Registering Compounds
Before uploading experiment data, compounds must be registered in the system. Compounds are registered by uploading an SDF (Structure Data File) containing molecular structures and properties.
How to Register
- Navigate to Register in the menu bar.
- Select an SDF file from your computer.
- Review the preview showing compounds found in the file.
- Click Confirm to register the compounds.
What Gets Extracted
The system uses RDKit to parse each molecule in the SDF file and extracts:
| Property | Source |
|---|---|
| Compound ID | From the "ID" or molecule name field in the SDF |
| CRO Compound ID | From the "Compound_ID" field (used for matching with CRO data) |
| Name | From Chemical_Name, Name, or molecule name fields |
| SMILES | Generated by RDKit from the molecular structure |
| Molecular Weight | From the SDF or calculated by RDKit |
| Molecular Formula | Calculated by RDKit |
| Structure | Stored as a mol block for rendering 2D structure images |
Duplicate Handling
If a compound with the same Compound ID already exists in the database, it will be skipped during registration. Existing compounds are not overwritten.
Tips
- Register compounds before uploading experiment data, so that compound IDs can be matched during the upload.
- The SDF file should contain the "ID" property for each compound. This is the primary identifier used throughout the application.
- The "Compound_ID" property (CRO compound ID) is used to match compounds when the CRO uses a different ID format.