The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary

The sharing and documentation of cardiovascular research data are essential for efficient use and reuse of data, thereby aiding scientific transparency, accelerating the progress of cardiovascular research and healthcare, and contributing to the reproducibility of research results. However, challenges remain. This position paper, written on behalf of and approved by the German Cardiac Society and German Centre for Cardiovascular Research, summarizes our current understanding of the challenges in cardiovascular research data management (RDM). These challenges include lack of time, awareness, incentives, and funding for implementing effective RDM; lack of standardization in RDM processes; a need to better identify meaningful and actionable data among the increasing volume and complexity of data being acquired; and a lack of understanding of the legal aspects of data sharing. While several tools exist to increase the degree to which data are findable, accessible, interoperable, and reusable (FAIR), more work is needed to lower the threshold for effective RDM not just in cardiovascular research but in all biomedical research, with data sharing and reuse being factored in at every stage of the scientific process. A culture of open science with FAIR research data should be fostered through education and training of early-career and established research professionals. Ultimately, FAIR RDM requires permanent, long-term effort at all levels. If outcomes can be shown to be superior and to promote better (and better value) science, modern RDM will make a positive difference to cardiovascular science and practice. The full position paper is available in the supplementary materials.

GBA/GBN-position on the feedback of incidental findings in biobank-based research: consensus-based workflow for hospital-based biobanks

Incidental research findings pose a considerable challenge to hospital-based research biobanks since they are acting as intermediaries between healthcare and research. In a joint action the centralized biobank ibdw (Interdisciplinary Bank of Biomaterials and Data Wuerzburg) together with local authorities drafted a coherent concept to manage incidental research findings in full compliance with relevant ethical and data privacy regulations. The concept was developed and elaborated in close collaboration with the German Biobank Alliance (GBA). Comprehensive documentation of all steps guarantees the traceability of the process. By a mandatory assessment of the findings prior to re-identification of the individual concerned, unnecessary measures can be avoided. The individual's "right not to know" is respected according to the stipulations of the informed consent. As a general principle any communication with the individual occurs exclusively through the hospital and by competent physicians with appropriate knowledge and communication skills. We propose this scheme as a blueprint for reporting workflows for incidental research findings at hospital-based biobanks.

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

BACKGROUND

Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability.

RESULTS

We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform.

CONCLUSIONS

Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

Liquid materials for biomedical research: a highly IT-integrated and automated biobanking solution

Various information technology (IT) infrastructures for biobanking, networks of biobanks and biomaterial management are described in the literature. As pre-analytical variables play a major role in the downstream interpretation of clinical as well as research results, their documentation is essential. A description for mainly automated documentation of the complete life-cycle of each biospecimen is lacking so far. Here, the example taken is from the University Medical Center Göttingen (UMG), where the workflow of liquid biomaterials is standardized between the central laboratory and the central biobank. The workflow of liquid biomaterials from sample withdrawal to long-term storage in a biobank was analyzed. Essential data such as time and temperature for processing and freezing can be automatically collected. The proposed solution involves only one major interface between the main IT systems of the laboratory and the biobank. It is key to talk to all the involved stakeholders to ensure a functional and accepted solution. Although IT components differ widely between clinics, the proposed way of documenting the complete life-cycle of each biospecimen can be transferred to other university medical centers. The complete documentation of the life-cycle of each biospecimen ensures a good interpretability of downstream routine as well as research results.

