{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T21:39:34Z","timestamp":1775165974163,"version":"3.50.1"},"reference-count":49,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T00:00:00Z","timestamp":1745366400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computers"],"abstract":"<jats:p>The advancement of biomedical research depends on efficient data sharing, integration, and annotation to ensure reproducibility, accessibility, and cross-disciplinary collaboration. International collaborative research is crucial for advancing biomedical science and innovation but often faces significant barriers, such as data sharing limitations, inefficient sample management, and scalability challenges. Existing infrastructures for biosample and data repositories face challenges limiting large-scale research efforts. This study presents a novel platform designed to address these issues, enabling researchers to conduct high-quality research more efficiently and at reduced costs. The platform employs a modular, distributed architecture that ensures high availability, redundancy, and interoperability among diverse stakeholders, as well as integrates advanced features, including secure access management, comprehensive query functionalities, real-time availability reporting, and robust data mining capabilities. In addition, this platform supports dynamic, multi-criteria searches tailored to disease-specific patient profiles and biosample-related data across pre-analytical, post-analytical, and cryo-storage processes. By evaluating the platform\u2019s modular architecture and pilot testing outcomes, this study demonstrates its potential to enhance interdisciplinary collaboration, streamline research workflows, and foster transformative advancements in biomedical research. The key is the innovation of a real-time dynamic e-consent (DRT e-consent) system, which allows donors to update their consent status in real time, ensuring compliance with ethical and regulatory frameworks such as GDPR and HIPAA. The system also supports multi-modal data integration, including genomic sequences, electronic health records (EHRs), and imaging data, enabling researchers to perform complex queries and generate comprehensive insights.<\/jats:p>","DOI":"10.3390\/computers14050157","type":"journal-article","created":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T10:40:48Z","timestamp":1745404848000},"page":"157","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Advanced Digital System for International Collaboration on Biosample-Oriented Research: A Multicriteria Query Tool for Real-Time Biosample and Patient Cohort Searches"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1664-7042","authenticated-orcid":false,"given":"Alexandros","family":"Fridas","sequence":"first","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4904-5624","authenticated-orcid":false,"given":"Anna","family":"Bourouliti","sequence":"additional","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]},{"given":"Loukia","family":"Touramanidou","sequence":"additional","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6218-7363","authenticated-orcid":false,"given":"Desislava","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6381-8326","authenticated-orcid":false,"given":"Kostantinos","family":"Votis","sequence":"additional","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]},{"given":"Panagiotis","family":"Katsaounis","sequence":"additional","affiliation":[{"name":"Metabio, 542 50 Thessaloniki, Greece"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12992-017-0319-4","article-title":"Good collaborative practice: Reforming capacity building governance of international health research partnerships","volume":"14","author":"Ward","year":"2018","journal-title":"Glob. 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Collaborations between health services and educational institutions to develop research capacity in health services and health service staff: A systematic scoping review. BMC Health Serv. Res., 24.","DOI":"10.1186\/s12913-024-11836-w"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e011973","DOI":"10.1136\/bmjopen-2016-011973","article-title":"Can an ethics officer role reduce delays in research ethics approval? A mixed-method evaluation of an improvement project","volume":"6","author":"Foy","year":"2016","journal-title":"BMJ Open"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/s12961-017-0246-0","article-title":"Ethical challenges for international collaborative research partnerships in the context of the Zika outbreak in the Dominican Republic: A qualitative case study","volume":"15","author":"Espinal","year":"2017","journal-title":"Health Res. Policy Syst."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10961-024-10083-9","article-title":"Collaborative research in healthcare: Uncovering the impact of industry collaboration on the service innovativeness of university hospitals","volume":"50","author":"Huynh","year":"2024","journal-title":"J. Technol. Transf."