Internal Data Model Research Articles

Enhancing RDM in Galaxy by integrating RO-Crate

Enhancing RDM in Galaxy by integrating RO-Crate

Реализация функции долговременного хранения научных данных большого объема в вычислительном центре

Long-term data storing is an important task for many modern scientific laboratories and datacenters. In order to reduce cost of digital information ownership, some solutions use magnetic tape technology and special software to control medium and data. Considering the on-site infrastructure specifics and well-established workflows of data processing, these organizations build and support such systems mainly by their own efforts, what becomes an important task in seeking to acquire the technological sovereignty. This paper describes long-term data storage issues in the computing center of the Zababakhin All-Russia Research Institute of Technical Physics where mathematical modeling computations generate vast amount of scientific data. The architecture and functional composition of the developed Archive Data Storage System are given as well as its internal data model, the chunk grouping rules, and the low-level tape format used. The measures taken to ensure an archived data consistency, methods of storage media management and issues of archival fund maintenance, are also considered. The calculation scheme of a typical archive system site’s hardware configuration, sufficient to process archiving data flows existing in datacenter, is given.

The use of modeling tools at the stages of database design

The article discusses the possibilities of using modeling tools at the stages of database design. Database design is one of the most complex and crucial tasks associated with the creation of an automated information system. As a result of solving this problem, the content of the database should be determined, an effective way for organizing data for all its future users, and data management tools. The main goal of this stage is to develop such a database scheme that it includes the necessary and sufficient data on information objects, their properties and relationships in accordance with the objects of the subject area and the processes of their transformation. The authors present the results of using modeling tools to solve the problems of the database design stage. Creating models is considered from the point of view of three-circuit architecture, the main principle of which is abstraction. To display the levels of data presentation, three related models have been developed: an external data model that displays the representations of each type of user existing in the organization (description of the subject area); a conceptual data model that displays a logical (or generalized) idea of data, independent of the type of database management system selected; an internal data model that displays the conceptual diagram in a specific way that is understandable to the selected target database management system. As an example of a subject area, the activity of a school of foreign languages is considered, namely, the registration of students in a school. The main problem is the large amount of information that is processed manually: paper forms of clients are drawn up, reports on the implementation of work are manually generated and filled out. It is necessary to develop a draft database for the registration of students of a school of foreign languages and to further implement it in the environment of the selected database management system.

Zenodo, an Archive and Publishing Repository: A tale of two herbarium specimen pilot projects

Zenodo (https://zenodo.org) is an open-access repository operated by CERN (European Organization for Nuclear Research), which provides researchers with an easy and stable platform to archive and publish their data and other output, such as software tools, manuals and project reports. In the context of the ICEDIG (Innovation and Consolidation for Large scale Digitisation of Natural Heritage) project, Zenodo was investigated for its usability as a platform where digitized images of collection specimens could be archived and published. In a production digitization pipeline, we foresee the automated archiving of daily image production. If Zenodo could be used for this purpose, such a process would also immediately mean that data and images are published FAIR-ly (Findable, Accessible, Interoperable and Reusable) within hours of their creation. To evaluate performance of the system, we first used a test dataset of 1800 herbarium specimen images, which was uploaded using Zenodo's API (Application Programming Interface) (Dillen et al. 2019). This dataset includes lossless TIFF images, label-segmented overlays and JSON-LD (JavaScript Object Notation for Linked Data) metadata using DwC (Darwin Core) terminology, constituting over 208 gigabytes of data. In addition, for all individual digital specimens the data about the specimen (in DwC) as well as metadata about its deposition on Zenodo (in Zenodo's internal data model) were available in multiple machine-readable formats. All data in DwC were provided as linked data with their DwC identifiers (e.g. http://rs.tdwg.org/dwc/terms/basisOfRecord). All individual specimens received minted DOIs (Digital Object Identifiers). A second upload of 280,000 herbarium JPEG images from a single institution (ca. 1 terabyte of data) with limited metadata (but using the same approach) was launched as well. In this presentation, the workflow for proper usage of the API will be described as well as some performance metrics, flexibilities and functionalities of the platform. Some issues and potential developments to tackle them will be discussed. Currently, the rate of ingestion into Zenodo seems only fast enough for small scale digitization pipelines. However, a modest improvement in transfer rate would make this a realistic proposition for large volume usage.

Data Model and Software Architecture for Business Process Model Generator

This paper describes the internal data model for a business process generator. Business process models are stored in an Event-driven process chain notation that provides a natural way to link the individual elements of a process. There is a software architecture that makes it easy to communicate with users as well as external systems.

Building an archive with Saada

Saada transforms a set of heterogeneous FITS files or VOTables of various categories (images, tables, spectra ...) in a database without writing code. Databases created with Saada come with a rich Web interface and an Application Programming Interface (API). They support the four most common VO services. Such databases can mix various categories of data in multiple collections. They allow a direct access to the original data while providing a homogenous view thanks to an internal data model compatible with the characterization axis defined by the VO. The data collections can be bound to each other with persistent links making relevant browsing paths and allowing data-mining oriented queries.

