Background: Developmental coordination disorder (DCD) is described as a motor skill disorder characterized by a marked impairment in the development of motor coordination abilities that significantly interferes with performance of daily activities and/or academic achievement. Since some electrophysiological studies suggest differences between children with/without motor development problems, we prepared an experimental protocol and performed electrophysiological experiments with the aim of making a step toward a possible diagnosis of this disorder using the event-related potentials (ERP) technique. The second aim is to properly annotate the obtained raw data with relevant metadata and promote their long-term sustainability. Results: The data from 32 school children (16 with possible DCD and 16 in the control group) were collected. Each dataset contains raw electroencephalography (EEG) data in the BrainVision format and provides sufficient metadata (such as age, gender, results of the motor test, and hearing thresholds) to allow other researchers to perform analysis. For each experiment, the percentage of ERP trials damaged by blinking artifacts was estimated. Furthermore, ERP trials were averaged across different participants and conditions, and the resulting plots are included in the manuscript. This should help researchers to estimate the usability of individual datasets for analysis. Conclusions: The aim of the whole project is to find out if it is possible to make any conclusions about DCD from EEG data obtained. For the purpose of further analysis, the data were collected and annotated respecting the current outcomes of the International Neuroinformatics Coordinating Facility Program on Standards for Data Sharing, the Task Force on Electrophysiology, and the group developing the Ontology for Experimental Neurophysiology. The data with metadata are stored in the EEG/ERP Portal.

• MeSH
• akustická stimulace MeSH
• datové kurátorství MeSH
• dítě MeSH
• elektroencefalografie MeSH
• evokované potenciály MeSH
• komorbidita MeSH
• kvantitativní znak dědičný MeSH
• lidé MeSH
• počítačová simulace MeSH
• poruchy motorických dovedností diagnóza   MeSH
• reakční čas MeSH
• reprodukovatelnost výsledků MeSH
• software MeSH
• světelná stimulace MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

The diagnosis of Sleep disorders, highly prevalent in the western countries, typically involves sophisticated procedures and equipments that are intrusive to the patient. Wrist actigraphy, on the contrary, is a non-invasive and low cost solution to gather data which can provide valuable information in the diagnosis of these disorders. The acquired data may be used to infer the Sleep/Wakefulness (SW) state of the patient during the circadian cycle and detect abnormal behavioral patterns associated with these disorders. In this paper a classifier based on Autoregressive (AR) model coefficients, among other features, is proposed to estimate the SW state. The real data, acquired from 23 healthy subjects during fourteen days each, was segmented by expert medical personal with the help of complementary information such as light intensity and Sleep e-Diary information. Monte Carlo tests with a Leave-One-Out Cross Validation (LOOCV) strategy were used to assess the performance of the classifier which achieves an accuracy of 96%.

• MeSH
• aktigrafie metody   MeSH
• automatizace MeSH
• automatizované zpracování dat metody   MeSH
• Bayesova věta MeSH
• bdění fyziologie   MeSH
• lidé MeSH
• poruchy spánku a bdění diagnóza   patofyziologie   MeSH
• reprodukovatelnost výsledků MeSH
• spánek fyziologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/.

• MeSH
• anotace sekvence MeSH
• databáze genetické * MeSH
• genetická variace genetika   MeSH
• genomika trendy   MeSH
• internet MeSH
• lidé MeSH
• mutace MeSH
• nádorový supresorový protein p53 genetika   MeSH
• software * MeSH
• výpočetní biologie trendy   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• lidé MeSH
• lipidomika * MeSH
• metabolomika * MeSH
• řízení kvality MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• dopisy MeSH
• komentáře MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.

• MeSH
• anotace sekvence MeSH
• databáze jako téma MeSH
• databáze proteinů * MeSH
• internet MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• lidé MeSH
• molekulární modely MeSH
• počítačová grafika MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza proteinů metody   MeSH
• šíření informací MeSH
• uživatelské rozhraní počítače * MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

• MeSH
• datové kurátorství MeSH
• registrace * MeSH
• software MeSH
• výpočetní biologie * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

One of the research projects running at the medical informatics department of the Institute of Computer Science AS CR explores the problem of medical information representation and development of electronic health record (EHR). With respect to this effort an interesting problem arises: how to transfer knowledge from a medical record written in a free text form into a structured electronic format represented by the EHR. Currently, this task was solved by writing extraction rules (regular expressions) for every element of information that is to be extracted from the medical record. However, such approach is very time consuming and requires supervision of a skilled programmer whenever the target area of medicine is changed. In this article we explore the possibility to mechanize this process by automatically generating the extraction rules from a pre-annotated corpus of medical records. Since we are currently in the phase of data acquisition and preliminary tests we will not present any final results, rather we will sketch the technologies we intend to use and describe the tools that were developed so far as a part of this project.

