Understanding Synonymy in Specify 7
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Synonymy is supported in all Specify trees, and the fundamental logic is consistent across all of them. This document specifically focuses on synonymy using taxonomic examples and describes its interaction with determination.
In museum collections and taxonomy, scientific names for organisms change over time. A name that was once considered valid may be superseded by another, becoming a synonym. Specify provides tools within the Taxon Tree to manage these relationships, ensuring that historical data is preserved while current records reflect the most up-to-date taxonomic understanding.
How Synonymy is Represented in Specify
When a taxon is treated as a synonym for another, Specify stores this relationship in two key ways: visually in the Taxon Tree and functionally within data forms.
In the Taxon Tree:
- Color Coding: A synonymized taxon node is displayed in a different color to distinguish it from accepted taxa. By default, this color is red, but it can be customized in User Preferences.
- Tooltip Information: When you hover your mouse over a synonymized node, a tooltip will appear that shows the accepted name it points to.
In Data Forms (Determinations):
The primary impact of synonymy is seen in the Determinations table, which links a Collection Object to a taxon. This table uses two fields to manage synonymy:
- Taxon: This field always stores the taxon name that was originally assigned to the specimen.
- Preferred Taxon: This field stores the currently accepted name for the taxon.
When a taxon is not a synonym, the Taxon and Preferred Taxon fields will contain the same name. However, if that taxon is later synonymized, the Taxon field remains unchanged, preserving the historical determination, while the Preferred Taxon field is updated to the new, accepted name. This ensures that data searches and reports can be run against the currently accepted taxonomy without losing the original data entry context.
How to Synonymize a Taxon
The synonymization process establishes a directional link from an unaccepted name to an accepted one.
- Navigate to the Taxon Tree by clicking the Trees icon in the main navigation bar.
- Select the node you wish to make the synonym (the unaccepted name).
- Click the
Synonymize icon in the toolbar. - Select the second node, which will be the accepted (or target) name.
- A confirmation dialog will appear. Click OK to complete the action.
The first node selected will now appear in red (by default) and will be treated as a synonym of the second node.
Rules and Restrictions for Synonymy
To maintain data integrity, Specify enforces several rules by default:
- Parent Nodes with Children: A taxon that has child nodes cannot be synonymized. You must first move or reassign its children to the new accepted taxon before you can synonymize the parent.
- Adding Children to Synonyms: You cannot add a child node to a taxon that is already a synonym of another name. New taxa must be added under an accepted parent.
- Rank Restrictions: Nodes at a rank higher than species (e.g., Genus, Family) can only be synonymized with other nodes of the same rank. Nodes at the species level or below can be synonymized more flexibly within and between ranks.
- Deletion: A taxon cannot be deleted if it is designated as the preferred name for a synonym.
Undoing a Synonymy
If a synonymy was made in error, you can undo it by selecting the synonymized (red) node and clicking the 
Undo Synonymy icon in the toolbar.
Synonymy vs. Merge
It is important to distinguish between synonymizing and merging nodes:
- Synonymize: Creates a taxonomic relationship. Both the synonym and the accepted taxon nodes remain in the tree, but one points to the other as the preferred name. This is used for taxonomic revisions.
Merge: Combines two duplicate nodes and their children into a single, correct node. The unwanted source node is deleted after its children are moved to the target node. This is used to correct data entry errors.
Advanced Configuration
For institutions that require more flexibility, the default restrictions on synonymizing nodes with children can be disabled for an entire database. Instructions for enabling this feature can be found in the guide: Enable Creating Children for Synonymized Nodes.
Downstream Synonymy
Synonymy does not cascade down the tree, meaning Specify does not automatically cascade synonymy from a genus to its species. When a genus is synonymized, it doesn’t always mean that all its child species transfer directly with the same specific epithet. For instance, Craginaster completa might become a synonym of a completely different species under Pseudananchys, not necessarily Pseudananchys completa. To maintain taxonomic accuracy, curators are required to handle each child taxon individually to ensure each synonymization is explicit and correct.