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Wiki source code of 1.4 Definitions

Last modified by publicadmin on 2025/12/16 13:04
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publicadmin 1.1 1 **Charité/BIH Infrastructure and Services**
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3 Various IT systems and services are integrated to provide networking, computing, storage, and other infrastructure required by the VRE. Services include transfer of data from existing research and clinical data sources (e.g., file stores, REDCap, PACS) into the Green Room; Hadoop and other systems deployed within the Health Data Platform; high performance computing clusters for running preprocessing pipelines; and backup, recovery, and data archival systems that ensure that data are kept safe and available at all times.
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5 **Data Controller**
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7 Has the meaning ascribed to it under GDPR.
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9 **Data Gateway API**
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11 An application programming interface that enables the Research Portal to exchange data and metadata with VRE systems and allows the VRE to be interoperable with other data platforms, data sources and systems.
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13 **Data Lake**
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15 A zone within the VRE in which data of any type can be received, stored, catalogued, and ultimately ingested into platform databases. Standard data models and ontologies are applied to allow datasets to be aggregated and processed. Data can be further de-identified here for broader sharing. Quality assurance, quality control and preprocessing pipelines prepare the data for visualisation and analysis.
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17 **Data Processor**
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19 Has the meaning ascribed to it under GDPR.
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21 **Dataset**
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23 A structured collection of data annotated with metadata that is typically associated with a specific project in the VRE.  Datasets can be versioned for data provenance and publication. 
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25 **Data Staging Pipelines**
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27 Workflows built into the VRE to allow automated processing of data. Pipelines help to eliminate or minimize manual intervention and facilitate a smooth flow of data from one stage to the next. Pipelines can be deployed to automate quality assurance, quality control, curation, validation, streaming, transformation, pre-processing, archival, and aggregation of data for downstream processes such as report generation, visualization, or query. 
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29 **Data Warehouse**
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31 A set of databases and services which transform diverse data into a unified, federated context. Federation is critical for harmonizing data and metadata so that information about participants and datasets can be queried, visualized, and analyzed across studies, data sources, and modalities. The Metadata Repository and Knowledge Graph implement standardized and extensible schemas to represent metadata derived from datasets as well as annotations generated by researchers.
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33 **GDPR**
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35 The European Union General Data Protection Regulation.
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37 **Green Room**
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39 An environment in which hospital data, such as data derived from electronic health records (EHRs), picture archiving and communication systems (PACS), laboratories, and other sources, can be de-identified, transformed, and prepared prior to being transferred to VRE Core systems and made available for research use.
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41 **Research Portal**
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43 The primary interface for researchers to access VRE functions and resources, including data capture tools, interactive dashboards and viewers, query tools, and analysis workspaces.
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45 **Virtual Research Environment**
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47 A platform designed by the Charité in collaboration with Indoc Research to facilitate secure data storage, analysis, and collaboration among members of a research project.
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49 **VRE Core**
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51 An environment in which de-identified hospital data, such as imaging, clinical and molecular data derived from electronic health records (EHRs) and other sources, can be securely stored, federated, and analyzed. Data is transferred to the VRE Core after undergoing de-identification and transformation pipelines in the VRE Green Room.
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53 **Workbench**
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55 A Workbench is a flexible and interactive environment in which users can access, visualise, and analyse their data with a range of analysis and visualisation tools. Workbenches are supported by underlying computing infrastructure and single sign-on protocols to permit data to be provisioned according to project and user role.
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58 ----
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60 **See Also: **
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62 [[About the VRE>>doc:Main.user_guide.About the VRE.About the VRE.WebHome]]
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64 [[Platform Architecture>>doc:Main.user_guide.About the VRE.Introduction]]
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66 ----
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73 Copyright © 2022, Indoc Research. This work is licensed under a [[Creative Commons Attribution-ShareAlike 4.0>>http://creativecommons.org/licenses/by-sa/4.0/ ||rel="noopener noreferrer" target="blank"]] International License.
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