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1. Droga Herbaty. Część II.

Author

DĄBROWSKI, GRZEGORZ

Abstract

Copyright of Wroclawskie Studia Wschodnie is the property of Wroclaw University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2022
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2. Droga Herbaty. Część I.

Author

Dąbrowski, Grzegorz

Abstract

Copyright of Wroclawskie Studia Wschodnie is the property of Wroclaw University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2021
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3. El camino del Té

Author

Gutiérrez Martínez, Olga Paola and Arévalo Agredo, Antonia

Subjects
Ceremonia japonesa del té, Antropología cultural, Chadō, Chanoyu, Dō, Té, Omotenashi
Abstract

El camino del Té realiza un análisis sobre la ceremonia del té japonesa (chanoyu) como camino de vida, explorando el legado histórico y cultural de Japón en ella, del que aprendices de la ceremonia del té nutren el aprendizaje corporal y cognitivo en su práctica. El chanoyu contiene una síntesis de los valores y principios presentes en la sociedad japonesa, traídos al conocimiento de algunos estudiosos del té en Medellín y Bogotá, los cuales están relacionados con asociaciones japonesas compuestas por descendientes de inmigrantes japoneses en Colombia y rescatan aspectos culturales de su herencia. Un ejercicio etnográfico de la vivencia del té y análisis de su influencia como filosofía, evidenciado en la identificación a nivel individual y social en grupo. La primera dimensión a comprender será la manifestación de la materialidad en la ceremonia del té como producción de arte desde cada uno de sus implementos hasta el gesto del cuerpo, y como a su vez, las expresiones de su materialidad desarrollan el omotenashi a varios aspectos de lo cotidiano: las relaciones sociales y la generación de negocio. La segunda dimensión es la lógica “El Camino” en su historia e interpretaciones, ya que la ceremonia del té es vista como una ventana hacia el alma de Japón por estudios culturales japoneses. The Way of Tea analyzes the Japanese tea ceremony (chanoyu) as a way of life, exploring the historical and cultural legacy of Japan in it, from which apprentices of the tea ceremony nurture bodily and cognitive learning in their practice. The chanoyu contains a synthesis of the values and principles present in Japanese society, brought to the knowledge of some scholars of tea in Medellín and Bogotá, which are related to Japanese associations made up of descendants of Japanese immigrants in Colombia and rescue cultural aspects of their inheritance. An ethnographic exercise of the experience of tea and analysis of its influence as a philosophy, evidenced in the identification at the individual and social level in a group. The first dimension to understand will be the manifestation of materiality in the tea ceremony as a production of art from each of its implements to the gesture of the body, and how, in turn, the expressions of its materiality develop the omotenashi to various aspects of everyday life: social relationships and business generation. The second dimension is the logic "The Way" in its history and interpretations, since the tea ceremony is seen as a window into the soul of Japan by Japanese cultural studies. Pregrado Antropólogo / Antropóloga

Published
2022
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5. Machado: open source genomics data integration framework

Author

Mudadu, Mauricio de Alvarenga, Zerlotini, Adhemar, MAURICIO DE ALVARENGA MUDADU, CNPTIA, and ADHEMAR ZERLOTINI NETO, CNPTIA.

Subjects
0106 biological sciences, Computer science, AcademicSubjects/SCI02254, Health Informatics, Genomics, computer.software_genre, 01 natural sciences, Transcriptome, World Wide Web, Chado, 03 medical and health sciences, Annotation, Software, Databases, Genetic, Technical Note, Web navigation, database, 030304 developmental biology, computer.programming_language, 0303 health sciences, Genome, business.industry, Database schema, Python (programming language), Multiomics, Computer Science Applications, Generic Model Organism Database, Search box, Dados genômicos, AcademicSubjects/SCI00960, Base de Dados, Haystack, business, computer, multiomics, Python, 010606 plant biology & botany, Data integration
Abstract

