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Construction and Use of Semantic Repository for Electrophysiological Experiments

MOUČEK, R., SMITKA, J., JEŽEK, P., MAUTNER, P., ČEPIČKA, L., HOLEČKOVÁ, I. Construction and Use of Semantic Repository for Electrophysiological Experiments. Stockholm, 2013.
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A need to store, organize, share and interpret data and metadata from electrophysiological experiments emerged also during our investigation of developmental coordination disorder in children. If classic data and metadata were successfully stored to the EEG/ERP portal, related studies, discussions, and partial interpretations remained unorganized and not searchable. Since the EEG/ERP portal (using a relational database) was not sufficiently prepared to store and process these unstructured texts, it was decided to find an appropriate solution to aggregate and store such data and facilitate subsequent search of relevant information. It was also necessary to use already existing description of data and domain knowledge in a form of semantic web structures. The OWLIM repository and the KIM platform were finally selected and used to store, annotate and search data. The KIM Platform supports semantic annotation of documents based on ontology, which is stored in the semantic repository. The annotated documents can be searched through; the use of ontological terms ensures more relevant results than a normal full-text search. To facilitate ontology development, a tool KIM-OWLImport was created. It is able to retrieve the selected ontology into the semantic repository in memory and modify it according to the rules defined by the KIM platform. The ontology then can be used for semantic annotation. To import documents into the KIM Platform a tool KIMBridge was developed. It runs as a service and periodically downloads new documents from selected data sources. Currently, KIMBridge supports downloading PDF documents from Google Drive and downloading discussions from the social network LinkedIn. Downloaded documents are annotated according to ontological prototype and indexed in the KIM Platform. Subsequent search is made through the web interface. This functionality was verified on a test set of domain documents.

Matching Pursuit for P300-based Brain-Computer Interfaces

VAŘEKA, L. Matching Pursuit for P300-based Brain-Computer Interfaces. In TSP 2012. neuveden: IEEE, 2012. s. 513-516. ISBN: 978-1-4673-1118-2
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"Since the evoked responses obtained by stimulation are much weaker than the continuous electroencephalographic signal, the correct signal analysis enhances stimulation-driven signal components. The paper proposes methods for event-related potential processing for brain-computer interfaces based on matching pursuit. The suggested method is compared with another simple method which is frequently used for feature extraction. A multi-layer perceptron was used for classification. The results can be used to improve the feature extraction for BCI systems."

Semantic Web in EEG/ERP Portal, Extending of Data Layer using Java Annotations

JEŽEK, P., MOUČEK, R. Semantic Web in EEG/ERP Portal, Extending of Data Layer using Java Annotations. In BIOSTEC 2012, HEALTHINF 2012. Setúbal: SciTePress, 2012. s. 350-353. ISBN: 978-989-8425-88-1
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Because the Semantic Web uses its technologies for presenting data/metadata on the web and common systems are based on object-oriented languages a need for suitable mapping is emerging. This paper describes the difficulties during transformation of data layer represented by object-oriented code into the semantic web structures (OWL, RDF). Since there is difference between semantic expressivity of these data representations it is necessary to fill this semantic gap. Authors investigate these differences in semantics and provide a preliminary idea to add missing semantics into the Java code using Java annotations. These annotations are consequently processed by the proposed framework. The transformation is demonstrated within the EEG/ERP Portal.

Neuroinformatics - Data management and analytic tools for EEG/ERP research

ŠTĚBETÁK, J., BRŮHA, P., MOUČEK, R. Neuroinformatics - Data management and analytic tools for EEG/ERP research. In Beyond AI: Interdisciplinary Aspects of Artifical Intelligence. Plzeň: ZČU, NTC, 2011. s. 91-95. ISBN: neuveden
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Brain research is currently a rapidly growing scientific field. Large amounts of data, various data formats and non-standardized domain descriptions lead to incompatible results and interpretations of neuroscientific data and to difficult communication between laboratories and scientific teams. Neuroinformatics, a newly established scientific field, provides integration across all levels and scales of neuroscience. Our research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP (electroencephalography, event-related potential) research.

PRESTI Neuroscience Stimuli Presentation Software

JAROŠ, P., HÁKA, P., MOUČEK, R. PRESTI Neuroscience Stimuli Presentation Software. In Proceedings International conference on knowledge management and information sharing. Setúbal: SciTePress, 2011. s. 390-393. ISBN: 978-989-8425-81-2
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This paper summarizes a new approach for creating test scenarios and stimuli presentation in neuroinformatics ERP experiments. The approach uses visual programming that allows creation of test scenarios without a need of any programming language knowledge. The newly designed programming language is described in this paper. Solution for weaknesses of visual programming is provided. The next part deals with performance of stimuli presentation software to ensure lowest possible latency between stimuli presentation and synchronisation with electroencephalograph.

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