Tuesday, July 28, 2015

Modelling taxonomic names in databases

Quick notes on modelling taxonomic names in databases, as part of an ongoing discussion elsewhere about this topic.

Simple model

One model that is widely used (e.g., ITIS, WoRMS) and which is explicit in Darwin Core Archive is something like this:


We have a table for taxa and we don't distinguish between taxa and their names. the taxonomic hierarchy is represented by the parentID field, which points to your parent. If you don't have a (non NULL) value for parentID you are not an accepted taxon (i.e., you are a synonym), and the field acceptedID points to the accepted taxon. Simple, fits in a single database table (or, let's be honest, and Excel spreadsheet).

The tradeoff is that you conflate names and taxa, you can't easily describe name-only relationships (e.g., homonyms, nomenclatural synonyms) without inventing "taxa" for each name.

Separating names and taxa

The next model, which I've drawn rather clunky below as if you were doing this in a relational database, is based on the TDWG LSID vocabularies. One day someone will explain why the biodiversity informatics community basically ignored this work, despite the fact that all the key nomenclators use it.


In this model we separate out names as first-class objects with globally unique identifiers. The taxa table refers to the names table when it mentions a name. Any relationships between names are handled separately from taxa, so we can easily handle things like replacement names for homonyms, basionyms, etc. Not that we can also remove a lot of extraneous stuff from the taxa table. For example, if we decide that Poissonia heterantha is the accepted name for a taxon, we don't need to create taxa for Coursetia heterantha or Tephrosia heterantha, because by definition those names are synonyms of Poissonia heterantha.

The other great advantage of this model is that it enables us to take the work the nomenclators have done straight without having to first shoe-horn it into the Darwin Core format, which assumes that everything is a taxon.