BackgroundGenome projects and multiomics experiments generate huge volumes of data that must be stored, mined and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for over a decade and have been implementing software libraries, toolkits, platforms, and databases to succeed in this matter. The GMOD’s (Generic Model Organism Database project) biological relational database schema, known as Chado, is one of the few successful open source initiatives, it is widely adopted and many softwares are able to connect to it.ResultsWe have been developing an open source software named Machado (https://github.com/lmb-embrapa/machado), a genomics data integration framework implemented in Python, to enable research groups to both store and browse, query, and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on the top of already existing databases. It has several data loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL and LSTrAP. There is an API to connect to JBrowse and a web browsing visualisation tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a google-like search i.e. single auto-complete search box that provides fast results and incremental filters.ConclusionMachado aims to be a modern object-relational framework that uses the latests Python libraries to produce an effective open source resource for genomics research.

Published
2020
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6. OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

Author

Miles, Alistair, Zhao, Jun, Klyne, Graham, White-Cooper, Helen, and Shotton, David

Abstract

Abstract: Motivation: Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. Results: We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData’s services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. Availability: The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license. [Copyright &y& Elsevier]

Published
2010
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7. Machado: Open source genomics data integration framework.

Author

Mudadu MA and Zerlotini A

Subjects
Genome, Software, Databases, Genetic, Genomics
Abstract

Background: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it., Findings: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters., Conclusion: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research., (© The Author(s) 2020. Published by Oxford University Press GigaScience.)

Published
2020
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9. CHADO as a Spiritual Discipline

Author

Richard Edward, Campbell

Subjects
Chado, Wabi, Chakai, Rikyu, Chanoyu, Non-discriminatory being, Shin gyo so, Dualistic Perception, Temae, Bosatsu, Wabicha, Non-differentiated self, Sokushin-jobutsu
Published
1997

10. Keeping Pichia pastoris up to date : Verbesserung der Pichia pastoris Genom Internet Ressourcen

Author

Kraus, Hans

Subjects
Komagataella pastoris, genome browser, Chado, Hefe, Pichia pastoris, methylotroph, Genombrowser, yeast, GBrowse
Abstract

In dieser Schrift wird die Installation des Genome Browsers GBrowse Version 2.39 dargestellt. Weiters wird die Reimplementierung der Leistungsmerkmale, die von Andreas Redl (Redl 2008) in GBrowse Version 1.69 eingebracht wurden, präsentiert. Die Einleitung enthält einen Überblick und Vergleich unterschiedlicher, frei erhältlicher, Genom Browser. Die Phylogenie von Pichia pastoris wird dargestellt. Einige der Gründe, warum P. pastoris gerne als Organismus für Genexpression gewählt wird, werden ebenfalls dargestellt. Die zusätzlichen Leistungsmerkmale, die Andreas Redl (Redl 2008) in GBrowse Version 1.69 eingebracht wurden, werden vorgestellt. Einer der Hauptteile dieser Arbeit beschreibt die Reimplementierung dieser Leistungsmerkmale in GBrowse Version 2.39 und die Datenvorbereitung für die drei P. pastoris Stämme DSMZ 70382, GS115 und CBS7435. Das Kapitel ‚Discussion’ stellt die Vorteile manuell kuratierter GFF3 Dateien gegenüber automatisch erstellten Dateien dar. Einige Probleme bei der Installation und Datenpräparation werden auch gebracht. Das Kapitel ‚Outlook’ schlägt die Implementierung zweier Hilfsscripts vor und die Ausnutzung des ‚Renderfarm’ GBrowse Version 2.39 Leistungsmerkmals. This paper presents the Installation of GBrowse 2.39 and the re-implementation of the additional features implemented by Andreas Redl (Redl 2008) for GBrowse 1.69. The introduction presents an overview and a comparison of some of the free available genome browsers. The phylogeny of Pichia pastoris is outlined and reasons for choosing P. pastoris are presented and the additional features in the GBrowse version 1.69 are described. Further the changes in the GBrowse version 2.39, the installation of this version from scratch, starting with the OS, are described. The appendix contains the command list for the installation. The re-implementation of the additional features and the reasons for the selection of algorithms are presented, also the data preparation for the three strains DSMZ 70382, GS115 and CBS7435. The ‘Discussion’ section discusses the merits of manually curated GFF3 data files and the problems of automatically creates ones. Further some of the installation and data preparation problems are also presented. The ‘Outlook’ chapter suggests the implementation of some helper scripts and the exploit of the ‘render farm’ feature as expansion for the new GBrowse version 2.39. vorgelegt von: Hans Kraus Masterarbeit Wien, FH Campus Wien 2012

