ARC Creator
by @ingogiebel
Create and populate Annotated Research Contexts (ARCs) following the nfdi4plants ARC specification. Use when creating a new ARC, adding studies/assays/workflows/runs, annotating ISA metadata, organizing research data into ARC structure, or pushing ARCs to a DataHUB. Guides the user interactively through all required and optional metadata fields.
clawhub install arc-creatorπ About This Skill
name: arc-creator description: Create and populate Annotated Research Contexts (ARCs) following the nfdi4plants ARC specification. Use when creating a new ARC, adding studies/assays/workflows/runs, annotating ISA metadata, organizing research data into ARC structure, or pushing ARCs to a DataHUB. Guides the user interactively through all required and optional metadata fields.
ARC Creator
Create FAIR Digital Objects following the nfdi4plants ARC specification v3.0.0.
Prerequisites
git and git-lfs installed~/bin/arc (optional but recommended)Interactive ARC Creation Workflow
Guide the user through these phases in order. Ask questions conversationally β don't dump all questions at once. Batch 2-4 related questions per message.
Phase 1: Investigation Setup
Ask the user:
1. Investigation identifier (short, lowercase-hyphenated, e.g. cold-stress-arabidopsis)
2. Title (concise name for the investigation)
3. Description (textual description of the research goals)
4. Where to store the ARC locally (suggest /home/uranus/arc-projects/)
Then run scripts/create_arc.sh and set investigation metadata via:
arc investigation update -i "" --title "" --description ""
Phase 2: Studies
For each study, ask:
1. Study identifier (e.g. plant-growth)
2. Title and description
3. Organism (for Characteristic [Organism])
4. Growth conditions (temperature, light, medium, etc.)
5. Source materials (what goes in β seeds, cell lines, etc.)
6. Sample materials (what comes out β leaves, roots, extracts, etc.)
7. Protocols β does the user have protocol documents to include?
8. Factors β what experimental variables are being tested? (e.g., temperature, genotype, treatment)
Create with:
arc study init --studyidentifier ""
arc study update --studyidentifier "" --title "" --description ""
Copy protocol files to studies/.
Copy resource files to studies/.
Phase 3: Assays
For each assay, ask:
1. Assay identifier (e.g. proteomics-ms, rnaseq, sugar-measurement)
2. Measurement type (e.g., protein expression profiling, transcription profiling, metabolite profiling)
3. Technology type (e.g., mass spectrometry, nucleotide sequencing, plate reader)
4. Technology platform (e.g., Illumina NovaSeq, Bruker timsTOF)
5. Data files β where are the raw data files? (will go into assays/)
6. Processed data β any processed output files?
7. Protocols β assay-specific protocols?
8. Performers β who performed this assay? (name, affiliation, role)
Create with:
arc assay init -a "" --measurementtype "" --technologytype ""
Copy data to assays/, protocols to assays/.
Phase 4: Workflows (optional)
Ask if there are computational analysis steps. For each:
1. Workflow identifier (e.g. deseq2-analysis, heatmap-generation)
2. Description of what it does
3. Code files (scripts, notebooks)
4. Dependencies (Python packages, R libraries, Docker image)
Place code in workflows/.
Note: workflow.cwl is REQUIRED by spec but often created later. Inform user.
Phase 5: Runs (optional)
Ask if there are computation outputs. For each: 1. Run identifier 2. Which workflow produced it 3. Output files (figures, tables, processed data)
Place outputs in runs/.
Phase 6: Contacts & Publications
Ask: 1. Investigation contacts (name, email, affiliation, role β at minimum the PI) 2. Publications (if any β DOI, PubMed ID, title, authors)
Add via:
arc investigation person register --lastname "" --firstname "" --email "" --affiliation ""
Phase 7: Git Commit & DataHUB Sync
1. Configure git user:
git config user.name ""
git config user.email ""
2. Commit:
git add -A
git commit -m "Initial ARC: "
3. Ask if the user wants to push to a DataHUB. If yes: - Ask which host (git.nfdi4plants.org, datahub.hhu.de, etc.) - Create remote repo (via browser or API) - Set remote and push
ISA Metadata Reference
For detailed ISA-XLSX fields, annotation table columns, and ontology references, read references/arc-spec.md.
Key Reminders
assays//dataset/ after initial placementgit lfs track "*.fastq.gz" "*.bam" "*.raw"arc --help βοΈ Configuration
git and git-lfs installed~/bin/arc (optional but recommended)