The ARC Creator skill is a powerful tool designed to help researchers create
and populate Annotated Research Contexts (ARCs) following the nfdi4plants ARC
specification. This skill guides users through the entire process of creating
FAIR Digital Objects, from initial investigation setup to final DataHUB
synchronization.
What is an ARC?
An Annotated Research Context (ARC) is a FAIR (Findable, Accessible,
Interoperable, Reusable) Digital Object that organizes research data,
metadata, and documentation following the nfdi4plants specification. ARCs
provide a structured way to capture the complete context of a research
investigation, making it easier to share, reproduce, and build upon scientific
work.
Key Features of the ARC Creator Skill
The ARC Creator skill offers several essential capabilities:
- Interactive Guidance : Walks users through metadata collection conversationally, asking questions in manageable batches
- Comprehensive Coverage : Handles investigation setup, studies, assays, workflows, runs, contacts, and publications
- Git Integration : Manages version control and DataHUB synchronization
- ISA Metadata Compliance : Ensures adherence to the nfdi4plants ARC specification v3.0.0
Prerequisites for Using ARC Creator
Before using the ARC Creator skill, ensure you have:
- git and git-lfs installed on your system
- The ARC Commander CLI available at ~/bin/arc (recommended but optional)
- A Personal Access Token for git.nfdi4plants.org or datahub.hhu.de (for DataHUB sync)
The Interactive ARC Creation Workflow
The skill guides users through seven distinct phases:
Phase 1: Investigation Setup
The skill begins by asking for basic investigation details:
- Investigation identifier (short, lowercase-hyphenated)
- Title and description of the research
- Local storage location for the ARC
It then creates the ARC structure and sets initial investigation metadata.
Phase 2: Studies
For each study, the skill collects:
- Study identifier and descriptive information
- Organism and growth conditions
- Source and sample materials
- Protocols and experimental factors
The skill then creates the study structure and copies relevant files to
appropriate directories.
Phase 3: Assays
For each assay, the skill gathers:
- Assay identifier and measurement type
- Technology details and platform information
- Data file locations and processed data
- Protocol documents and performer information
The skill creates the assay structure and organizes data files appropriately.
Phase 4: Workflows (Optional)
If computational analysis is involved, the skill asks about:
- Workflow identifiers and descriptions
- Code files and dependencies
- Scripts, notebooks, and required libraries
Workflow files are placed in the workflows directory.
Phase 5: Runs (Optional)
For computational outputs, the skill collects:
- Run identifiers and associated workflows
- Output files including figures, tables, and processed data
Phase 6: Contacts and Publications
The skill gathers information about:
- Investigation contacts (names, emails, affiliations, roles)
- Publications with DOIs, PubMed IDs, titles, and authors
Phase 7: Git Commit and DataHUB Sync
Finally, the skill:
- Configures git user information
- Commits all changes with an appropriate message
- Offers to push to a DataHUB if desired
Key Reminders for ARC Users
The skill emphasizes several important principles:
- Assay data is immutable once placed in the dataset directory
- Studies describe materials while assays describe measurements
- Workflows contain code while runs contain outputs
- Git LFS should be used for large files (>100 MB)
- ARCs should not be stored on OneDrive/Dropbox to avoid conflicts
Benefits of Using ARC Creator
Researchers benefit from using the ARC Creator skill in multiple ways:
- Standardization : Ensures consistent metadata collection and organization
- Completeness : Guides users to include all necessary information
- FAIR Compliance : Helps create research objects that meet FAIR principles
- Reproducibility : Captures complete research context for future reproduction
- Shareability : Creates well-structured ARCs ready for sharing and publication
Technical Implementation
The skill leverages the ARC Commander CLI for many operations, providing a
user-friendly interface to complex command-line tools. It handles file
organization, metadata annotation, and git operations automatically, reducing
the technical burden on researchers.
Conclusion
The ARC Creator skill is an invaluable tool for researchers working with the
nfdi4plants ARC specification. By providing interactive guidance through the
entire ARC creation process, it ensures that research data is properly
organized, documented, and prepared for FAIR sharing. Whether you're creating
a new ARC, adding studies, or preparing data for DataHUB synchronization, this
skill streamlines the process and helps maintain high standards of research
data management.
Skill can be found at:
creator/SKILL.md>
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