Architecting FAIR Digital Objects and Computational Workflows: Interoperable Metadata, Persistent Identification, and Reproducible Research Infrastructures
Department of Information Studies University of Copenhagen Denmark
Abstract
The exponential growth of data intensive research across life sciences, Earth sciences, and computational domains has exposed profound challenges in interoperability, reproducibility, and long term stewardship of digital research assets. The FAIR principles have provided a normative framework for making digital objects Findable, Accessible, Interoperable, and Reusable. However, the operationalization of FAIR at scale requires coordinated infrastructures that integrate persistent identifiers, semantic web standards, research object packaging, workflow provenance capture, and policy aligned governance mechanisms. This article presents a comprehensive theoretical and architectural synthesis of interoperable FAIR digital objects and computational workflows grounded in contemporary specifications and community driven implementations. Drawing on standards such as the Digital Object Interface Protocol specification, PROV O, RDF 1.1, Schema.org, OCFL, BagIt, IEEE 2791 2020, and RO Crate, as well as community platforms including myExperiment, Whole Tale, OpenAIRE, the NCI Genomic Data Commons, and EOSC interoperability frameworks, this study constructs a layered conceptual model for digital object management. The analysis examines metadata modeling through Bioschemas and Science on Schema.org, ontology reuse, machine actionable data management plans, and persistent identifier design patterns. Particular emphasis is placed on computational workflow reproducibility using engines such as Snakemake and Galaxy, software distribution ecosystems such as Bioconda, cross platform packaging in Debian, and provenance frameworks including CWLProv and Pegasus. The article critically interrogates socio technical tensions between researcher usability and stewardship compliance, drawing on debates about data management fatigue and lifestyle oriented FAIR practice. It advances a detailed interoperability architecture integrating digital object identifiers, research object crates, linked data graphs, and repository storage layouts compliant with OCFL and BagIt. Through extensive theoretical elaboration, the paper articulates governance principles for data commons, cross domain metadata harmonization, and standards based international genomic data sharing. The findings demonstrate that sustainable FAIR infrastructures emerge not from isolated tools but from coordinated ecosystems combining persistent identity, semantic richness, workflow transparency, and institutional stewardship cultures. The study concludes by outlining policy, technical, and cultural pathways toward machine actionable, reproducible, and globally interoperable research environments.
Keywords
FAIR digital objects, research objects, computational workflows, interoperability standards
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