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Complete SmartAdd Workflow

This guide walks you through the entire workflow from uploading data to importing it into Chemotion.

Workflow Overview​

graph LR
    A[Upload Data] --> B[Explore & Prepare]
    B --> C[Organize Reactions & Samples]
    C --> D[Export ZIP]
    D --> E[Import to Chemotion]

Step 1: Upload Data​

Upload Your Files​

Upload your analytical data and related files to SmartAdd. The files will be stored in the input area, ready for you to organize into samples and reactions.

Option A: Upload Individual Files​

  1. Drag analytical files (spectra, MOL files, images, etc.) directly into the "Drag files here" area
  2. Files are processed and appear in the input list view on the left
  3. Files are ready to be assigned to samples and reactions

Option B: Upload a ZIP Archive​

  1. Prepare a ZIP file containing your analytical data and related files
  2. Drag the ZIP file into the upload area
  3. SmartAdd extracts all contents automatically
  4. All files appear in the input list view
No Pre-Organization Required
  • ZIP files don't need to follow any specific folder structure
  • SmartAdd extracts all files regardless of how they're organized
  • You'll build the sample/reaction structure manually in the next steps
  • Focus on using clear, descriptive filenames for easier assignment later

File Naming Tips​

Use clear filenames to make assignment easier:

  • ✅ Good: compound_A_1H_NMR_400MHz.jdx
  • ✅ Good: sample_001_structure.mol
  • ✅ Good: data@#$_final_v2.txt
  • ✅ Good: file1.jdx

Supported File Types​

  • Spectra: NMR data files
  • Structure Files: MOL, text files
  • Images: PNG, JPG
  • Text Files: Metadata, notes, experimental details
  • Archives: ZIP files containing any of the above

Step 2: Create & Organize Structure​

Build Your Collection Manually​

Now you'll create the structure by manually adding samples and reactions, then assigning your uploaded files to them.

Understanding the Tree Hierarchy​

SmartAdd uses this hierarchy (as shown in the right panel):

📦 Collection (Assignment Tree)
  ├─ 🧪 Reaction 1
  │   ├─ 📋 Sample 1 (Reactant)
  │   │   └─ 📊 Analyses
  │   │       └─ 📊 Analysis (e.g., NMR)
  │   │           └─ 📁 Datasets
  │   │               └─ 📄 Files
  │   └─ 📋 Sample 2 (Product)
  │       └─ 📊 Analyses
  └─ 📋 Sample 3 (Standalone)
      └─ 📊 Analyses

Typical hierarchy: Reactions → Samples → Analyses → Analysis → Datasets → Files

How to Build Your Structure​

There are multiple ways to build and organize your collection:

Method 1: Using Action Buttons​

  1. Add Samples: Click "Add Sample" button in the right panel
  2. Add Reactions: Click "Add Reaction" button to create reaction nodes
  3. Assign Files: Drag files from the input list (left) to samples/analyses in the tree (right)
  4. Edit Properties: Click any node to edit its properties in the properties panel

Method 2: Using Quick Add Buttons​

  • Plus Button Next to Reaction: Click the + button next to any reaction node to quickly add samples to that reaction

Method 3: Using Context Menu (Right-Click)​

Right-click on any node in the tree to open a context menu with options:

  • Edit Name: Rename the selected item
  • Add Sample: Add a sample (when right-clicking on reaction)
  • Add Analysis: Add analysis to a sample
  • Add Dataset: Add dataset to an analysis
  • Delete: Remove the selected item and its children
Multiple Ways to Work

Choose the method that feels most natural to you! The context menu (right-click) is especially useful for quickly adding nested items without navigating through menus.

Editing Properties​

Select any node in the tree to edit its properties:

Sample Properties​

FieldDescriptionExample
NameSample identifier"Compound A"
SMILESMolecular structure (validated)"CC(=O)OC1=CC=CC=C1C(=O)O"
AmountQuantity with units"100 mg"
PurityPercentage"98.5%"
LocationStorage location"Freezer A, Shelf 2"
Sample TypeCategory of sample"Product" / "Starting Material"
DescriptionAdditional notes"Synthesized on 2024-01-15"
SMILES Validation

SmartAdd provides real-time validation for SMILES notation. When entering molecular structures:

  • Syntax is checked automatically
  • Invalid structures are highlighted
  • Prevents export of incorrect molecular data

Reaction Properties​

FieldDescriptionExample
NameReaction identifier"Suzuki Coupling"
SamplesMultiple samples supportedAdd reactants, products, solvents
Sample RolesReactant/Product/SolventAutomatically sorted by role
Reaction Scheme TypeVisual scheme formatDefine for proper visualization
RF ValueTLC reference"0.65"
DescriptionReaction conditions"Room temp, 24h, N2 atmosphere"
Multi-Sample Reactions

