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Framework for Collection of Electrophysiology Data

JEŽEK, P., MOUČEK, R., KRAUZ, J., HOŠEK, J., FRANC, Y.L., WACHTLER, T., GREWE, J. Framework for Collection of Electrophysiology Data. In Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2015. s. 558-565. ISBN: 978-989-758-068-0
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Experiments in electrophysiology produce a lot of unstructured metadata collected in electrophysiology databases. The data are usually accessed through a web interface implemented on the top of data model respecting given data format. A lot of experiments are conducted outside the laboratory where access to these databases is not always available. The usage of mobile devices such as tablets or smart phones seems to be a practical solution, but users would welcome the same structured user interface such as they know from a common computer. When user interfaces of electrophysiology databases are tailored to a unique data struc- ture, they cannot be easily reused on a mobile device. As a solution, a mapping of a general data structure to a graphical template is proposed. This mapping is implemented in a framework that generates a template representing the database structure. The parsing process is driven by supplemented annotations added to the code. Next, an Android tool visualizing a graphical layout generated from the template is developed. A use case study is presented on a database of EEG/ERP experiments.

Tool Facilitating Construction of Ontologies on the KIM Platform

MOUČEK, R., SMITKA, S., JEŽEK, P. Tool Facilitating Construction of Ontologies on the KIM Platform. In HealthINF 2015 ? Proceedings of the International Conference on Health Informatics. Setúbal: SciTePress, 2015. s. 659-665. ISBN: 978-989-758-068-0
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During research based on experimental work vast amounts of data and associated metadata are usually produced. This is also the case of experimental work using the techniques of electroencephalography and event related potentials. The collected data and associated metadata have to be stored, analyzed, and eventually shared among research groups. Besides storing data and metadata from experiments, it is often beneficial to collect additional information from other sources related to the kind of experiment performed. These information sources are mostly scientific and technical publications, manuals describing the used infrastructure, and topical discussions appearing on the web. This article deals with selection and use of a semantic repository for such information sources. Development of a simple prototype ontology is shortly presented and a tool that facilitates construction of ontologies on the KIM platform is described. Sets of test documents are used to verify the functionality of the tool.

Archetypes Development in Electrophysiology Domain - Electroencephalography as a Personal EHR System Module

PAPEŽ, V., MOUČEK, R. Archetypes Development in Electrophysiology Domain - Electroencephalography as a Personal EHR System Module. In HEALTHINF 2015 ? 8th International Conference on Health Informatics. Setúbal: SciTePress, 2015. s. 611-616. ISBN: 978-989-758-068-0
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The work presents the concept of a new personal electronic health record (EHR) system. The system is based on openEHR standards/framework. A fundamental part of openEHR is domain description by two layer modelling - reference data models and archetypes. Archetypes are building blocks of the EHR system, which provide structure and semantics for stored data. As common ontologies and terminologies, even archetypes are based on reusability. Although the public archetype repositories (clinical knowledge managers, CKM) contain hundreds of archetypes from various domains, the electrophysiology domain is not described yet. The work is focused on the development of the archetypes dealing with the electroencephalography domain.

Prototypes of software portal and stimulation device for electrophysiological research

MOUČEK, R., MAUTNER, P., JEŽEK, P., NOVOTNÝ, J., BYDŽOVSKÝ, M., RINKES, J., PROKOP, T., ŠTĚBETÁK, J., BRŮHA, P. Prototypes of software portal and stimulation device for electrophysiological research. Washington, 2014.
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This abstract focuses on recent conceptual improvements of two software and hardware prototypes that can be easily integrated into various electrophysiological laboratory systems: the EEG/ERP Portal (EEGbase) and a stimulation device for cognitive research. The EEG/ERP Portal is a web based application for long-term storage, management, processing and sharing of electrophysiological data. It was designed and developed using robust open source technologies and semantic web resources to ensure future extensibility of the application and sustainability of stored data/metadata. The Portal suffered from low flexibility with respect to the scope of the electrophysiological domain and covered a small number of laboratory needs in terms of the variety of stored metadata and customization of the user interface. As a solution, we left the idea of using high level concepts of the Semantic Web and individually applied selected best practices of this approach. This also includes the use of a non-relational database for storing and retrieving metadata. The stimulation device for cognitive research is an ARM based Cortex microcontroller including firmware and optional control software for creating various experiments in which the subject is stimulated by visual and/or auditory stimuli. It works in three modes: 1- sequential stimulation mode in which stimuli are presented sequentially respecting their probability, 2- simultaneous stimulation mode in which stimuli are presented simultaneously with corresponding frequencies, 3- stimulation mode with waiting for pressing a response. Stimulation outputs can be e.g. simple LEDs, LED panels, patterns presented on small LCD displays, simple tones of various frequencies and lengths, or sounds stored in wav files. The stimulator designed for research laboratories is mobile, enables synchronization with recording devices and can be connected to conventional equipment.

Effects of a personal electronic health record system on a reasoning of neuro-electrophysiology experiments.

PAPEŽ, V., MOUČEK, R., JEŽEK, P., ŘONDÍK, T. Effects of a personal electronic health record system on a reasoning of neuro-electrophysiology experiments.. Washingzon, 2014.
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The concept of a new user-centric personal electronic health record system is focused mainly on storing gathered user?s bio data independently on the domain, EEG included. Unambiguous data description by controlled vocabularies and ontologies allows analysis across these domains and it may help to reveal non-trivial consequences.

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