Benchling's Bioregistry acts as data repository for an organization's biological entities. It is used to track these biological entities through the entire research process and across several groups. Since this data is being shared across several internal groups, it must be kept error-free in order to make sure the most accurate scientific conclusions are made.
This document will go over how Benchling validates your organization's registry to ensure data integrity.
We're launching this update on a rolling basis, so please contact our support team if you would like to us to enable it for you.
Once enabled, you can further leverage our unique constraint feature to ensure unique DNA or AA bases. This ensures you are only registering unique DNA or Amino Acids bases. Further configurations can also check if the metadata (ie. schema links, part links, and etc.) are filled out correctly according to the uniqueness constraints for each schema.
Note: Users can change these "uniqueness constraints" within their organization's registry settings.
Benchling will not allow the import to proceed until these errors are resolved.
After registration, these entities metadata can be occasionally modified by users - potentially by mistake. These errors can cause unseen errors that can affect downstream experiments.
Several things can invalidate a registered entity:
- Editing fields such that two entities contain exactly similar metadata.
- Removing metadata that was initially required for registration.
- Archiving an entity/part that was linked to a required field.
To identify these errors, Benchling will periodically perform validation checks on the registry and will mark and provide information on the invalid entries.
The next section will go over several features that Benchling uses to notifies users that their registry contains invalidated entities.
- A user will receive an email notification if they invalidate an entity by modifying its metadata
- Invalidated entities will have a red "Failed" tag next to it.
- Clicking into the "Failed" entity will provide more information on what is causing the failed validation check and how to fix said errors.
Note: Click into the "?" icon to get more information about the error type.
- Users can screen for invalidated entities by navigating to Benchling's search bar and filtering based on "Validation Status".
- Invalidated entities that are "@-mentioned" will be indicated with a red chip, however it does NOT stop a user from utilizing it - users can still click the chip to get the entity information.
- Invalidated entities can be manually overridden only by registry admins. However all organization members will be able to see that the validation check was overridden.
Note: These checks can be overrode in bulk.
- To resolve uniqueness conflicts, unregister one of the duplicates and re-register it to merge it into the other entity that remained registered.
Example: "Plasmid A" and "Plasmid B" were registered in the Bioregistry, and a user changes one of the fields in the plasmids such that they both had similar metadata. Benchling will invalidate these entities. If a user checks his notes, unregisters Plasmid A, and re-registers it, "Plasmid A" will be merged to "Plasmid B". All notes and linkages associated with "Plasmid A" will be transferred to "Plasmid B".
Note: The entity being merged will also have all of its associated batches transferred to the registered entity with new ID's.