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Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin‐Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland‐Reyes S, Strambio‐De‐Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J. Toward a common standard for data and specimen provenance in life sciences. Learn Health Syst 2024; 8:e10365. [PMID: 38249839 PMCID: PMC10797572 DOI: 10.1002/lrh2.10365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 01/23/2024] Open
Abstract
Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.
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Affiliation(s)
- Rudolf Wittner
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Petr Holub
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Cecilia Mascia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | - Francesca Frexia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | | | - Clare Allocca
- National Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Fay Betsou
- Biological Resource Center of Institut Pasteur (CRBIP)ParisFrance
| | - Tony Burdett
- EMBL's European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ibon Cancio
- Plentzia Marine Station (PiE‐UPV/EHU)University of the Basque Country, EMBRC‐SpainBilbaoSpain
| | | | | | | | | | | | - Mark Elliot
- Department of Social Statistics, School of Social SciencesUniversity of ManchesterManchesterUK
| | - Katrina Exter
- Flanders Marine Institute (VLIZ), EMBRC‐BelgiumOstendBelgium
| | - Carole Goble
- Department of Computer ScienceUniversity of ManchesterManchesterUK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS gGmbH)HeidelbergGermany
| | | | | | - Simone Leo
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | - Anna Marsano
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Marco Mattavelli
- SCI‐STI‐MMÉcole Politechnique Fédérale de LausanneLausanneSwitzerland
| | - Josh Moore
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
- German BioImaging–Gesellschaft für Mikroskopie und Bildanalyse e.V.KonstanzGermany
| | - Hiroki Nakae
- Japan bio‐Measurement and Analysis ConsortiumTokyoJapan
| | - Isabelle Perseil
- INSERM–Institut National de la Sante et de la Recherche MedicaleParisFrance
| | - Ayat Salman
- Standards Council of CanadaOttawaOntarioCanada
- Canadian Primary Care Sentinel Surveillance Network (CPCSSN) Department of Family MedicineQueen's UniversityKingstonOntarioCanada
| | - James Sluka
- Biocomplexity InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Stian Soiland‐Reyes
- Department of Computer ScienceUniversity of ManchesterManchesterUK
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Michael Sussman
- US Department of AgricultureWashingtonDistrict of ColumbiaUSA
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
| | | | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw)WürzburgGermany
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Plass M, Wittner R, Holub P, Frexia F, Mascia C, Gallo M, Müller H, Geiger J. Provenance of specimen and data - A prerequisite for AI development in computational pathology. N Biotechnol 2023; 78:22-28. [PMID: 37758054 DOI: 10.1016/j.nbt.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 09/30/2023]
Abstract
AI development in biotechnology relies on high-quality data to train and validate algorithms. The FAIR principles (Findable, Accessible, Interoperable, and Reusable) and regulatory frameworks such as the In Vitro Diagnostic Regulation (IVDR) and the Medical Device Regulation (MDR) specify requirements on specimen and data provenance to ensure the quality and traceability of data used in AI development. In this paper, a framework is presented for recording and publishing provenance information to meet these requirements. The framework is based on the use of standardized models and protocols, such as the W3C PROV model and the ISO 23494 series, to capture and record provenance information at various stages of the data generation and analysis process. The framework and use case illustrate the role of provenance information in supporting the development of high-quality AI algorithms in biotechnology. Finally, the principles of the framework are illustrated in a simple computational pathology use case, showing how specimen and data provenance can be used in the development and documentation of an AI algorithm. The use case demonstrates the importance of managing and integrating distributed provenance information and highlights the complex task of considering factors such as semantic interoperability, confidentiality, and the verification of authenticity and integrity.
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Affiliation(s)
- Markus Plass
- Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria.
| | - Rudolf Wittner
- Masaryk University, Šumavská 416/15, 602 00 Brno, Czechia
| | - Petr Holub
- Masaryk University, Šumavská 416/15, 602 00 Brno, Czechia
| | | | | | - Matej Gallo
- Masaryk University, Šumavská 416/15, 602 00 Brno, Czechia
| | - Heimo Müller
- Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Jörg Geiger
- Uni Würzburg, Straubmühlweg 2a, 97078 Würzburg, Germany
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Wittner R, Mascia C, Gallo M, Frexia F, Müller H, Plass M, Geiger J, Holub P. Lightweight Distributed Provenance Model for Complex Real-world Environments. Sci Data 2022; 9:503. [PMID: 35977957 PMCID: PMC9383664 DOI: 10.1038/s41597-022-01537-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each organization can document only parts of the objects life cycle. As a result, interconnection of distributed provenance parts forms distributed provenance chains. Dependant on the actual provenance content, complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline — starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data (images, annotations, clinical data), ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain.
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Affiliation(s)
- Rudolf Wittner
- BBMRI-ERIC, Neue Stiftingtalstrasse 2, 8010, Graz, Austria.,Faculty of Informatics, Masaryk University, Botanická 68a, 602 00, Brno, Czech Republic.,Institute of Computer Science, Masaryk University, Šumavská 416/15, 602 00, Brno, Czech Republic
| | - Cecilia Mascia
- CRS4 - Center for Advanced Studies, Research and Development in Sardinia, Loc. Piscina Manna, 09050, Pula, CA, Italy
| | - Matej Gallo
- Faculty of Informatics, Masaryk University, Botanická 68a, 602 00, Brno, Czech Republic
| | - Francesca Frexia
- CRS4 - Center for Advanced Studies, Research and Development in Sardinia, Loc. Piscina Manna, 09050, Pula, CA, Italy
| | - Heimo Müller
- BBMRI-ERIC, Neue Stiftingtalstrasse 2, 8010, Graz, Austria.,Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 2, 8010, Graz, Austria
| | - Markus Plass
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 2, 8010, Graz, Austria
| | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), University and University Hospital of Würzburg, 97080, Würzburg, Germany
| | - Petr Holub
- BBMRI-ERIC, Neue Stiftingtalstrasse 2, 8010, Graz, Austria. .,Institute of Computer Science, Masaryk University, Šumavská 416/15, 602 00, Brno, Czech Republic.
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