SmartAdd supports adding multiple samples to a single reaction with:

  • Automatic smart sorting based on roles
  • Clear organization of reactants, products, and solvents
  • Proper hierarchical structure for complex reactions

Analysis Properties​

FieldDescriptionExample
TypeAnalysis technique"NMR" / "IR" / "MS"
Type OntologyStandardized classificationSelect from dropdown
File AttachmentsAssociated data filesSpectra, logs, images
StatusProcessing status"Complete" / "Pending"
Dataset InclusionInclude/exclude from exportControl export contents
DescriptionAnalysis notes"400 MHz, CDCl3"
Dataset Management

Use dataset inclusion/exclusion to control what gets exported to Chemotion:

  • Exclude preliminary or failed analyses
  • Include only validated data
  • Flexible organization for clean exports

Step 3: Organize Reactions & Samples​

Creating Samples​

  1. Click the Add Sample button in the right panel
  2. A new sample node appears in the assignment tree
  3. Edit the sample properties (name, SMILES, amount, etc.)
  4. Assign MOL files or spectra by dragging from the input list

Creating Reactions​

  1. Click the Add Reaction button in the right panel
  2. A new reaction node appears in the tree
  3. Add samples to the reaction
  4. Assign sample roles (reactant/product/solvent)

Linking Files to Samples/Analyses​

Drag and drop files from left panel to right panel:

  1. Locate your file in the input list (left panel)
  2. Drag it to the appropriate sample or analysis node (right panel)
  3. The file is now attached and will be included in the export

Organizing Multiple Samples in Reactions​

SmartAdd supports multi-sample reactions with automatic smart sorting:

  1. Add multiple samples to a reaction
  2. Assign roles to each sample:
    • Reactants: Starting materials
    • Products: Desired outcomes
    • Solvents: Reaction medium
  3. Samples are automatically sorted by role
  4. Define reaction scheme type for proper visualization

Step 4: Review & Validate​

Before exporting, verify:

Data Completeness Checklist​

  • All samples created and have meaningful names
  • SMILES notation entered and validated for molecular structures
  • MOL files assigned to appropriate samples
  • Amounts include units (mg, g, mol, mL)
  • Reactions created with samples added
  • Reaction roles are correctly assigned (reactant/product/solvent)
  • Multi-sample reactions properly organized with smart sorting
  • Files from input list dragged to correct samples/analyses
  • Analysis types are properly categorized
  • Dataset inclusion/exclusion configured correctly
  • Descriptions provide adequate context

Quality Checks​

  1. Navigate through the tree - Ensure logical structure
  2. Check input list - Verify all important files have been assigned (unassigned files won't be exported)
  3. Spot-check properties - Verify key fields are filled
  4. Review relationships - Confirm sample-reaction-analysis links
  5. Expand nodes - Ensure all files are visible under correct analyses/analysis/datasets

Step 5: Export for Chemotion​

You now have two export options:

Option A: Download as ZIP​

  1. Click Download as ZIP in the left panel
  2. Choose a save location
  3. The ZIP file is generated with Chemotion-compatible structure
  4. Manually upload to Chemotion later

Option B: Direct Upload to Chemotion (New!)​

  1. Click Upload to Chemotion ELN from the export menu
  2. Enter Server Details:
  3. Authenticate:
    • Enter your Chemotion username
    • Enter your password
    • Secure authentication with session management
  4. Upload: SmartAdd uploads your collection directly to Chemotion
    • No manual download needed
    • Automatic session handling

What's Included in the Export?​

  • ✅ All samples with properties and validated SMILES
  • ✅ Reactions with multiple samples and smart role sorting
  • ✅ Analyses with classifications and selected datasets
  • ✅ All attached files
  • ✅ Metadata in Chemotion format
Direct Upload Benefits

The direct upload feature eliminates manual steps:

  • No need to download and re-upload files
  • Faster workflow
  • Automatic authentication
  • Server connectivity verification

Step 6: Import into Chemotion​

For ZIP Downloads (Option A)​

  1. Open Chemotion ELN
  2. Navigate to Import section
  3. Select the exported ZIP file
  4. Confirm and complete the import

For Direct Uploads (Option B)​

The import is handled automatically! After successful upload:

  1. Open your Chemotion ELN
  2. Navigate to your collections
  3. Your data is already there after few seconds of upload - ready to use!

Post-Import Verification​

After importing into Chemotion:

  • Review imported samples
  • Verify reaction schemes
  • Check that all files are accessible
  • Confirm metadata integrity

Tips for Efficient Workflow​

  1. Work in batches: Process similar samples together
  2. Use templates: Develop naming conventions for consistency
  3. Save checkpoints: Export intermediate ZIPs as backups
  4. Validate early: Check properties as you go, not at the end