Published
2012

11. Japansk tecermoni och religion

Author

Hillås, Gunnel

Subjects
Chado, Philosophy, Ethics and Religion, teceremoni, Filosofi, etik och religion
Published
2009

12. dictyBase 2015: Expanding data and annotations in a new software environment.

Author

Basu S, Fey P, Jimenez-Morales D, Dodson RJ, and Chisholm RL

Subjects
Animals, Data Curation standards, Dictyostelium metabolism, Genetic Association Studies, Molecular Sequence Annotation methods, Molecular Sequence Annotation standards, Data Curation methods, Databases, Genetic, Dictyostelium genetics, Software
Abstract

dictyBase is the model organism database for the social amoeba Dictyostelium discoideum and related species. The primary mission of dictyBase is to provide the biomedical research community with well-integrated high quality data, and tools that enable original research. Data presented at dictyBase is obtained from sequencing centers, groups performing high throughput experiments such as large-scale mutagenesis studies, and RNAseq data, as well as a growing number of manually added functional gene annotations from the published literature, including Gene Ontology, strain, and phenotype annotations. Through the Dicty Stock Center we provide the community with an impressive amount of annotated strains and plasmids. Recently, dictyBase accomplished a major overhaul to adapt an outdated infrastructure to the current technological advances, thus facilitating the implementation of innovative tools and comparative genomics. It also provides new strategies for high quality annotations that enable bench researchers to benefit from the rapidly increasing volume of available data. dictyBase is highly responsive to its users needs, building a successful relationship that capitalizes on the vast efforts of the Dictyostelium research community. dictyBase has become the trusted data resource for Dictyostelium investigators, other investigators or organizations seeking information about Dictyostelium, as well as educators who use this model system., (© 2015 Wiley Periodicals, Inc.)

Published
2015
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13. Direct Radical Intuition: toward an 'Architecture of Presence' through Japanese ZEN Aesthetics

Author

Ellis, Charles

Subjects
Architecture, zen, architecture, wabi, ki, aikido, chado
Abstract

Currently the field of architectural thinking is steeped in Western discourse. The INTENTIONS of this research are to reveal how ideas of a Direct Radical intuition as an Eastern perspective can be infused into a field of Western dominated architectural thinking paradigm. This investigation into the landscape of architectural theory proposes that a study of Japanese Zen Buddhist aesthetics through ‘Direct Radical intuition’ will draw us toward an ‘Architecture of Presence.’ The formation of Japanese philosophical and religious thoughts will go through EXPLORATIONS culminating in two Buddhist principles; wabi (beautiful poverty) through chado, or ‘the way of tea’ and ki (life force) through aikido, or ‘the way of harmony’ that were absorbed by Zen. Additionally, an examination of selected Western philosophical thought in Phenomenology and Post Modernism that aligns with or is contrary to aesthetics of Zen will be used to further clarify the ASSOCIATIONS to these principles. Finally, an analysis of selected projects by Japanese architect Tadao Ando will further reveal how the proclivity toward aesthetic principles of Zen can illuminate CONNECTIONS for a visible architectural expression. A synthesis of this study will result in an assimilation of terms in alliance with ‘Direct Radical Intuition’ that has at its essence a ‘concrete pragmatism’ and ‘creative spontaneity’ disclosing a means of navigating through the architectural design and construction process. A comprehension of the architectural issues with transparency imbued with ‘Direct Radical intuition’ allows the designer to look within and beyond self and culturally imposed boundaries. This insight leads toward an ‘Architecture of Presence’ that is rooted in fundamental aspects of human activity and ascension toward a nourishment of the human spirit. This imminent enrichment facilitates the empowerment of IMPLICATIONS toward individual, cultural and social place in the larger context of a compassionate global integration.

