The HELM Monomer Curation App is a tool for managing monomer libraries for the HELM functionality in Signals. Users can bulk upload monomers into libraries, view those libraries and their monomers, and deprecate and restore individual monomers.
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
The HELM Libraries page lists all the monomers available in the selected library. By default, the HELM Libraries page is displayed on the homepage when the HELM Monomer Curation App is launched.
All the monomers available in the selected library are listed in the HELM Libraries page, and for each monomer listed, the following details are displayed:
- Structure
- Symbol
- Polymer Type
- Monomer Type
- Name
- Natural Analog
- Version
- Status
- Library
The first 20 monomers in the library are displayed by default.
Note: All Libraries is specified as the default value in the Libraries dropdown; hence, all monomers available in all the libraries are listed in the HELM Libraries page. The All Libraries dropdown lists the three standard libraries and the custom libraries that were created and activated in Signals.
Note: Custom libraries are available only for users who have specific access rights/privileges to those libraries.
The HELM Monomer Curation app consists of the following three standard 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.
Note: The standard libraries can be viewed but cannot be changed (no monomers can be added, removed, deprecated, or edited).
Reports
The Reports page displays information about the bulk import of monomers. It is displayed by default when bulk import of monomers is initiated. To access the Reports page, select Reports on the Home page of the HELM Monomer Curation app.
The Reports page displays the following information about the bulk 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 of the monomer is created. Once a monomer is added to a custom library, it cannot be deleted. However, you can choose to deprecate the active version of the monomer.
Note: This is an Admin feature, and Admin rights are needed to deprecate an active monomer or to restore a deprecated monomer to Active state.
Monomers cannot be deleted during an editing operation because they may have been used in an editing operation and so may be present in CDXML files. If a CDXML file that contains a deleted monomer is imported into the editor, it is treated as a new monomer. Keeping the deleted monomers guarantees that if the library has ever contained the monomer, the monomer 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.