Taxonomy

A specimen in Arctos can be identified to a name, or to a taxonomic concept. The vast majority of identifications in Arctos use names.

Names

Names (scientific_name) are just strings, of the form Genus or Genus species or Genus species inf. infra. In other databases these are known as ‘canonical names’. They have no authors associated with them. Creating them is easy, via the GUI or via a bulk loader.

Note that the taxon_name table uses scientific_name as its primary key.

Taxonomy search options in Arctos

Taxonomic search can be performed:

1. via the Record Search GUI (at https://arctos.database.museum/search.cfm),
2. via ‘Find Records in Arctos with…’ buttons on the Name page (https://arctos.database.museum/name/),
3. via writing a Query string for https://arctos.database.museum/search.cfm?, or
4. (via the SQL interface)

The behavior of options 1-3 (above) is documented below, ordered from more specific searching to less specific:

• Query taxon_name_id=ID&identification_order=1 (via Name page, ‘Used in Identifications’, with added &identification_order=1):
  • Returns all specimens with the current (ID order = 1) identification for a name
• Query taxon_name_id=ID&identification_order=>0 (via Name page, ‘Used in Accepted Identifications’):
  • Returns all specimens with accepted identification (ID order = 1, 2, 3…) for a name
• Query taxon_name_id=ID (via Name page, ‘Used in Identifications’):
  • Returns all specimens with identifications for a name, irrespective of the ID order (including ID order=0, depreciated names)
• Query scientific_name=NAME (via Name page, ‘Used in Identification, less Strict’, or via the Catalog Record Search page):
  • Returns all specimens with identifications for a name, irrespective of the ID order, allowing for partial matches to the name
• Query taxon_name=NAME (via Name page, ‘Used or Related to Used’, or via the Catalog Record Search page):
  • Returns i) all specimens with identifications to a name (any ID order), ii) all specimens identified to a synonym of an accepted name, or iii) all specimens identified to the accepted name of a synonym. Synonymy is determined in two ways:
    • via the name’s Related Names (taxon_relations table) and
    • via the taxonomic hierarchy of a name (taxon_terms table): if a classification for a name in the accepted Source contains a name that is different from the original name, the different name is considered a related name. For example, World Flora Online provides the classification of the accepted name for any synonyms, permitting searching for both accepted name and synonyms.

Entering names into Arctos

The name associated with an identification should be the name on the label, not the synonym of the name (see this issue).

Classifications

For each name there may be several classifications that match the scientific_name; in this context ‘classification’ means a set of non-hierarchical terms (e.g., display_name or author_text) and hierarchical classes (e.g., order, family) for each name. Each classification exists in a ‘source (e.g., ‘Arctos Plants’, ‘WoRMS’). A collection (e.g., UAM:Herb`) ranks the sources that should be used for their classification (in ‘Manage Collection’). At ALA we use three: ‘Arctos Plants’ > ‘WoRMS’ > ‘Arctos’ (a legacy source). If there is no classification for a name in the first source, then the second is searched, and so on. The risk of this fallback is that a name in a secondary source will be a homonym (same name, different meaning), and the family, order and even kingdom may appear incorrect for the specimen. Eventually it will be better to have all names in ‘Arctos Plants’ and deactivate the fallbacks.

Currently (2024-02-29) there are 804 names used in ALA identifications that do not have a classification in these three sources (see SQL, and this issue).

It is not enforced in the database that there is only one classification per source per name, and if there are more, the hierarchical terms get merged, possibly even for homonyms (see this issue). So it is a good idea to make sure that the name usages for ALA have a single classification per source per name (on 2024-02-29 this is true, SQL).

A proposal for a new Classification source

[in progress]

The problem with existing classifications:

• Arctos Plants is an old and very uneven classification (add stats on names with family, etc).
• The new WFO in Arctos comes via Global Names, which gives the classification of the accepted name for a synonym, not the classification of the synonym itself. It also lacks key metadata for the name (display name, etc.). WFO also (appropriately) lists multiple classifications for the same canonical name where different instances (with diff. authors) exits. In Arctos this creates data retrieval and display problems.

A problem with the current taxonomy model in Arctos:

• Arctos only uses canonical names as name objects, so there is no way to distinguish the same name with different authors.
• Arctos also specifies synonymy among canonical names, which again precludes differentiating among synonymies that depend on variations in author string.

A proposed new classification (‘Alaska plants’) will:

• Synonymy: Use the new Flora of Alaska checklist as a rank 1 source for synonymy and accepted status, and use WFO as a rank 2 source.
• Classification: Use WFO as the source of higher taxonomy above genus

• Only have one instance of each canonical name. Where a name exists in FoAK, that will be the full name chosen. For WFO? What strategy? How frequent is this an issue?

  Alnus sinuata a good example

How specimens are searched for:

The code is at https://github.com/ArctosDB/arctos-dev/blob/main/3.2.9/search.cfm

From the taxonomy search page, these are the inputs:

• Exact match to name, identification order = 1: search.cfm?taxon_name_id=
• Exact match to name, identification order = 1 or more: search.cfm?taxon_name_id=...&identification_order=%3E0
• “Used in identification, less strict match”, ?i.e., Exact match to name, any identification order?: search.cfm?scientific_name=...
• Name used or related to used (looking up synonyms): search.cfm?taxon_name=...

Best practice: Add verbatim identification to get the Author string.

Complete transcription: https://arctos.database.museum/guid/UAM:Herb:108266

Update: https://handbook.arctosdb.org/how_to/How_to_Search_for_Specimens_with_Identification_and_Taxonomy.html

Taxonomic concepts

(to follow)