Integration of pathway data as prior knowledge into methods for network reconstruction

Hundreds of databases offer vast amounts of literature knowledge about biological signaling networks. However, this knowledge is rarely integrated into current bioinformatic analyzes due to challenges in the programmatic access and transformation of this data. This thesis focuses on the integration of prior knowledge into methods for network reconstruction. The motivation is to improve the performance of bioinformatic algorithms and methods by facilitating the integration of available pathway data as prior knowledge. First, the fundamentals of biological networks and pathways, their encoding using ontologies, methods for network reconstruction, and high-throughput gene expression technologies are introduced. Three central results are presented in this work: First, the novel software package rBiopaxParser, which enables the generic import of BioPAX-encoded pathway databases into the R Project for Statistical Computing. An overview of the functionality, the internal data model and visulization options is given. Second, a proof-of-concept implementation of the transformation and merging of pathway data to be used as prior knowledge for methods for network reconstruction is presented. The interactomes, the entirety of interactions, of three databases, Reactome, Pathway Interaction Database, and BioCarta, are generated and merged as a basis for prior pathway knowledge. Third, network reconstruction using Nested Effects Models is performed based on the generated prior knowledge networks and experimental high-throughput data of 16 gene knockdowns in breast cancer cell lines. Finally, this thesis compares the implemented software to similar concurrent developments and discusses the generated prior knowledge and the results of network reconstruction.

Extraction of standardized archetyped data from Electronic Health Record systems based on the Entity-Attribute-Value Model

Objective The ISO/EN 13606 Electronic Health Record architecture standard permits semantically interoperable exchange of Electronic Health Record data by using archetypes to define the structure and semantics of Electronic Health Record contents. Practical implementations of the ISO/EN 13606 standard have been scarcely reported on, and none of the publications describes in detail an efficient technique of archetype-compliant data extraction from an Electronic Health Record system. We address this research issue in the present report, and focus on a specific class of largely research-oriented Electronic Health Record systems which are internally based on the Entity-Attribute-Value Model. Method We propose an approach for extracting data described by archetypes from an Entity-Attribute-Value based Electronic Health Record system in an ISO/EN 13606-conformant manner. The approach is based on mapping from the structure of exported source documents to the archetype. It is implemented via standard XML technologies. Results We tested our approach on an Electronic Health Record system employed for clinical research at the Medical University of Vienna. Using test data defined by three different archetypes, source documents were successfully extracted as archetype-conformant ISO/EN 13606 Electronic Health Record extracts. Conclusions Electronic Health Record data may be effectively extracted from Entity-Attribute-Value based Electronic Health Record systems using the suggested approach. As a prerequisite for applying our approach, the internal data model of the Electronic Health Record system and the archetype must overlap in a way that a semantic mapping between them is possible. The system must further provide an XML interface which permits the export of the source documents in conventional format. The export must include data and metadata that are mandatorily postulated by the archetype and the ISO/EN 13606 Reference Model.

Autoplot: a browser for scientific data on the web

Autoplot is software developed for the Virtual Observatories in Heliophysics to provide intelligent and automated plotting capabilities for many typical data products that are stored in a variety of file formats or databases. Autoplot has proven to be a flexible tool for exploring, accessing, and viewing data resources as typically found on the web, usually in the form of a directory containing data files with multiple parameters contained in each file. Data from a data source is abstracted into a common internal data model called QDataSet. Autoplot is built from individually useful components, and can be extended and reused to create specialized data handling and analysis applications and is being used in a variety of science visualization and analysis applications. Although originally developed for viewing heliophysics-related time series and spectrograms, its flexible and generic data representation model makes it potentially useful for the Earth sciences.

웹 문서의 의미적 연관성 기술을 위한 온톨로지 에디터

웹의 확산과 더불어 웹상에 존재하는 정보의 양은 예측할 수 없을 정도로 증가하였고, 웹 사용자의 이용수준과 요구 사항도 매우 다양하고 복잡해졌다. 사용자가 원하는 정보와 의미적으로 정확히 일치하는 정보들을 검색하기 위해서는 웹 정보에 대한 정확한 의미 부여와 웹 정보 사이의 의미적 연관성을 기술할 수 있는 지식 표현 수단으로써 온톨로지가 필요하다. 이러한 필요성에 따라 W3C에서는 웹 자원에 대한 의미 표현 기술로 OWL(Web Ontology Language)이라는 웹 온톨로지 언어를 발표하였으나 아직 이를 효과적으로 생성, 편집할 수 있는 전용 에디터(editor)의 개발은 아직 미비한 실정이다. 따라서 본 논문에서는 웹 문서들 간의 의미적 연관성을 기술할 수 있는 OWL을 직관적인 인터페이스(interface)로 생성 및 편집할 수 있도록 OWL Parser, Internal DataModel, Visualization Module을 제공하는 온톨로지 에디터를 설계하고 구현하였다. As the internet continues to grow, the quantity of information on the Web increases beyond measure. The internet users' abilities and requirements to use information also become varied and complicated. Ontology can describe correct meaning of web resource and relationships between web resources. And it can extract conformable information that a user wants. Accordingly, we need the ontology to represent knowledge. W3C announced OWL(Web Ontology Language), a meaning description technology for such web resources. But, the development of a professional use of tools that can compose and edit effectively is not yet developed adequately. In this paper, we design and implement an Ontology editor which generates and edits OWL documents through intuitional interface, with a OWL parser, a Internal DataModel, and a Serializer.

