Bulk Upload

Upload is the process of calling the registration service to register a set of compounds automatically based on a predefined configurable set of business rules (validation, standardization, structure checking).

• Supported formats

• Upload options

  • Multi-value input delimiter

  • ID-based fields

• Upload compounds, salts and solvates

The Upload page consists of two main sections, the File uploader and the All uploads.

The Upload page with the recent uploads

An SD file can be dragged and dropped into the File uploader, but you can also browse for files or paste as texts.

Supported formats

The Upload page is designed to simultaneously handle multiple submissions imported from an SD file according to configurable system settings.

The following molecule formats are supported: SDF, SMILES, SMARTS, MRV, CSV.

{info} In the case of SDF files the structure field is mandatory. When the "structure" part is "empty" a No structure registration is triggered. More details can be found at the Uploading No structures.

The structure within the CSV file can be in Chemaxon Extended SMARTS (1), SMARTS (2), Chemaxon Extended SMILES (3), or SMILES (4) format.

{info} Since version 22.19.0 the UTF-8 BOM file encoding is supported.

{info} In the CSV file, the header is mandatory, columns can be comma or semicolon separated. The first column must be the structure column followed by any other fields.

{info} The structure column can contain a valid chemical file format as listed above for registering Single structure, or can be left empty for registering No-structures. At least one field (e.g. Id or additional data) must be mapped prior to initiating the upload process or the upload will fail.

{info} Note that in case of CSV files the system might not automatically recognize the fields, so manual mapping should be made in order to successfully upload the file.

Upload options

You can reach the upload options by clicking on the gear wheel icon on the Upload page.

Multi-value input delimiter

Since version 20.8.0 a multi-value input delimiter can be defined in the Upload options. Field value splitting is supported for both SDF and CSV. If CSV is chosen, CSV delimiter and multi-value delimiter must be different and CSV delimiter must not be contained within multi-value delimiter. The delimiter is chosen for the uploaded file and not per field. ‘Enable multi-value input’ must be true for the given field in order to attempt to split field values.

Upload options icon	Defining a delimiter	Delimiter mapping

ID-based fields

Since version 21.3.0 ‘File contains dictionary item IDs, instead of values’ option can be used in the Upload options.

'File contains dictionary item IDs, instead of values' checkbox

The effect of the 'File contains dictionary item IDs, instead of values' checkbox:

• ID-based fields:

  When this checkbox is ON: File contains dictionary item IDs, instead of values.

  When this checkbox is OFF: File contains values.

• Non-ID-based fields:

  Non-ID-based fields are not affected.

When you use the Append field feature and choose a Value from the drop-down, that id-value pair will be used. You will see the Value on the UI, also when the checkbox is ON or OFF.

Upload compounds, salts and solvates

From the Upload page compounds and salts/solvates can be bulk registered:

• Upload compounds
  • Upload summary page
• Upload salts and solvates