Lightweight Distributed Provenance Model for Complex Real–world Environments

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.

“Be sustainable”: EOSC‐Life recommendations for implementation of FAIR principles in life science data handling

“…EOSC‐Life has facilitated the development of the Common Provenance Model (Wittner et al , 2022). It introduces a framework to handle distributed provenance information [R5] .…”

Toward a common standard for data and specimen provenance in life sciences

“…Industrial collaboration is established by grounding the standardization effort in the ISO, where industry experts drive all aspects of a standard development process through their involvement in the ISO Technical Committees. The presented ISO standard development is thus considered a standardized instance of a publicly available provenance model 33 developed in parallel under the auspices of the EOSC-Life project. 57 Another challenge is the continuous dissemination and periodic revision of the standard once published.…”

“…The presented ISO standard development is thus considered a standardized instance of a publicly available provenance model 33 developed in parallel under the auspices of the EOSC-Life project. 57 Another challenge is the continuous dissemination and periodic revision of the standard once published. Though ISO standards are not "open access," they can be purchased for a moderate fee § § or accessed through institutional libraries, and, barring any patent restrictions, can be freely implemented, for instance, in Open Source software.…”

“…The Common Provenance Model can be seen as a current state-of-theart provenance model for distributed provenance, which is the most advanced provenance model that aims to provide a foundation for distributed provenance chains. 33 The development of the CPM was piloted using a distributed research pipeline covering biological material acquisition and storage, sample processing, data generation, and data processing. The prototype implementation of provenance generation was provided for the computational steps of the research pipeline.…”

“…The figure cited from. 33 complemented by a specialized profile to capture the provenance of workflow runs. § 6.…”