BackgroundBiobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of biobank-related data. Hitherto no ontology provided the coverage needed to capture a broad spectrum of biobank user scenarios.MethodsBased in the principles laid out by the Open Biological and Biomedical Ontologies Foundry two biobanking ontologies have been developed. These two ontologies were merged using a modular approach consistent with the initial development principles. The merging was facilitated by the fact that both ontologies use the same Upper Ontology and re-use classes from a similar set of pre-existing ontologies.ResultsBased on the two previous ontologies the Ontology for Biobanking (http://purl.obolibrary.org/obo/obib.owl) was created. Due to the fact that there was no overlap between the two source ontologies the coverage of the resulting ontology is significantly larger than of the two source ontologies. The ontology is successfully used in managing biobank information of the Penn Medicine BioBank.ConclusionsSharing development principles and Upper Ontologies facilitates subsequent merging of ontologies to achieve a broader coverage.
Patients and healthcare providers are important partners in cancer biobanking and research. Until now, however, there have been a limited number of scalable approaches to engage patients and providers as true collaborators in biobanking studies. The National Cancer Institute's Cancer Moonshot Biobank is a new engagement-centered project whose goal is to accelerate cancer research on drug resistance and sensitivity. This ambitious undertaking will involve the collection and distribution of longitudinal cancer biospecimens from over 1000 research participants receiving standard of care therapy at participating NCI Community Oncology Research Program (NCORP) institutions. Participants will be asked to donate blood and tissue at various time points including at baseline, during treatment, and at progression, if applicable. Engagement is a core component of the project given the longitudinal nature of the project, and the importance of participants and providers to its success. We define engagement as the establishment of an ongoing trusting and mutually vested relationship between study participants, healthcare providers and the Biobank. The three main engagement components of the Cancer Moonshot Biobank are: 1. External Scientific Panel (ESP): An extramural team of physicians, patient advocates, communication and biobanking experts who give input on various aspects of Biobank engagement 2. Local engagement activities at NCORP Sites 3. An online Participant and Provider Engagement (PPE) portal The PPE portal will be the main platform for direct interface between the Biobank and its participants, healthcare providers, as well as the public, and will serve as an archetype within NCI for the development of a unified portal for future NCI projects. Through the PPE portal, participants and providers will receive program updates, securely access documents including their biomarker test results and signed consent forms, and access educational material and other community resources. We describe ideation, design, and content creation for the PPE portal. Strategies for usability testing, integration of feedback, procedures for design and content iteration, as well as lessons learned are also discussed. Through the creation of NCI's PPE portal we aim to provide a valuable resource to participants and providers who are part of the Cancer Moonshot Biobank, while at the same time facilitating adoption of online engagement strategies within NCI and beyond. Citation Format: Esmeralda Casas-Silva, Helena J. Ellis, Veena Gopalakrishnan, Carol J. Weil, Abhi Rao, Lokesh Agrawal, Ping Guan, Natalie Madero, Jane W. Wanyiri, Jeffrey McLean, Mark A. Jensen, James Suh, Sean McDermott, P. Mickey Williams, Helen M. Moore, Laura Kadamus, Ainsley Adao, Rhett Beattie, Frank Ali, Debapriya Sarkar. Fostering research participation through NCI's Cancer Moonshot Biobank engagement portal [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4352.
Biobanking at Duke University has existed for decades and has grown over time in silos and based on specialized needs, as is true with most biomedical research centers. These silos developed informatics systems to support their own individual requirements, with no regard for semantic or syntactic interoperability. Duke undertook an initiative to implement an enterprise-wide biobanking information system to serve its many diverse biobanking entities. A significant part of this initiative was the development of a common terminology for use in the commercial software platform. Common terminology provides the foundation for interoperability across biobanks for data and information sharing. We engaged experts in research, informatics, and biobanking through a consensus-driven process to agree on 361 terms and their definitions that encompass the lifecycle of a biospecimen. Existing standards, common terms, and data elements from published articles provided a foundation on which to build the biobanking terminology; a broader set of stakeholders then provided additional input and feedback in a secondary vetting process. The resulting standardized biobanking terminology is now available for sharing with the biobanking community to serve as a foundation for other institutions who are considering a similar initiative.
Human biospecimens represent invaluable resources to advance molecular medicine, epidemiology, and biomarker discovery/validation, among other biomedical research. Biobanks typically cryopreserve biospecimens to safeguard their biochemical composition. However, exposing specimens repeatedly to freeze/thaw cycles can degrade their integrity in unforeseen ways. Those biobanks storing liquid samples, thus, regularly make a fundamental compromise at collection time between freezing samples in many small volumes (e.g., 0.5 mL or smaller) or in fewer, larger volumes (e.g., 1.8 mL). The former eliminates the need to expose samples to repeated freeze/thaw cycling, although increasing up-front labor costs, consumables used, and cold storage space requirements. The latter decreases up-front labor costs, consumables, and cold storage requirements, yet exposes samples repeatedly to damaging freeze/thaw cycles when smaller aliquots are needed for analysis. The Rhode Island BioBank at Brown University (RIBB) thoroughly evaluated the performance of an original technology that minimizes a sample's exposure to freeze/thaw cycling by enabling the automated extraction of frozen aliquots from one single frozen parent sample without thawing it. A technology that eliminates unnecessary sample exposures to freeze/thaw cycles could help protect sample integrity, extend its useful life, and effectively rectify and eliminate the aforementioned need to compromise. This report presents the results of the evaluation, and conclusively demonstrates the technology's ability to extract multiple uniform frozen aliquots from a single cryotube of never-thawed frozen human plasma, which faithfully represent the parent sample when analyzed for typical biochemical analytes, showing a coefficient of variability lower than 5.5%.
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