The Use of Translational Research Platforms in Clinical and Biomedical Data Exploration

Skolariki, Konstantina; Avramouli, Antigoni

doi:10.1007/978-3-319-56246-9_25

Cited by 6 publications

(3 citation statements)

References 17 publications

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“…24 feasibility tools were found. The "Georgetown Database of Cancer (G-DOC)" [14] tool and the "Cancer Translational Research Informatics Platform (caTRIP)" [14] were removed from further investigation because they turned out not to be open source, after deeper investigation. No openly available source code could also be found for the "Electronic Health Records Systems for Clinical Research (EHR4CR)" project [15].…”

Section: Identified Feasibility Toolsmentioning

confidence: 99%

“…No openly available source code could also be found for the "Electronic Health Records Systems for Clinical Research (EHR4CR)" project [15]. The tools "cBioPortal" [14], "Biology-Related Information Storage Kit (BRISK)" [14], "COVID-19 Exchange Data Platform (CODEX)" [16], "integrated clinical omics database (iCOD)" [14], "integrating data for analysis, anonymization and sharing (iDASH)" [14], "Informatics for Integrating Biology and the Bedside (i2b2) Query & Analysis Tool" [16,17], "Medical-Blocks" [18], "tranSMART" [6,16] and "Medex" [19] are central research data platforms or platforms built around a single database. Although in principle possible to adopt, we consider the effort required to customize them to be very high and have therefore not included them in the further evaluation.…”

Section: Identified Feasibility Toolsmentioning

confidence: 99%

“…In addition, tools with a different focus were not investigated further, i.e. the tool "Oncology Data Retrieval Systems (OncDRS)" [14] with a focus on genomic data and "DataSHIELD" [22] which is a multi-purpose tool for distributed computing. Finally the "COVID-Curated and the Open aNalysis aNd rEsearCh platform (CO-CONNECT)" [23] was excluded as the project terminated in October 2022 and there is no indication for further provision or development.…”

Section: Identified Feasibility Toolsmentioning

confidence: 99%

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Adaptability of Existing Feasibility Tools for Clinical Study Research Data Platforms

Witte,

Schoneberg,

Hanss

et al. 2023

German Medical Data Sciences 2023 – Science. Close to People.

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Introduction: The increasing need for secondary use of clinical study data requires FAIR infrastructures, i.e. provide findable, accessible, interoperable and reusable data. It is crucial for data scientists to assess the number and distribution of cohorts that meet complex combinations of criteria defined by the research question. This so-called feasibility test is increasingly offered as a self-service, where scientists can filter the available data according to specific parameters. Early feasibility tools have been developed for biosamples or image collections. They are of high interest for clinical study platforms that federate multiple studies and data types, but they pose specific requirements on the integration of data sources and data protection. Methods: Mandatory and desired requirements for such tools were acquired from two user groups — primary users and staff managing a platform’s transfer office. Open Source feasibility tools were sought by different literature search strategies and evaluated on their adaptability to the requirements. Results: We identified seven feasibility tools that we evaluated based on six mandatory properties. Discussion: We determined five feasibility tools to be most promising candidates for adaption to a clinical study research data platform, the Clinical Communication Platform, the German Portal for Medical Research Data, the Feasibility Explorer, Medical Controlling, and the Sample Locator.

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Section: Identified Feasibility Toolsmentioning

confidence: 99%