A method for integrating multiple components in a decision support system

We present a flexible, extensible method for integrating multiple tools into a single large decision support system (DSS) using a forest ecosystem management DSS (NED-2) as an example. In our approach, a rich ontology for the target domain is developed and implemented in the internal data model for the DSS. Semi-autonomous agents control external components and communicate using a blackboard. We illustrate how this multi-agent approach with its blackboard architecture supports the expansion of a DSS (in this case, NED-2) to incorporate new models and decision support tools as they become available. The exemplar NED-2 DSS developed using this method is a goal-driven DSS that integrates a sophisticated inventory system, treatment plan development, growth-and-yield models, wildlife models, fire risk models, knowledge based systems for goal satisfaction analysis, and a powerful report generation system.

Design Choices when Architecting Visualizations

In this paper, we focus on some of the key design decisions we faced during the process of architecting a visualization system and present some possible choices, with their associated advantages and disadvantages. We frame this discussion within the context of Rivet, our general visualization environment designed for rapidly prototyping interactive, exploratory visualization tools for analysis. As we designed increasingly sophisticated visualizations, we needed to refine Rivet in order to be able to create these richer displays for larger and more complex data sets. The design decisions we discuss in this paper include the internal data model, data access, semantic meta-data information the visualization can use to create effective visual encodings, the need for data transformations in a visualization tool, modular objects for flexibility, and the tradeoff between simplicity and expressiveness when providing methods for creating visualizations.

UPGRADE: A Framework for Building Graph-Based Interactive Tools

Construction of interactive tools for visual languages is a challenging task. The UPGRADE framework leverages tool builders by integrating application logic and GUI components. It is based on attributed graphs as its internal data model. At the user interface (external representation), graphs can be rendered in multiple ways, including graphics, trees, text and tables. The framework is open, e.g., third-party viewer components may be plugged into the framework.

Java power tools

The Java Power Tools or JPT is a Java toolkit designed to enable students to rapidly develop graphical user interfaces in freshman computer science programming projects. Because it is simple to create GUIs using JPT, students can focus on the more fundamental issues of computer science rather than on widget management. In a separate article[4], we will discuss with examples how the JPT can help freshman students to learn about the basics of algorithms, data structures, classes, and interface design. In this article, we will focus on how the JPT itself can be used as an extended case study of object-oriented design principles in a more advanced course.The fundamental design principles of the JPT are that the elements of a graphical user interface should be able to be combined recursively as nested views and that the communication between these views and the internal data models should be as automatic as possible. In particular, in JPT, the totality of user input from a complex view can be easily converted into a corresponding data model and any input errors will be detected and corrected along the way. This ease of communication is achieved by using string objects as a lingua franca for views and models and by using parsing when appropriate to automatically check for errors and trigger recovery. The JPT achieves its power by a combination of computer science and software design principles. Recursion, abstraction, and encapsulation are systematically used to create GUI tools of great flexibility. It should be noted that a much simpler pedagogical package for Java IO was recently presented in [9].

A multi-view VR interface for 3D GIS

Virtual reality is becoming a popular tool to visualize 3D GIS data. Direct interaction with the GIS data, however, is often limited. In this paper, we present a multi-view approach to support 3D GIS interaction within VR-environments. The multi-view approach is based on three types of visualization: plan view, model view and world view. The plan view visualizes the data as a conventional cartographic map. The model view provides a 3D bird's-eye view on a partly symbolic and simplified 3D representation of the data. The world view gives the full immersive and photo-realistic 3D display. These views or modes can be used simultaneously or intermittently, and each provides a repertoire of interaction possibilities that is apt — but not necessarily limited — to that kind of visualization and interaction. This multi-view approach is implemented in the Karma VI system, using existing GIS and VR technology. We describe the multi-view approach, the system components and the internal data models, and how CAD models can be imported and be made consistent with the GIS data.

Choice of conceptual and internal data model in a data base management system (DBMS) with a layered structure

Choice of conceptual and internal data model in a data base management system (DBMS) with a layered structure