Position Statement from the German Biobank Alliance on the Cooperation Between Academic Biobanks and Industry Partners

Under the umbrella of the German Biobank Node (GBN), 11 biobanks and two IT development centers are funded by the Federal Ministry of Education and Research (BMBF) to work together in the German Biobank Alliance (GBA). Their common aim is to make existing biomaterials hosted by different biobanks nationally and internationally available for biomedical research. This position article reflects and summarizes contributions and comments made during a GBA workshop, on the cooperation between academic biobanks and pharmaceutical and diagnostics companies that took place in Leipzig on the 21st of June 2018. It documents key points agreed on by all participating biobanks during the workshop thereby addressing several of the challenges identified. Although there are various possibilities for cooperation between academic biobanks and industry, this position article focuses exclusively on projects where academic biobanks give access to their biosamples and related data to industry partners. In doing so it considers the general conditions/framework and procedures in the German biobanking environment and raises ethical, legal, and procedural issues to be addressed when initiating such collaborations. It intends to furnish a basis for further activities to foster cooperation with industry and to push an overarching national coordination process. The final aim is to develop GBN-recommendations. Of course, many hospitals already have clear regulations on collaboration(s) with industry partners. These naturally take precedence for the GBA biobanks. However, where interest exists, GBN/GBA recommendations could help to induce changes to existing local policies nonetheless.

The Global Genome Biodiversity Network (GGBN) Data Standard specification

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.

Database URL:http://terms.tdwg.org/wiki/GGBN_Data_Standard

"Life in Data"--Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data

INTRODUCTION

Clinical, biodiversity, and environmental biobanks share many data standards, but there is a lack of harmonization on how data are defined and used among biobank fields. This article reports the outcome of an interactive, multidisciplinary session at a meeting of the European, Middle Eastern, and African Society for Biopreservation and Biobanking (ESBB) designed to encourage a 'learning-from-each-other' approach to achieve consensus on data needs and data management across biobank communities.

MATERIALS, METHODS, AND RESULTS

The Enviro-Bio and ESBBperanto Working Groups of the ESBB co-organized an interactive session at the 2013 conference (Verona, Italy), presenting data associated with biobanking processes, using examples from across different fields. One-hundred-sixty (160) diverse biobank participants were provided electronic voting devices with real-time screen display of responses to questions posed during the session. The importance of data standards and robust data management was recognized across the conference cohort, along with the need to raise awareness about these issues within and across different biobank sectors.

DISCUSSION AND CONCLUSION

While interactive sessions require a commitment of time and resources, and must be carefully coordinated for consistency and continuity, they stimulate the audience to be pro-active and direct the course of the session. This effective method was used to gauge opinions about significant topics across different biobanking communities. The votes revealed the need to: (a) educate biobanks in the use of data management tools and standards, and (b) encourage a more cohesive approach for how data and samples are tracked, exchanged, and standardized across biobanking communities. Recommendations for future interactive sessions are presented based on lessons learned.

How to design biospecimen identifiers and integrate relevant functionalities into your biospecimen management system

Effective tracking of biospecimens within a biobank requires that each biospecimen has a unique identifier (ID). This ID can be found on the sample container as well as in the biospecimen management system. In the latter, the biospecimen ID is the key to annotation data such as location, quality, and sample processing. Guidelines such as the Best Practices from the International Society of Biological and Environmental Repositories only state that a unique identifier should be issued for each sample. However, to our knowledge, all guidelines lack a specific description of how to actually generate such an ID and how this can be supported by an IT system. Here, we provide a guide for biobankers on how to generate a biospecimen ID for your biobank. We also provide an example of how to apply this guide using a longitudinal multi-center research project (and its biobank). Starting with a description of the biobank's purpose and workflows through to collecting requirements from stakeholders and relevant documents (i.e., guidelines or data protection concepts), and existing IT-systems, we describe in detail how a concept to develop an ID system can be developed from this information. The concept contains two parts: one is the generation of the biospecimen ID according to the requirements of stakeholders, existing documentation such as guidelines or data protection concepts, and existing IT-infrastructures, and the second is the implementation of the biospecimen IDs and related functionalities covering the handling of individual biospecimens within an existing biospecimen management system. From describing the concept, the article moves on to how the new concept supports both existing or planned biobank workflows. Finally, the implementation and validation step is outlined to the reader and practical hints are provided for each step.

