Evidence map›Paper›PMID 42400369›Full record

ArticleJournal of integrative bioinformatics2026

Fusion of computational and experimental provenance in RO-Crate.

Caroline Ott, Kevin Schneider, Heinrich Lukas Weil, Florian Wetzels, David Zimmer, Christoph Garth, Timo Mühlhaus

Abstract read
In one paragraph

Article in Journal of integrative bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Caroline OttDepartment of Biology, Computational Systems Biology, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://csbiology.github.io/.ORCID https://orcid.org/0000-0003-1512-9504
Kevin SchneiderDepartment of Biology, Computational Systems Biology, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://csbiology.github.io/.
Heinrich Lukas WeilDepartment of Biology, Computational Systems Biology, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://csbiology.github.io/.
Florian WetzelsDepartment of Computer Science, Visualization & HCI, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://vis.cs.rptu.de/.
David ZimmerDepartment of Biology, Computational Systems Biology, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://csbiology.github.io/.
Christoph GarthDepartment of Computer Science, Visualization & HCI, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://vis.cs.rptu.de/.
Timo MühlhausDepartment of Biology, Computational Systems Biology, RPTU Kaiserslautern-Landau, D-67663 Kaiserslautern, Germany, https://csbiology.github.io/.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Modern research projects typically involve several measurement techniques and computational analyses, resulting in complex, multimodal research data objects. While the FAIR Principles provide a framework for making data Findable, Accessible, Interoperable, and Reusable, researchers must still apply community standards for each data type, where available. This challenge is particularly pronounced in computational analyses and workflows, where high methodological diversity makes it difficult to create meaningful FAIR Digital Objects that also capture experimental provenance. Such objects must describe the full research process by interlinking experimental and computational steps in a unified, queryable provenance model. The ISA framework captures laboratory protocols and processes, while computational analyses are described using workflow-centric models such as Workflow (Run) RO-Crate, which separate workflow definitions from execution traces. Despite conceptual similarities, these approaches remain largely disconnected. This paper presents the ARC Workflow Run RO-Crate profile, which aligns ISA-based experimental provenance with computational workflow and execution metadata in a single, standards-compliant container. It enables shared semantics and makes experimental assays and workflow runs interoperable within a coherent provenance graph interpretable by both ISA- and workflow-aware tools. At the same time, the profile harmonizes experimental and computational provenance and remains compatible with existing (Workflow) RO-Crate and ISA tooling ecosystems.

Indexed as

Computational BiologySoftwareWorkflowFAIRFDOresearch data managementRO-Crateworkflows

Identifiers

PMID42400369
PMCPMC13526443

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.