Elab2ARC: A Browser-Based Workspace for Converting Free-Text Protocols into rich FAIR digital objects

elab2ARC is a client-side, browser-based workspace that automates the conversion of free-text eLabFTW electronic laboratory notebook records into FAIR-compliant, version-controlled Annotated Research Contexts (ARCs) for seamless sharing and archiving without disrupting daily laboratory workflows.

The Gist

Imagine a scientist's daily work as a messy, handwritten diary kept in a digital notebook. This is what an Electronic Laboratory Notebook (ELN) is like. While it's great for writing down what happened during the day, it's terrible for computers to read. It's like writing a recipe in a secret code; a human chef can understand it, but a robot kitchen can't. Because of this, when scientists want to share their work or publish it, they have to spend hours manually rewriting their notes into a clean, standardized format that computers can understand.

Elab2ARC is a new tool designed to fix this headache. Think of it as a smart translator and organizer that lives inside your web browser. Here is how it works, using simple comparisons:

• The Source Material: It starts with data from a popular open-source notebook called eLabFTW. This is the "messy diary" mentioned earlier.
• The Transformation: Elab2ARC acts like a digital moving company. Instead of you packing boxes one by one, it automatically grabs your notes, your lists of steps (protocols), and your photos or files (attachments). It then repacks them into a very specific, organized format called an ARC (Annotated Research Context).
• The Destination: This new format is like a perfectly labeled shipping crate that follows strict international rules (called ISA-compliant). This ensures that anyone, anywhere, and any computer can understand exactly what the experiment was, how it was done, and what the results were. This is what scientists call making data FAIR (Findable, Accessible, Interoperable, and Reusable).
• Privacy First: A key feature is that all the "packing" happens right on your own computer (client-side). It's like doing your packing in your own living room before the truck arrives, rather than sending your belongings to a warehouse first. This means you stay in total control of your data until you are ready to send it to the PLANTdataHUB repository.
• The "Magic" Helper: If your notes are written in long, free-flowing paragraphs, the tool can use a smart AI assistant (an LLM) to read them and suggest a structured outline. However, it doesn't do the final job for you; it just hands you a draft to review and edit, ensuring a human is always the one making the final decisions.

The Bottom Line:
Elab2ARC doesn't ask scientists to change how they work every day. You can keep writing your messy, free-text notes in your usual notebook. The tool is designed to be used only when a project is finished. It takes the work you've already done, organizes it automatically into a format ready for publication and long-term storage, and saves you from the tedious task of rewriting everything from scratch.

Technical Summary

Technical Summary: Elab2ARC

Problem Statement
While Electronic Laboratory Notebooks (ELNs) are ubiquitous in life sciences, their inherent notebook format often hinders machine-readability and compliance with FAIR (Findable, Accessible, Interoperable, Reusable) principles. This structural limitation creates a significant bottleneck: researchers must expend considerable manual effort to restructure raw ELN records into publication-ready, machine-actionable formats. This process is not only time-consuming but also prone to error, delaying the sharing and long-term archiving of experimental data.

Methodology
To address this, the authors present elab2ARC, a browser-based workspace designed to automate the transformation of open-source eLabFTW records into Annotated Research Contexts (ARCs). The system operates through the following technical workflow:

• Data Retrieval: Utilizing the eLabFTW API, elab2ARC fetches administrative metadata, experimental protocols, and file attachments directly from the source ELN.
• Client-Side Processing: All data processing occurs locally within the user's browser. This architecture ensures that user data remains under the researcher's control prior to any submission, addressing privacy and data sovereignty concerns.
• Structural Transformation: The system reorganizes the retrieved unstructured or semi-structured data into ISA (Investigation-Study-Assay) compliant tables and links associated datasets, effectively converting "notebook" entries into version-controlled, FAIR-aligned research objects.
• LLM-Assisted Extraction: An optional workflow integrates Large Language Models (LLMs) to extract structured metadata from free-text protocols. Crucially, this feature generates editable drafts rather than final outputs, preserving human oversight and allowing researchers to verify and refine the extracted data before finalization.
• Output and Submission: The final output is an ARC, which can be submitted to the PLANTdataHUB repository for sharing and archiving.

Key Contributions
The primary contribution of this work is the development of a practical, non-intrusive tool that bridges the gap between daily laboratory documentation and FAIR data standards. Key technical contributions include:

1. Seamless Integration: The tool reuses existing eLabFTW documentation without requiring changes to the researchers' daily laboratory practices or workflow.
2. Automation of Restructuring: It automates the labor-intensive task of converting free-text protocols and attachments into structured, ISA-compliant formats.
3. Human-in-the-Loop AI: It introduces a cautious, editable approach to using LLMs for metadata extraction, balancing automation efficiency with the necessity of human validation.
4. Data Sovereignty: By performing all processing client-side, the system ensures that sensitive data is not exposed to external servers before the user is ready to submit.

Results and Claims
The paper demonstrates that elab2ARC successfully converts eLabFTW records into ARCs, providing a viable pathway for the FAIR-aligned sharing and long-term archiving of life-science experimental records. The system is designed specifically for use at the point of project completion, facilitating the transition from internal documentation to external publication and repository submission.

Significance
The significance of elab2ARC lies in its ability to offer a practical solution to the "FAIR gap" in life sciences. By automating the conversion of widely used ELN data into version-controlled, ISA-compliant objects, it reduces the manual burden on researchers and enables the creation of rich digital objects that are machine-readable and ready for reuse. The tool represents a step toward making experimental records more accessible and interoperable without disrupting the established workflows of scientific laboratories.