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Li, X., and Cong, Y. (2024). Exploring barriers and ethical challenges to medical data sharing: Perspectives from Chinese researchers. BMC Med. Ethics, 25.","DOI":"10.1186\/s12910-024-01135-8"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Kosiol, J., Silvester, T., Cooper, H., Alford, S., and Fraser, L. (2024). Revolutionising health and social care: Innovative solutions for a brighter tomorrow\u2014A systematic review of the literature. BMC Health Serv. Res., 24.","DOI":"10.1186\/s12913-024-11099-5"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/scipol\/scab010","article-title":"Benefits, Motivations, and Challenges of International Collaborative Research: A Sociology of Science Case Study","volume":"48","author":"Dusdal","year":"2021","journal-title":"Sci. Public Policy"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.promfg.2017.08.021","article-title":"Managing Knowledge\u2013The Importance of Databases in the Scientific Production","volume":"12","author":"Figueiredo","year":"2017","journal-title":"Procedia Manuf."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Mikhael, E.M., Al-Jumaili, A.A., Jamal, M.Y., and Abdulazeez, Z.D. (2025). Current status and perceived challenges of collaborative research in a leading pharmacy college in Iraq: A qualitative study. BMC Med. Educ., 25.","DOI":"10.1186\/s12909-025-06653-6"},{"key":"ref_14","first-page":"100120","article-title":"Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience","volume":"3","author":"Muenzen","year":"2022","journal-title":"HGG Adv."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/s42488-020-00040-0","article-title":"An overview of biomedical platforms for managing research data","volume":"3","author":"Navale","year":"2021","journal-title":"J. Data Inf. Manag."},{"key":"ref_16","unstructured":"Winickoff, D.E., Kreiling, L., Borowiecki, M., Garden, H., and Philp, J. (2025, February 05). Collaborative Platforms for Emerging Technology: Creating Convergence Spaces. Available online: http:\/\/www.oecd.org\/termsandconditions."},{"key":"ref_17","unstructured":"(2025, April 22). Metabio\u2013Metabio. Available online: https:\/\/metab.io\/."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Dowling, N.M., Bolt, D.M., Deng, S., and Li, C. (2016). Measurement and control of bias in patient reported outcomes using multidimensional item response theory. BMC Med. Res. Methodol., 16.","DOI":"10.1186\/s12874-016-0161-z"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.csbj.2019.03.010","article-title":"Informed Consent in Biomedical Research","volume":"17","author":"Dankar","year":"2019","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41746-020-0302-y","article-title":"Digitizing clinical trials","volume":"3","author":"Inan","year":"2020","journal-title":"NPJ Digit. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.radonc.2020.09.054","article-title":"From multisource data to clinical decision aids in radiation oncology: The need for a clinical data science community","volume":"153","author":"Kazmierska","year":"2020","journal-title":"Radiother. Oncol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1080\/08989621.2020.1774373","article-title":"International scientific collaborative activities and barriers to them in eight societies","volume":"27","author":"Matthews","year":"2020","journal-title":"Account. Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1111\/cts.12559","article-title":"Innovation at the Intersection of Clinical Trials and Real-World Data Science to Advance Patient Care","volume":"11","author":"Swift","year":"2018","journal-title":"Clin. Transl. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Torab-Miandoab, A., Samad-Soltani, T., Jodati, A., and Rezaei-Hachesu, P. (2023). Interoperability of heterogeneous health information systems: A systematic literature review. BMC Med. Inform. Decis. Mak., 23.","DOI":"10.1186\/s12911-023-02115-5"},{"key":"ref_25","first-page":"20","article-title":"Improving Interoperability between Registries and EHRs","volume":"2018","author":"Blumenthal","year":"2018","journal-title":"AMIA Summits Transl. Sci. Proc."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.semradonc.2019.05.010","article-title":"The Evolving Use of Electronic Health Records (EHR) for Research","volume":"29","author":"Kim","year":"2019","journal-title":"Semin. Radiat. Oncol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e7476","DOI":"10.2196\/medinform.7476","article-title":"Health Information Technology (HIT) Adaptation: Refocusing on the Journey to Successful HIT Implementation","volume":"5","author":"Yen","year":"2017","journal-title":"JMIR Med. Inform."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e35724","DOI":"10.2196\/35724","article-title":"Fast Healthcare Interoperability Resources (FHIR) for Interoperability in Health Research: Systematic Review","volume":"10","author":"Vorisek","year":"2022","journal-title":"JMIR Med. Inform."},{"key":"ref_29","unstructured":"(2025, April 22). ISO\/IEC 27001:2022\u2014Information Security Management Systems. Available online: https:\/\/www.iso.org\/standard\/27001."},{"key":"ref_30","unstructured":"(2025, April 22). General Data Protection Regulation (GDPR) Compliance Guidelines. Available online: https:\/\/gdpr.eu\/."},{"key":"ref_31","unstructured":"(2025, April 22). HIPAA Home|HHS.gov, Available online: https:\/\/www.hhs.gov\/programs\/hipaa\/index.html."