The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

• MeSH
• databáze proteinů * MeSH
• konformace proteinů MeSH
• shluková analýza MeSH
• software * MeSH
• správnost dat MeSH
• uživatelské rozhraní počítače MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

OBJECTIVES: Our main objective is to design a method of, and supporting software for, interactive correction and semantic annotation of narrative clinical reports, which would allow for their easier and less erroneous processing outside their original context: first, by physicians unfamiliar with the original language (and possibly also the source specialty), and second, by tools requiring structured information, such as decision-support systems. Our additional goal is to gain insights into the process of narrative report creation, including the errors and ambiguities arising therein, and also into the process of report annotation by clinical terms. Finally, we also aim to provide a dataset of ground-truth transformations (specific for Czech as the source language), set up by expert physicians, which can be reused in the future for subsequent analytical studies and for training automated transformation procedures. METHODS: A three-phase preprocessing method has been developed to support secondary use of narrative clinical reports in electronic health record. Narrative clinical reports are narrative texts of healthcare documentation often stored in electronic health records. In the first phase a narrative clinical report is tokenized. In the second phase the tokenized clinical report is normalized. The normalized clinical report is easily readable for health professionals with the knowledge of the language used in the narrative clinical report. In the third phase the normalized clinical report is enriched with extracted structured information. The final result of the third phase is a semi-structured normalized clinical report where the extracted clinical terms are matched to codebook terms. Software tools for interactive correction, expansion and semantic annotation of narrative clinical reports has been developed and the three-phase preprocessing method validated in the cardiology area. RESULTS: The three-phase preprocessing method was validated on 49 anonymous Czech narrative clinical reports in the field of cardiology. Descriptive statistics from the database of accomplished transformations has been calculated. Two cardiologists participated in the annotation phase. The first cardiologist annotated 1500 clinical terms found in 49 narrative clinical reports to codebook terms using the classification systems ICD 10, SNOMED CT, LOINC and LEKY. The second cardiologist validated annotations of the first cardiologist. The correct clinical terms and the codebook terms have been stored in a database. CONCLUSIONS: We extracted structured information from Czech narrative clinical reports by the proposed three-phase preprocessing method and linked it to electronic health records. The software tool, although generic, is tailored for Czech as the specific language of electronic health record pool under study. This will provide a potential etalon for porting this approach to dozens of other less-spoken languages. Structured information can support medical decision making, quality assurance tasks and further medical research.

• MeSH
• elektronické zdravotní záznamy normy   MeSH
• mezinárodní klasifikace nemocí MeSH
• psaní normy   MeSH
• řízený slovník * MeSH
• sémantika * MeSH
• směrnice jako téma MeSH
• smysluplné využití normy   MeSH
• software MeSH
• správnost dat MeSH
• strojové učení * MeSH
• uživatelské rozhraní počítače MeSH
• zpracování přirozeného jazyka * MeSH
• zpracování textu normy   MeSH
• Publikační typ
• časopisecké články MeSH

The mixed research design is a progressive methodological discourse that combines the advantages of quantitative and qualitative methods. Its possibilities of application are, however, dependent on the efficiency with which the particular research techniques are used and combined. The aim of the paper is to introduce the possible combination of Hypothesis with EyeTribe tracker. The Hypothesis is intended for quantitative data acquisition and the EyeTribe is intended for qualitative (eye-tracking) data recording. In the first part of the paper, Hypothesis software is described. The Hypothesis platform provides an environment for web-based computerized experiment design and mass data collection. Then, evaluation of the accuracy of data recorded by EyeTribe tracker was performed with the use of concurrent recording together with the SMI RED 250 eye-tracker. Both qualitative and quantitative results showed that data accuracy is sufficient for cartographic research. In the third part of the paper, a system for connecting EyeTribe tracker and Hypothesis software is presented. The interconnection was performed with the help of developed web application HypOgama. The created system uses open-source software OGAMA for recording the eye-movements of participants together with quantitative data from Hypothesis. The final part of the paper describes the integrated research system combining Hypothesis and EyeTribe.

• MeSH
• lidé MeSH
• pohyby očí * MeSH
• software * MeSH
• správnost dat MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

PURPOSE: We aimed (1) to describe and evaluate the "EPIC-Soft DataEntry" application developed as a user-friendly data entry tool for pan-European and national food consumption surveys among infants and children, and (2) to compare two food record-based dietary assessment methods in terms of food description and quantification using data quality indicators. EPIC-Soft DataEntry was used for both methods. METHODS: Two pilot studies were performed in both Belgium and Czech Republic in a total of 376 children (3 months to 10 year olds): one using a consecutive 3-day food diary; and the second with two non-consecutive 1-day food diaries with data entry during a completion interview. The collected dietary data were compared between the two dietary assessment methods by country and by age groups: (i) <1 year; (ii) 1-3 years; (iii) >3-10 years. RESULTS: Overall, 70% of the interviewers evaluated the work with EPIC-Soft DataEntry as easy. With both dietary assessment methods, an equally high proportion of specific food names (e.g., "yoghurt, strawberry") were reported, where only between 5 and 15% of foods were non-specified (e.g., "yoghurt, n.s."). The two 1-day food diaries yielded a higher proportion of foods with detailed description. For example, in the age category of 1-3 year olds in Belgium, for 7 out of 16 systematic questions on food description (e.g., "preservation method,") specific answers were significantly higher (all P < 0.03). The proportion of missing quantities of consumed foods was comparable between the two methods. CONCLUSIONS: The EPIC-Soft DataEntry application was positively evaluated by the majority of the interviewers. Two non-consecutive 1-day food diaries with data entry during a completion interview provide a more detailed description of consumed foods as compared with a 3-day food diary.

• MeSH
• databáze faktografické MeSH
• dieta - přehledy * MeSH
• dieta MeSH
• dietní záznamy * MeSH
• dítě MeSH
• hodnocení stavu výživy * MeSH
• hodnotící studie jako téma MeSH
• kojenec MeSH
• lidé MeSH
• pilotní projekty MeSH
• předškolní dítě MeSH
• software MeSH
• správnost dat MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Belgie MeSH
• Česká republika MeSH

• MeSH
• analýza přežití MeSH
• kalibrace MeSH
• kohortové studie MeSH
• lékařská informatika metody   MeSH
• lidé MeSH
• nádory prsu * MeSH
• prognóza * MeSH
• retrospektivní studie MeSH
• software MeSH
• správnost dat MeSH
• statistika jako téma MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• práce podpořená grantem MeSH