ARC Creator

Create FAIR Digital Objects following the nfdi4plants ARC specification v3.0.0.

Prerequisites

• git and git-lfs installed
• ARC Commander CLI at ~/bin/arc (optional but recommended)
• For DataHUB sync: Personal Access Token for git.nfdi4plants.org or datahub.hhu.de

Interactive ARC Creation Workflow

Guide the user through these phases in order. Ask questions conversationally — don't dump all questions at once. Batch 2-4 related questions per message.

Phase 1: Investigation Setup

Ask the user:

• Investigation identifier (short, lowercase-hyphenated, e.g. cold-stress-arabidopsis)
• Title (concise name for the investigation)
• Description (textual description of the research goals)
• Where to store the ARC locally (suggest /home/uranus/arc-projects//)

arc investigation update -i "<id>" --title "<title>" --description "<desc>"

Phase 2: Studies

For each study, ask:

• Study identifier (e.g. plant-growth)
• Title and description
• Organism (for Characteristic [Organism])
• Growth conditions (temperature, light, medium, etc.)
• Source materials (what goes in — seeds, cell lines, etc.)
• Sample materials (what comes out — leaves, roots, extracts, etc.)
• Protocols — does the user have protocol documents to include?
• Factors — what experimental variables are being tested? (e.g., temperature, genotype, treatment)

arc study init --studyidentifier "<id>"
arc study update --studyidentifier "<id>" --title "<title>" --description "<desc>"

Copy protocol files to studies//protocols/. Copy resource files to studies//resources/.

Phase 3: Assays

For each assay, ask:

• Assay identifier (e.g. proteomics-ms, rnaseq, sugar-measurement)
• Measurement type (e.g., protein expression profiling, transcription profiling, metabolite profiling)
• Technology type (e.g., mass spectrometry, nucleotide sequencing, plate reader)
• Technology platform (e.g., Illumina NovaSeq, Bruker timsTOF)
• Data files — where are the raw data files? (will go into assays//dataset/)
• Processed data — any processed output files?
• Protocols — assay-specific protocols?
• Performers — who performed this assay? (name, affiliation, role)

arc assay init -a "<id>" --measurementtype "<type>" --technologytype "<tech>"

Copy data to assays//dataset/, protocols to assays//protocols/.

Phase 4: Workflows (optional)

Ask if there are computational analysis steps. For each:

• Workflow identifier (e.g. deseq2-analysis, heatmap-generation)
• Description of what it does
• Code files (scripts, notebooks)
• Dependencies (Python packages, R libraries, Docker image)

Phase 5: Runs (optional)

Ask if there are computation outputs. For each:

• Run identifier
• Which workflow produced it
• Output files (figures, tables, processed data)

Phase 6: Contacts & Publications

Ask:

• Investigation contacts (name, email, affiliation, role — at minimum the PI)
• Publications (if any — DOI, PubMed ID, title, authors)

arc investigation person register --lastname "<last>" --firstname "<first>" --email "<email>" --affiliation "<aff>"

Phase 7: Git Commit & DataHUB Sync

• Configure git user:

git config user.name "<name>"
git config user.email "<email>"

• Commit:

git add -A
git commit -m "Initial ARC: <investigation title>"

• 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

• Assay data is immutable — never modify files in assays//dataset/ after initial placement
• Studies describe materials, assays describe measurements
• Workflows are code, runs are outputs
• Git LFS for files > 100 MB: git lfs track ".fastq.gz" ".bam" "*.raw"
• Don't store ARCs on OneDrive/Dropbox — Git + cloud sync causes conflicts
• ARC Commander CLI reference: arc --help