elab2ARC

elab2ARC is a tool for converting eLabFTW experiments into Annotated Research Context (ARC) format. It allows researchers to easily fetch experiment data from eLabFTW instances and update or push these files to DataHUB in ARC format. The application streamlines the management of data from lab experiments to repositories, improving efficiency in scientific data handling.

Why is elab2ARC needed?

Many researchers rely on electronic lab notebooks (ELNs) to document their experiments due to their flexibility in handling free-form text and supporting data files up to 100 MB. However, when metadata standardization becomes necessary or when raw data files exceed the file size limit, other research data standards, such as Annotated Research Context (ARC), may be required.

ARC offers robust metadata annotation tools and customizable templates that help standardize the unstructured content typically found in ELNs. Additionally, ARC supports large files up to 10 GB, making it an excellent complement to ELNs like eLabFTW, which are not designed to handle raw data storage or larger file sizes.

Manually transferring metadata from ELNs to ARC can be both error-prone and time-consuming. To address this challenge, elab2ARC provides an efficient solution by automating the extraction, transformation, and loading (ETL) of data from ELN records into ARC-compliant structures. This tool streamlines the process, reduces errors, and ensures consistency, enhancing research data management workflows.

Features of elab2ARC

elab2ARC simplifies converting eLabFTW experiment data into Annotated Research Context (ARC) format. Key features include:

Direct Data Retrieval: Extracts experiment data from eLabFTW using experiment IDs and API keys.
ARC Conversion: Transforms data into ARC format, organizing protocols, datasets, and metadata.
DataHub Integration: Automates ARC file updates and pushes them to a DataHub repository.
Multi-Instance Support: Manages data from multiple eLabFTW instances seamlessly.

These features streamline workflows, ensuring efficient and standardized data management.

Setting up Tokens for elab2ARC

Create an Personal Access Token in DataHUB

This guide shows you how to generate a Personal Access Token (PAT). The PAT can be used to authenticate your local machine to communicate with your DataHUB account.

Sign in to the DataHUB
Navigate to the user settings
Go to the Access Tokens settings
Fill all required information:
- Token name: e.g. the name of the machine to be linked (“Office PC”) (1)
- Expiration date (optional) (2)
- Select a scope: e.g. api (3)
Click “Create personal access token” (4)
Your new personal access token appears on top. Copy (1) it somewhere safe for later use.

Create an eLabFTW API key

Login to your eLabFTW instance
Navigate to User Settings
Navigate to API KEYS Tab. Enter a name and a Read Only permissions
Save the key securely, as it will only be displayed once. Treat it like a password, as it grants access to eLabFTW.

How to use elab2ARC

Open the tools page: elab2ARC.

Add Tokens

In the Tokens tab, select your eLabFTW Instance or add Instance [1]
Paste eLabFTW API key [2]
Paste DataHUB Project Access Token [3]

Select eLabFTW experiment/resource

In the Home tab, select [1] your eLabFTW Experiment/Resource or enter the corresponding ID [2]. Use commas to separate multiple IDs.
Click Submission [3] to fetch entries.
Check Status [4] provides detailed information about the submission.
Preview [5] opens the eLabFTW tab and shows more information about the eLabFTW entry. Here you can also select linked Experiments/Resources for conversion.

Preview eLabFTW entry

In the eLabFTW tab, you get detailed information about your eLabFTW entry.

Main text of the entry [1]
administrative Metadata [2]
linked Resources and Experiments [3]
and Attachments [4] With the checkboxes, you can select entries for conversion.

Select ARC & Start Conversion

In the ARCs tab, select the ARC into which the elabFTW entry should be converted.
You can use an existing ARC by clicking the Convert to assay button [1] or create a new ARC with the Create a new ARC button [2].
Use Start Conversion button [3] to start the elab2ARC conversion.

Conversion

The elab2ARC tool will automatically convert your elabFTW experiments into ARC format

create a new assay folder with eLabFTW experiment name as assay name (green)
create the assay folder structure (dataset/protocols/isa.assay)
convert experiment main text into a .md file and store it in the protocol folder (purple)
add all attachments of the eLabFTW experiment into the dataset folder (yellow)
enter name/email/affiliation of the eLabFTW experiment metadata into the isa.assay sheet