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1007\/s00145-019-09319-x","article-title":"TFHE: Fast Fully Homomorphic Encryption Over the Torus","volume":"33","author":"Chillotti","year":"2020","journal-title":"J. Cryptol."},{"key":"ref_33","unstructured":"Dingledy, F.W., and Matamoros, A.B. (2021, May 25). What Is Digital Rights Management?. Available online: https:\/\/scholarship.law.wm.edu\/libpubs\/122."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"45","DOI":"10.36401\/IDDB-21-01","article-title":"Real-Time Dynamic Tiered e-Consent: A Novel Tool for Patients\u2019 Engagement and Common Ontology System for the Management of Medical Data","volume":"1","author":"Ivanova","year":"2021","journal-title":"Innov. Digit. Health Diagn. Biomark."},{"key":"ref_35","first-page":"1","article-title":"NIST Special Publication 800-162 Guide to Attribute Based Access Control (ABAC) Definition and Considerations","volume":"800","author":"Hu","year":"2014","journal-title":"NIST Spec. Publ."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lapatas, V., Stefanidakis, M., Jimenez, R.C., Via, A., and Schneider, M.V. (2015). Data integration in biological research: An overview. J. Biol. Res., 22.","DOI":"10.1186\/s40709-015-0032-5"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1038\/s41597-024-03449-z","article-title":"Biomedical Data Repository Concepts and Management Principles","volume":"11","author":"Lin","year":"2024","journal-title":"Sci. Data"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Shanahan, H., and Bezuidenhout, L. (2022). Rethinking the A in FAIR Data: Issues of Data Access and Accessibility in Research. Front. Res. Metr. Anal., 7.","DOI":"10.3389\/frma.2022.912456"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1038\/s41390-024-03039-0","article-title":"Approaches to protocol standardization and data harmonization in the ECHO-wide cohort study","volume":"95","author":"Jacobson","year":"2024","journal-title":"Pediatr. Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e30363","DOI":"10.2196\/30363","article-title":"The Use of CDISC Standards for Real-World Data (RWD): Expert Perspectives from a Qualitative Delphi Survey","volume":"10","author":"Facile","year":"2022","journal-title":"JMIR Med. Inform."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Kush, R.D., Warzel, D., Kush, M.A., Sherman, A., Navarro, E.A., Fitzmartin, R., P\u00e9tavy, F., Galvez, J., Becnel, L.B., and Zhou, F.L. (2020). FAIR data sharing: The roles of common data elements and harmonization. J. Biomed. Inform., 107.","DOI":"10.1016\/j.jbi.2020.103421"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Hoffman, N., Alkhatib, R., and Gaede, K.I. (2024). Data Management in Biobanking: Strategies, Challenges, and Future Directions. BioTech, 13.","DOI":"10.3390\/biotech13030034"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Jacquier, E., Laurent-Puig, P., Badoual, C., Burgun, A., and Mamzer, M.F. (2021). Facing new challenges to informed consent processes in the context of translational research: The case in CARPEM consortium. BMC Med. Ethics, 22.","DOI":"10.1186\/s12910-021-00592-9"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s40246-018-0147-5","article-title":"The development of large-scale de-identified biomedical databases in the age of genomics-principles and challenges","volume":"12","author":"Dankar","year":"2018","journal-title":"Hum. Genom."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1186\/s12967-021-03147-z","article-title":"From biobank and data silos into a data commons: Convergence to support translational medicine","volume":"19","author":"Asiimwe","year":"2021","journal-title":"J. Transl. Med."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"100913","DOI":"10.1016\/j.patter.2023.100913","article-title":"Learning across diverse biomedical data modalities and cohorts: Challenges and opportunities for innovation","volume":"5","author":"Rajendran","year":"2024","journal-title":"Patterns"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"464-e20","DOI":"10.1634\/theoncologist.2014-0431","article-title":"The project data sphere initiative: Accelerating cancer research by sharing data","volume":"20","author":"Green","year":"2015","journal-title":"Oncologist"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2119","DOI":"10.1001\/jama.2015.3595","article-title":"The precision medicine initiative: A new national effort","volume":"313","author":"Ashley","year":"2015","journal-title":"JAMA"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1038\/s41698-017-0016-z","article-title":"Precision medicine: The foundation of future cancer therapeutics","volume":"1","author":"Shin","year":"2017","journal-title":"NPJ Precis. Oncol."}],"container-title":["Computers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-431X\/14\/5\/157\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:20:14Z","timestamp":1760030414000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-431X\/14\/5\/157"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,23]]},"references-count":49,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["computers14050157"],"URL":"https:\/\/doi.org\/10.3390\/computers14050157","relation":{},"ISSN":["2073-431X"],"issn-type":[{"value":"2073-431X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,23]]}}}