Overview of Arctos taxonomy

(See https://arctosdb.org/documentation/identification/taxonomy/ for an overview of the structure of taxonomy in Arctos, examples of some methods of locating specimens by taxonomy, and the implications of various search fields.)

Choosing a taxonomy source

Collections choose one taxonomy source (under Manage Collection) to represent “specimen taxonomy” (by way of appropriate ranked terms being linked to specimens in table FLAT). While any number of sources are available, they can be categorized into three functional groups. Which group a particular source falls into may depend on the actions of other collections and personal connections to the publishers of the source.

1) Shared local source

These sources are managed locally (through Arctos tools), and used by multiple collections. Changes to the source will need to be coordinated amongst the users. This is the common situation, with most collections using the “Arctos” source, which is derived from the old “band-aid” flat table. This approach allows local collaboration (eg, CollectionA contributes information about TaxonA while simultaneously receiving information about TaxonB from CollectionB).

2) Remote sources

These sources come into Arctos through GlobalNames and cannot be changed locally. Using these sources probably requires a line of communication with the resource, so that new names may be added and updates may be implemented. Despite the multitude of well-funded taxonomy initiatives publishing data to the Internet, no source has yet proven comprehensive and responsive enough for this approach to work.

3) Unshared local sources

These differ from shared local sources only in that other collections do not use them; you must curate the data for all taxonomy that is attached to your specimens, and the changes you make affect only your specimens.

Flat and “collection taxonomy”

When a collection’s preferred source contains for a name one appropriate ranked term, that term is pushed to FLAT as “collection’s taxonomy assertion.” When a collection’s preferred source does not contain a single ranked term – due perhaps to not applying a rank to the term commonly associated with family, or having multiple opinions of family in a classification, or having multiple classifications containing different terms of rank family, or having no classifications, or having no classifications containing a term ranked family – then NULL is saved to FLAT as family; the collection is effectively not asserting family membership for the specimen.

Coming Soon….

We are collaborating with the GlobalNames project to make available a production instance of GNITE, which will allow users to pull in data, modify it in a simple hierarchical structure not plagued by alternate opinions and homonyms, and save the data back to GlobalNames where it becomes available in Arctos. Data sources can come from anything in GlobalNames (including the “Arctos” source), and may be merged, split, and sorted as appropriate. This functionality should be applicable to all categories of taxonomic sources. Several “components” are still missing:

  • GNITE itself
  • Functionality to publish data from GNITE to GlobalNames
  • “Push alerts” from GlobalNames to Arctos, indicating that a classification has been updated and should be pulled into Arctos.
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