Nomenclature in Species+

The Simplified Entity Relationship Diagram can be accessed to provide clarity and aid in the understanding of the descriptions below.

Taxon concepts

The basic entity that underpins the Species+ database is a "taxon concept". A taxon concept is a unique combination of a scientific name and its corresponding author/year. Each taxon concept has an automatically generated unique numeric identifier and a “rank” property, indicating its place in the taxonomic hierarchy. "Ranks" include: kingdom, phylum, class, order, family, subfamily, species, subspecies, and variety.

Accepted names vs synonyms

Another property of a taxon concept is its name status. This property is used to differentiate between accepted names and synonyms. Both accepted names and synonyms are types of taxon concepts, uniquely identified by a numeric ID.

Accepted names have a "parent" property, whereby they can be arranged in a taxonomic tree. Synonyms do not require a parent property to be defined; they are linked to the taxonomic tree by means of a synonymy relationship, whereby a given accepted name can have several synonyms and a synonym can be linked to several accepted names.

Permanent identifiers

The numeric identifiers of taxon concepts are permanent and represent the same scientific name and author/year combination at all times. It is possible for a taxon concept to undergo certain changes, such higher taxonomy changes (e.g. relocation to a different family) or name status changes (e.g. promoting a synonym to an accepted name). Yet, its identifier will remain the same.

Other data entities

The following entities are in place:

• Common names
  Multilingual. Some languages have better coverage than others.
• Distributions
  Geographical occurrence of a taxon concept, at the level of countries and territories. Additional information on distribution status (e.g. extinct, uncertain) is included.
• Distribution references
  Publications on which distribution information is based.
• Taxon concept references
  Publications describing the taxon concept, with indication of whether they are CITES standard nomenclature references.
• CITES listings
  CITES Appendix listings and reservations, both current and historic.
• CITES quotas
  Both current and historic.
• CITES suspensions
  Both current and historic.
• EU annexes
  Both current and historic.
• EU suspensions
  Both current and historic.
• EU opinions
  Both current and historic.

Changes to taxon concepts tree

Taxon concepts might be subject to a number of nomenclature changes, such as splits (i.e. one taxon concept splitting into two or more taxon concepts) lumps (i.e. two or more taxon concepts lumping into one taxon concept) or name status swap (i.e. a synonym becoming an accepted name, or vice versa).The taxon concept, name status and unique identifier considerations outlined above are at the core of the nomenclature changes management process in Species+. The example below illustrates the expected effects that a split will have on the underlying structure.

Example: Elevation of the subspecies Antilocapra americana mexicana to species level, resulting in Antilocapra americana splitting into two taxa: Antilocapra americana and Antilocapra mexicana.

Effects on taxon concepts:

• No changes to the name status or higher taxonomy for Antilocapra americana. The species may, however, undergo changes of distribution and list of synonyms and descendents and a "nomenclature note" would be added to this species to indicate that a split took place.
• A new taxon concept, Antilocapra mexicana, is created. As this scientific name did not previously exist, a new unique identifier would be created.
• The taxon concept Antilocapra americana mexicana (representing the subspecies being elevated as part of the split) undergoes changes to its name status, as it changes from an accepted name to a synonym of the newly created species Antilocapra mexicana. It maintains its original unique identifier. By becoming a synonym, A. a. mexicana would no longer be associated with a "parent" taxon and its only connection to the taxonomic tree is as a synonym.

Effects on associated data entities:

The split may require that some information, such as common names, distribution, legislation, etc, would need to be copied or transferred from Antilocapra americana to Antilocapra mexicana. For example, historic CITES listing information might need to be copied over to the newly created species, whereas distribution information might be divided between the two newly split species according to the range of the new taxa. This transfer of data is carried out by UNEP-WCMC at the time of the nomenclature updates.

Consequences for the API

Nomenclature changes typically involve a large number of operations and a formal representation of the different types of changes is not straightforward. The API does not aim to expose that formal representation or the log of all changes performed as that would require API consumers to build complex logic around parsing and processing particular steps, and the integration would be susceptible to adjustments in the way nomenclature changes are handled.

Instead, the API exposes the current state of data with enough information to detect changes to relevant structures in the destination system. Because all operations that affect a particular taxon concept automatically update the timestamp of the last modification, API consumers will know which taxa were changed by fetching the list of taxa changed since the last run of the synchronisation mechanism. The assumption is that API consumers will store the Species+ identifier in their systems. With that in place, new taxa can be detected by the fact that a given identifier is not present in the destination database and changes to the taxonomic tree can be detected by comparing the parent property.