Anforderungen an eine standortübergreifende Biobanken-IT-Infrastruktur

Schüttler, Christina; Buschhüter, N.; Döllinger, C.; Ebert, L.; Hummel, Michael; Linde, José Manuel Jerez; Prokosch, Hans‐Ulrich; Proynova, Rumyana; Lablans, Martin

doi:10.1007/s00292-018-0435-9

Cited by 15 publications

(9 citation statements)

References 8 publications

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“…An additional functionality that distinguishes the Sample Locator from the search applications under review is that it limits the results visualization to the aggregated sample count from the whole GBA network for anonymous researchers. Only after a researcher’s authentication and log-in, the counts per biobank location are additionally displayed [ 6 ]. Further, after the search, the Sample Locator forwards the user directly to the Negotiator, a dedicated communication tool to help request material from relevant biobanks and negotiate the terms involved based on the actual planned research project.…”

Section: Discussionmentioning

confidence: 99%

“…To align with the overarching goal of improving patient care by strengthening medical research, increased efforts have recently been made to support the secondary use of data generated in the treatment context [ 1 - 4 ]. In Germany, initiatives such as the Medical Informatics Initiative [ 5 ] or the German Biobank Alliance (GBA) [ 6 ] have emerged to establish an appropriate infrastructure for this endeavor. Coordinated by the German Biobank Node (GBN), the GBA has taken up the challenge of creating a cross-location biobank network to support biospecimen-based research projects.…”

Section: Introductionmentioning

confidence: 99%

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A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study

Schüttler¹,

Huth²,

Jagwitz-Biegnitz³

et al. 2020

J Med Internet Res

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Background The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. Objective To ensure the sustainable use of such a tool, we included researchers as participants in an end user–based usability evaluation. Methods To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. Results Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). Conclusions The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study

Schüttler¹,

Huth²,

Jagwitz-Biegnitz³

et al. 2020

J Med Internet Res

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“…Consequently, MIRACUM (Medical Informatics in Research and Care in University Medicine) [9], one of the four MII consortia, has set itself the task of carrying out a comparative evaluation of existing tools with regard to their usability to identify the most user-friendly system, and thus forms the best basis for developing a harmonized tool. As the implementation of such a platform was intended to take place as quickly as possible, a preselection of three implementations already used in the consortium (also freely accessible for researchers in Germany) was made for the usability evaluation: the MIRACUM i2b2 (Informatics for Integrating Biology and the Bedside) [10] feasibility platform, OHDSI's (Observational Health Data Sciences and Informatics) ATLAS [11,12], and the Sample Locator [13] of the German Biobank Alliance (GBA) [14,15]. The selection was based on the fact that they differed greatly in terms of complexity and functionality, so good coverage was expected.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Three Feasibility Tools for Identifying Patient Data and Biospecimen Availability: Comparative Usability Study (Preprint)

Schüttler¹,

Prokosch²,

Sedlmayr³

et al. 2020

Preprint

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BACKGROUND To meet the growing importance of real-word data analysis, clinical data and biosamples must be timely made available. Feasibility platforms are often the first contact point for determining the availability of such data for specific research questions. Therefore, a user-friendly interface should be provided to enable access to this information easily. The German Medical Informatics Initiative also aims to establish such a platform for its infrastructure. Although some of these platforms are actively used, their tools still have limitations. Consequently, the Medical Informatics Initiative consortium MIRACUM (Medical Informatics in Research and Care in University Medicine) committed itself to analyzing the pros and cons of existing solutions and to designing an optimized graphical feasibility user interface. OBJECTIVE The aim of this study is to identify the system that is most user-friendly and thus forms the best basis for developing a harmonized tool. To achieve this goal, we carried out a comparative usability evaluation of existing tools used by researchers acting as end users. METHODS The evaluation included three preselected search tools and was conducted as a qualitative exploratory study with a randomized design over a period of 6 weeks. The tools in question were the MIRACUM i2b2 (Informatics for Integrating Biology and the Bedside) feasibility platform, OHDSI’s (Observational Health Data Sciences and Informatics) ATLAS, and the Sample Locator of the German Biobank Alliance. The evaluation was conducted in the form of a web-based usability test (usability walkthrough combined with a web-based questionnaire) with participants aged between 26 and 63 years who work as medical doctors. RESULTS In total, 17 study participants evaluated the three tools. The overall evaluation of usability, which was based on the System Usability Scale, showed that the Sample Locator, with a mean System Usability Scale score of 77.03 (SD 20.62), was significantly superior to the other two tools (Wilcoxon test; Sample Locator vs i2b2: P=.047; Sample Locator vs ATLAS: P=.001). i2b2, with a score of 59.83 (SD 25.36), performed significantly better than ATLAS, which had a score of 27.81 (SD 21.79; Wilcoxon test; i2b2 vs ATLAS: P=.005). The analysis of the material generated by the usability walkthrough method confirmed these findings. ATLAS caused the most usability problems (n=66), followed by i2b2 (n=48) and the Sample Locator (n=22). Moreover, the Sample Locator achieved the highest ratings with respect to additional questions regarding satisfaction with the tools. CONCLUSIONS This study provides data to develop a suitable basis for the selection of a harmonized tool for feasibility studies via concrete evaluation and a comparison of the usability of three different types of query builders. The feedback obtained from the participants during the usability test made it possible to identify user problems and positive design aspects of the individual tools and compare them qualitatively.

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“…The definition of machine-interpretable, complex mappings has already been investigated in the past (see, e.g., Mate et al 52 ). The German Biobank Node and German Biobank Alliance projects, 10 23 53 which are working on establishing the German national node for BBMRI-ERIC and whose members are active contributors to the Samply software environment, are currently discussing how the MDR could be extended to store such transformation rules.…”

Section: Discussion and Outlookmentioning

confidence: 99%

Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC

et al. 2019

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Background High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks. Objectives To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task. Methods Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application. Results The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients. Conclusion A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.

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Anforderungen an eine standortübergreifende Biobanken-IT-Infrastruktur

Cited by 15 publications

References 8 publications

A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study

A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study

Evaluation of Three Feasibility Tools for Identifying Patient Data and Biospecimen Availability: Comparative Usability Study (Preprint)

Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC

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