Published
2011

14. Téets väg

Author

Hallengren, Anders and Hallengren, Anders

Abstract

A brief history of the introduction and ritualization of tea, and how it became fashionable. This minor contribution also outlines a linguistic theory of how the two principal groups in the naming of this worldwide beverage can be explained by the two most important commercial routes—one WNW by land including the ancient Silk and Caravan roads—carrying North Chinese ‘chá’; the other WSW in more recent times by ship in the European Age of Sail (trading South-East Chinese ‘te’ or ‘ta’—at the Amoy and Quanzhou harbours, from Guangzhou and other ports of the South), and thus be derived from the modes of conveyance! The reason as well as the usage depend on linguistic geography, but above all the time slots of contact zones, specific transportation networks and waterways. The Swedish title of the article, meaning ‘The Way of Tea’, furthermore is an allusion to the Japanese tea ceremony, the cha-do, which is also touched upon in this context.

Published
1979

15. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Bahurek, Tomáš, Martínek, Tomáš, Vogel, Ivan, and Bahurek, Tomáš

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

16. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Bahurek, Tomáš, Martínek, Tomáš, Vogel, Ivan, and Bahurek, Tomáš

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

17. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Martínek, Tomáš, and Vogel, Ivan

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

18. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Martínek, Tomáš, and Vogel, Ivan

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

19. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Martínek, Tomáš, and Vogel, Ivan

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

20. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Martínek, Tomáš, and Vogel, Ivan

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

21. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Bahurek, Tomáš, Martínek, Tomáš, Vogel, Ivan, and Bahurek, Tomáš

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

22. Dotazovací jazyk pro databáze biologických dat

Author

Martínek, Tomáš, Vogel, Ivan, Bahurek, Tomáš, Martínek, Tomáš, Vogel, Ivan, and Bahurek, Tomáš

Abstract

S rapidně stoupajícím množstvím biologických dat stoupá i důležitost biologických databází. U těchto databází je nezbytné objevování znalostí (nalezení spojitostí, které nebyli známé v čase vkládání dat). K získávání znalostí z biologických databází je nutná konstrukce složitých SQL dotazů, což vyžaduje pokročilou znalost SQL a použitého databázového sché- matu. Biologové většinou tyto znalosti nemají, proto je potřeba nástroje, který by poskytl intuitivnějšího rozhrání pro tyto databáze. Tato práce navrhuje ChQL, intuitivní dotazovací jazyk pro databázi biologických dat Chado. ChQL umožňuje biologům poskládat dotaz za použití pojmů, které dobře znají bez nutnosti znát SQL nebo použité schéma. Tato práce implementuje aplikaci pro dotazování databáze Chado pomocí ChQL. Webové rozhrání provede uživatele procesem zostavení věty jazyka ChQL. Aplikace přeloží tuto větu do SQL dotazu, odešle jej do databáze Chado a zobrazí vrácená data v tabulce. Výsledky jsou vyhodnoceny testováním dotazů na reálných datech., With rising amount of biological data, biological databases are becoming more important each day. Knowledge discovery (identification of connections that were unknown at the time of data entry) is an essential aspect of these databases. To gain knowledge from these databases one has to construct complicated SQL queries, which requires advanced knowledge of SQL language and used database schema. Biologists usually don't have this knowledge, which creates need for tool, that would offer more intuitive interface for querying biological databases. This work proposes ChQL, an intuitive query language for biological database Chado. ChQL allows biologists to assemble query using terms they are familiar without knowledge of SQL language or Chado database schema. This work implements application for querying Chado database using ChQL. Web interface guides user through process of assembling sentence in ChQL. Application translates this sentence to SQL query, sends it to Chado database and displays returned data in table. Results are evaluated by testing queries on real data.

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