• MeSH
• elektronické zdravotní záznamy * MeSH
• lékařská informatika * MeSH
• lidé MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database. In total, 760 487 protein domains from 42 371 protein models were mapped to hg19 coordinates and made publicly available for search or download (www.prot2hg.com). In addition, this annotation was implemented into the genomics research platform GENESIS in order to query nearly 8000 exomes and genomes of families with rare Mendelian disorders (tgp-foundation.org). When applied to patient genetic data, we found that rare (<1%) variants in the Genome Aggregation Database were significantly more annotated onto a protein domain in comparison to common (>1%) variants. Similarly, variants described as pathogenic or likely pathogenic in ClinVar were more likely to be annotated onto a domain. In addition, we tested a dataset consisting of 60 causal variants in a cohort of patients with epileptic encephalopathy and found that 71% of them (43 variants) were propagated onto protein domains. In summary, we developed a resource that annotates variants in the coding part of the genome onto conserved protein domains in order to increase variant prioritization efficiency.Database URL: www.prot2hg.com.

• MeSH
• anotace sekvence metody   MeSH
• data mining metody   MeSH
• databáze genetické * MeSH
• datové kurátorství metody   MeSH
• genetická variace * MeSH
• genom lidský genetika   MeSH
• genomika metody   MeSH
• internet MeSH
• lidé MeSH
• proteinové domény genetika   MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevated temperatures or in the presence of salts. Since experimental screening for stabilizing mutations is typically laborious and expensive, in silico predictors are often used for narrowing down the mutational landscape. The recent advances in machine learning and artificial intelligence further facilitate the development of such computational tools. However, the accuracy of these predictors strongly depends on the quality and amount of data used for training and testing, which have often been reported as the current bottleneck of the approach. To address this problem, we present a novel database of experimental thermostability data for single-point mutants FireProtDB. The database combines the published datasets, data extracted manually from the recent literature, and the data collected in our laboratory. Its user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or mutation and (ii) the construction of highly customized and machine learning-friendly datasets using advanced searching and filtering. The database is freely available at https://loschmidt.chemi.muni.cz/fireprotdb.

• MeSH
• anotace sekvence MeSH
• bodová mutace * MeSH
• databáze proteinů * MeSH
• datové soubory jako téma MeSH
• internet MeSH
• molekulární modely MeSH
• proteiny chemie   genetika   MeSH
• software MeSH
• stabilita proteinů MeSH
• strojové učení statistika a číselné údaje   MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Objectives: A significant portion of care related to cardiorespiratory diseases is provided at home, usually but not exclusively, after the discharge of a patient from hospital. It is the purpose of the present study to present the technical means which we have developed, in order to support the adaptation of the continuity of care of cardiorespiratory diseases at home. Methods: We have developed an integrated system that includes: first, a prototype laptop-based portable monitoring system that comprises low-cost commercially available components, which enable the periodical or continuous monitoring of vital signs at home; second, software supporting medical decision-making related to tachycardia and ventricular fibrillation, as well as fuzzy-rules-based software supporting home-ventilation optimization; third, a typical continuity of care record (CCR) adapted to support also the creation of a homecare plan; and finally, a prototype ontology, based upon the HL7 clinical document architecture (CDA), serving as basis for the development of semantically annotated web services that allow for the exchange and retrieval of homecare information. Results: The flexible design and the adaptable data-exchange mechanism of the developed system result in a useful and standard-compliant tool, for cardiorespiratory disease-related homecare. Conclusions: The ongoing laboratory testing of the system shows that it is able to contribute to an effective and low-cost package solution, supporting patient supervision and treatment. Furthermore, semantic web technologies prove to be the perfect solution for both the conceptualization of a continuity of care data exchange procedure and for the integration of the structured medical data.

• MeSH
• informační systémy normy   MeSH
• internet MeSH
• kardiovaskulární nemoci MeSH
• kontinuita péče o pacienty MeSH
• lidé MeSH
• sémantika MeSH
• služby domácí péče MeSH
• systémová integrace MeSH
• telemetrie metody   přístrojové vybavení   MeSH
• ukládání a vyhledávání informací metody   MeSH
• zajištění kvality zdravotní péče metody   MeSH
• Check Tag
• lidé MeSH