Learn about the Signals HELM Monomer Curation App

The HELM Monomer Curation app allows the management of monomer libraries for the HELM feature in Signals. The HELM Monomer Curation app enables a curator to view and add monomers to custom libraries and manage their contents.

Detailed reports are provided on bulk import so that users can identify problems with the uploaded monomers. Rules can be applied to control how a monomer is added when duplicates are detected in the destination library.

HELM Libraries page

The HELM Monomer Curation app consists of the following three predefined libraries:

• Natural Monomers – Natural Amino Acids, FASTA OR monomers, and RNA monomers.
• Pistoia Alliance Monomers – Predefined monomers from Pistoia Alliance.
• Signals Monomers – Predefined monomers from Signals.

Notes:

• The All Libraries dropdown is displayed as the default value. It includes both the activated predefined libraries, and any custom libraries created and activated in Signals.

• Custom libraries are available only for users having specific privileges.

• Predefined libraries can be viewed but cannot be changed (no monomers can be added, removed, deprecated, or edited).

The HELM Libraries page lists all monomers available per library. For each monomer the following details are shown:

• Structure
• Symbol
• Polymer Type
• Monomer Type
• Name
• Natural Analog
• Version
• Status
• Library

The first 20 monomers in the library are displayed by default.

Reports page

The Reports page displays information about imported monomers in bulk. It is displayed by default when bulk import of monomers is performed. To access the Reports page, select Reports on the HELM Monomer Curation app.

The Reports page displays the following information about the import:

• Name – Name of the .json file imported.
• Library – Library to which the monomers were imported.
• Date Created – Date of the import.
• Status – Status of the import, which can be:
  • Waiting – Waiting for the import to begin.
  • Importing – Import is in progress.
  • Completed – Import of monomers is successful and complete.
  • Failed – Import of monomers failed and no monomers were imported.
• Duration – Time taken for import process to be completed.
• New Monomers – Number of monomers added to the library for the first time.
• New Versions – Number of new versions of monomers imported. When a monomer already exists in a library, a new version can be created under Duplicate Resolution in the Bulk Import page.
• Failed – Number of monomers that could not be imported.

Versioning and Deprecating

Each time a monomer is imported, a new version is created. Once a monomer has been added to a custom library, it cannot be deleted; however, the curator has the option to deprecate the active version of the monomer.

This functionality is an administrator feature, requiring the appropriate privileges to deprecate an active monomer or to restore a deprecated monomer to an active state.

Monomers cannot be deleted during editing operations because they may have been utilized and may exist within CDXML files. If a CDXML file containing a deleted monomer is imported into the editor, it would be treated as a new monomer. Retaining deleted monomers ensures that if the library has ever included the monomer, it will be recognized in all subsequent imports.

Sorting

Entries in the HELM Libraries page and the Reports page can be sorted based on any field. However, sorting by the Structure field in the HELM Libraries page is not possible. To sort, select the field name. A small arrow on the right side of the field name indicates the sorting order. An upward arrow indicates ascending order, and a downward arrow indicates descending order.