with a primary focus on those that can be used free of charge. In addition, it compares different approaches to expressing RDB-to-RDF mappings. The review shows that these systems represent a viable method providing sufficient performance. Their real-life performance is demonstrated on data and queries coming from the neXtProt project.

• Klíčová slova
• RDB-to-RDF mapping, Relational database, Resource Description Framework, SPARQL,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH