The Compounds collection is where all the compounds' chemical properties and other information are documented. As in other collections, fields in the Compounds collection are customizable, and additional fields may be added to describe the compounds.
There are two main ways to populate the compounds collection- either add them one by one or import in bulk.
Add a single compound by filling out a new compound form:
Go to the compound collection index page.
Click on 'New compound' button at the top right corner to open a form showing the fields chosen to appear in that collection.
Populated the fields with the required information and saved them to create a new item.
The compound collection is integrated with a chemical structure editor, which allows for drawing chemical structures or uploading existing structure files. For more information on the editor click here.
Once saved the chemical properties (if enabled) of this specific compound are added automatically to the form.
Bulk import
Labguru compounds collection offers two main options to perform bulk compound import - by using an Excel template or SDF file upload.
Excel template:
Importing compounds using the Excel template allows users to create new compounds, update existing compounds as well as add stocks or update existing stocks, all at the same time.
Go to the compound collection index page.
Click on the 3 dots and select Import/Update.
On the New Import page, download Labguru’s import template (.xlsx format).
The compounds' structure may be described either by using SMILES (simplified molecular-input line-entry system) in the Structure (SMILES) header, or by using InChI (International Chemical Identifier) in the Structure (InChI) header.
Please note that if both structure fields are populated (SMILES and InChI), the structure will be determined according to the InChI notation inserted.
Make sure to follow the general import instructions and upload the filled Excel file.
SDF files upload:
Importing compounds by uploading an SDF file allows users to create new compounds and generate a new stock for each imported compound. In case one of the imported compound's structure already exists in the collection, a stock will be generated for the original compound in the collection having this structure.
The final number of imported compounds as well as the number of duplicates found will be listed in the SDF import summary.
The generated stocks will be located in a temporary box named after the SDF file.
To upload a SDF file:
Go to the compound collection index page.
Click on the 3 dots and select Import/Update.
Upload the designated SDF file in step 3 on the New Import page.
An SDF mapping wizard will open that will allow allocating the SDF attributes correctly to existing or new data fields in the compounds collection.
Compounds can be added to the compounds collection via the Compound and Reaction elements in the ELN.
Every compound added (drawn or uploaded via file) to the compound and/or reaction element will be added to the compound collection.
To learn more about the compound and reaction element in experiments click here.