A framework for biobank sustainability

Each year funding agencies and academic institutions spend millions of dollars and euros on biobanking. All funding providers assume that after initial investments biobanks should be able to operate sustainably. However the topic of sustainability is challenging for the discipline of biobanking for several major reasons: the diversity in the biobanking landscape, the different purposes of biobanks, the fact that biobanks are dissimilar to other research infrastructures and the absence of universally understood or applicable value metrics for funders and other stakeholders. In this article our aim is to delineate a framework to allow more effective discussion and action around approaches for improving biobank sustainability. The term sustainability is often used to mean fiscally self-sustaining, but this restricted definition is not sufficient for biobanking. Instead we propose that biobank sustainability should be considered within a framework of three dimensions - financial, operational, and social. In each dimension, areas of focus or elements are identified that may allow different types of biobanks to distinguish and evaluate the relevance, likelihood, and impact of each element, as well as the risks to the biobank of failure to address them. Examples of practical solutions, tools and strategies to address biobank sustainability are also discussed.

Changing requirements and resulting needs for IT-infrastructure for longitudinal research in the neurosciences

The observation of growing "difficulties" in IT-infrastructures in neuroscience research during the last years led to a search for reasons and an analysis on how this phenomenon is reflected in the scientific literature. With a retrospective analysis of nine examples of multicenter research projects in the neurosciences and a literature review the observation was systematically analyzed. Results show that the rise in complexity mainly stems from two reasons: (1) more and more need for information on quality and context of research data (metadata) and (2) long-term requirements to handle the consent and identity/pseudonyms of study participants and biomaterials in relation to legal requirements. The combination of these two aspects together with very long study times and data evaluation periods are components of the subjectively perceived "difficulties". A direct consequence of this result is that big multicenter trials are becoming part of integrated research data environments and are not standing alone for themselves anymore. This drives up the resource needs regarding the IT-infrastructure in neuroscience research. In contrast to these findings, literature on this development is scarce and the problem probably underestimated.

Improving IT-Support for Biobank Users

To improve IT-support for biobank users by the Department of Medical Informatics (MI) a questionnaire was designed addressing topics regarding the provided software and the IT-support. Different stakeholders of supported projects were identified and the interviews were performed with five users. The developed questionnaire consisted of five sections and 50 questions. The results of the interviews showed an overall satisfaction with the software and the support. Differences were identified between "long-term" and "short-term" users. Most improvements should be made in the usability of the software. Furthermore, the interviewees showed a great interest in a user-group to discuss and compare the functionalities and workflows of the different research groups. The results of the interviews will be used to make a prioritized list of improvements for the software. After validating the questionnaire users of the other IT-Systems provided by the MI will be interviewed.

Suitability of customer relationship management systems for the management of study participants in biomedical research

BACKGROUND

Longitudinal biomedical research projects study patients or participants over a course of time. No IT solution is known that can manage study participants, enhance quality of data, support re-contacting of participants, plan study visits, and keep track of informed consent procedures and recruitments that may be subject to change over time. In business settings management of personal is one of the major aspects of customer relationship management systems (CRMS).

OBJECTIVES

To evaluate whether CRMS are suitable IT solutions for study participant management in biomedical research.

METHODS

Three boards of experts in the field of biomedical research were consulted to get an insight into recent IT developments regarding study participant management systems (SPMS). Subsequently, a requirements analysis was performed with stakeholders of a major biomedical research project. The successive suitability evaluation was based on the comparison of the identified requirements with the features of six CRMS.

RESULTS

Independently of each other, the interviewed expert boards confirmed that there is no generic IT solution for the management of participants. Sixty-four requirements were identified and prioritized in a requirements analysis. The best CRMS was able to fulfill forty-two of these requirements. The non-fulfilled requirements demand an adaption of the CRMS, consuming time and resources, reducing the update compatibility, the system's suitability, and the security of the CRMS.

CONCLUSIONS

A specific solution for the SPMS is favored instead of a generic and commercially-oriented CRMS. Therefore, the development of a small and specific SPMS solution was commenced and is currently on the way to completion.