" --description "<desc>" ``` ### 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 — seeds, cell lines, etc.) 6. **Sample materials** (what comes out — leaves, roots, extracts, etc.) 7. **Protocols** — does the user have protocol documents to include? 8. **Factors** — what experimental variables are being tested? (e.g., temperature, genotype, treatment) Create with: ```bash arc study init --studyidentifier "<id>" arc study update --studyidentifier "<id>" --title "<title>" --description "<desc>" ``` Copy protocol files to `studies/<id>/protocols/`. Copy resource files to `studies/<id>/resources/`. ### 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** — where are the raw data files? (will go into `assays/<id>/dataset/`) 6. **Processed data** — any processed output files? 7. **Protocols** — assay-specific protocols? 8. **Performers** — who performed this assay? (name, affiliation, role) Create with: ```bash arc assay init -a "<id>" --measurementtype "<type>" --technologytype "<tech>" ``` Copy data to `assays/<id>/dataset/`, protocols to `assays/<id>/protocols/`. ### 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/<id>/`. 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/<id>/`. ### Phase 6: Contacts & Publications Ask: 1. **Investigation contacts** (name, email, affiliation, role — at minimum the PI) 2. **Publications** (if any — DOI, PubMed ID, title, authors) Add via: ```bash arc investigation person register --lastname "<last>" --firstname "<first>" --email "<email>" --affiliation "<aff>" ``` ### Phase 7: Git Commit & DataHUB Sync 1. Configure git user: ```bash git config user.name "<name>" git config user.email "<email>" ``` 2. Commit: ```bash git add -A git commit -m "Initial ARC: <investigation title>" ``` 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 - **Assay data is immutable** — never modify files in `assays/<id>/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 <subcommand> --help` </article></body></html>

--- 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 - 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: 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: ```bash arc investigation update -i "" --title "" --description "<desc>" ``` ### 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 — seeds, cell lines, etc.) 6. **Sample materials** (what comes out — leaves, roots, extracts, etc.) 7. **Protocols** — does the user have protocol documents to include? 8. **Factors** — what experimental variables are being tested? (e.g., temperature, genotype, treatment) Create with: ```bash arc study init --studyidentifier "<id>" arc study update --studyidentifier "<id>" --title "<title>" --description "<desc>" ``` Copy protocol files to `studies/<id>/protocols/`. Copy resource files to `studies/<id>/resources/`. ### 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** — where are the raw data files? (will go into `assays/<id>/dataset/`) 6. **Processed data** — any processed output files? 7. **Protocols** — assay-specific protocols? 8. **Performers** — who performed this assay? (name, affiliation, role) Create with: ```bash arc assay init -a "<id>" --measurementtype "<type>" --technologytype "<tech>" ``` Copy data to `assays/<id>/dataset/`, protocols to `assays/<id>/protocols/`. ### 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/<id>/`. 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/<id>/`. ### Phase 6: Contacts & Publications Ask: 1. **Investigation contacts** (name, email, affiliation, role — at minimum the PI) 2. **Publications** (if any — DOI, PubMed ID, title, authors) Add via: ```bash arc investigation person register --lastname "<last>" --firstname "<first>" --email "<email>" --affiliation "<aff>" ``` ### Phase 7: Git Commit & DataHUB Sync 1. Configure git user: ```bash git config user.name "<name>" git config user.email "<email>" ``` 2. Commit: ```bash git add -A git commit -m "Initial ARC: <investigation title>" ``` 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 - **Assay data is immutable** — never modify files in `assays/<id>/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 <subcommand> --help` </article></body></html>

arc-creator

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