Taxonomy

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Taxonomy is the formal hierarchical naming system applied to biological organisms. In this database, each taxon that might be used in a determination is stored in its own row with its own hierarchy. This structure was created in anticipation of a more robust structure, hopefully implemented as an external webservice. Despite tremendous funding, no such services exist so we continue with our table and some SQL code.

The names in the taxonomy table are therefore intended to be a formal taxonomic authority. Constructions from formal names, such as interspecific hybrids, or vague determinations (e.g., “Sorex sp.”) are not admissible. Such determinations are constructed outside of the taxonomy table.  Here we have formal names; elsewhere we have determinations.

Scientific Name is a machine-generated field, usually a concatenation of the three values for genus, species, and subspecies (subspecies is often null). For plants, three-part Scientific Names include the Infraspecific Rank between species and “subspecies.” To designate less explicit determinations such, as identification to family, Scientific Name is the most explicit taxon in the record.  The examples below (using truncated higher taxonomy) demonstrate this principle:

Family	Genus	Species	Subspecies	Scientific Name
Canidae	Canis	lupus	ligoni	Canis lupus ligoni
Canidae	Canis	lupus	{null}	Canis lupus
Canidae	Canis	{null}	{null}	Canis
Canidae	{null}	{null}	{null}	Canidae

An exception to this pattern are records including a designation of subgenus.  Subgenera are displayed only in the absence of a value for species, i.e., subgenus is the most specific value.  (Undisplayed subgenera still enable querying by subgenus.)

Family	Genus	Subgenus	Species	Scientific Name
Canidae	Canis	Canis	lupus	Canis lupus
Canidae	Canis	Canis	{null}	Canis (Canis)

Display Name is Scientific Name plus Code-compliant HTML markup and includes author strings.

Infraspecific Ranks are categories of description below the level of species. In zoology, subspecies is the only infraspecific rank generally used. In botany, “variety” (var.) and “forma” (fo.) are used in addition to subspecies (subsp.). This field should always be null in zoological records, and it should always be used in three-part botanical names.  There is a controlled vocabulary.

• Salix polaris subsp. pseudopolaris
• Trichophorum pumilum var. Rollandii

Author Text
is the name of the author(s) of the scientific name, and sometimes the year of publication, as it appears following the name. Infraspecific Author serves the same purpose for infraspecific names. Some examples:

• Balaena mysticetus Linnaeus, 1758
• Sibbaldus musculus (Linnaeus, 1758)
• Salix glauca L.
• Trichophorum pumilum (M. Vahl) Schinz & Thell
• Trichophorum pumilum (Vahl) Thell. var. rollandii (Fernald) Hulten

The format follows different conventions in botany and zoology, but the presence or absence of parenthesis, is important and should be as it appears in the Source Authority for the record. Botanical names often use the Kew Abbreviation of the author’s name.

Taxon Status is an optional description of the formal disposition of a taxonomic name.  There is a controlled vocabulary.

Nomenclatural Code refers to the formal standards that govern the format and priority of a name.  The two most established codes are the International Code of Zoological Nomenclature (ICZN) and the International Code for Botanical Nomenclature (ICBN).  Within Arctos, the value for Nomenclautural Code function to control how names are formatted and how they may be entered. Vocabulary is controlled by a Code Table.

Named Hybrids are single botanical names that have been applied to interspecific hybrids. For example, the hybrid offspring of sedges Carex limosa and Carex salina has been named Carex ×limosoides J.Cay. (This is distinct from a hybrid determination, which would be constructed with two names; e.g., “Carex limosa X Carex salina.”) The conventions “x_limosoides” “X_limosoides” are frequently seen. In fact, the character is not a conventional X, but rather the mathematical times sign, and the Taxonomy Editing screen is equipped to insert this character into the Species field. Named Hybrids should have the relationship “hybrid offspring of” to each of the parental species.

Higher Taxonomy is handled by having higher taxonomic categories in each record (row). These include Kingdom, Phylum, Class, Subclass, Order, Suborder, Family, Subfamily, and Tribe. Classes are defined and controlled in a code table. Subgenus is also available but rarely used. Each record should include Kingdom, Phylum, Class, Order, and Family except where an inexplicit determination such as “Carnivora” precludes the use of lower taxa. Use Suborder, Subfamily, and Tribe only where you can provide this information in all records for the respective Orders, Families, or Subfamilies. In other words, do not put in the Subfamily unless you do so for all records of that Family.

Development of more than the minimal data described above might best await an adequate shared web service.

Full Taxon Name is a concatenation of all values from Higher Taxonomy plus Genus, Species and Subspecies. This value is machine generated, and used for broad searches where the user may not know the taxonomic rank of a search term.

Common Names are intended to help users find what they are looking for, and not to propagate any exclusive standard. A taxon may have several common names, in several languages and using several types of characters, and they can all be included. The same common name may apply to more than one taxon. For example, the term “common shrew” has been published for Sorex cinereus in North America and for Sorex araneus in Europe. Common names have not been capitalized except when they draw on a particular standard such as that of the American Ornithological Union (AOU Checklist).  Adjectival forms of proper names are capitalized (e.g., “Alaska marmot”).

Source Authority gives a source for the “scientific-name” parts of a taxonomic record. (The authority does not necessarily apply to the higher taxonomy included in the record.) These authorities are mostly general taxonomic treatments broad scope. Many, such as “UAM,” “MVZ,” or “MSB,” are legacy data from those institutions. So far, the most explicit value for this field is “original description,” which is intended to mean that the person creating record got it from the original description of the taxon which should be referred to in the Author Text field.

Valid Catalog Term flag is a toggle that controls the acceptability of a taxon for use in new determinations.  If the taxon is currently considered scientifically acceptable, then the value should be “yes.”  If the taxon is an invalid synonym for another name, the value should be “no.”  This flag prevents invalid names from being entered as new determinations.  Invalid scientific names are available in Arctos for use in historic determinations and for use where the specimen has been cited in literature.  Ideally, “invalid” taxa should have a relationship to a valid taxon.

Taxon Relations are comprised of a relationship type, a related taxon, and an authority for the relationship. The related taxon is another record in the taxonomy table.

Relationship Authority is an open text field, and it may be null. Presumably the Source Authority for an accepted taxon is adequate documentation, but if not, then Relationship Authority could cite a publication or the name of an expert to whom the relationship is attributed.

Most Taxon Relations represent synonymy among taxa. As evolutionary relationships and nomenclature are revisited, changes in taxonomy are suggested, and either accepted or rejected. Which changes are accepted, and by whom, is a routine issue. Therefore, keeping track of synonomy in the database can be important to users. If they cannot find material they are seeking under one name, they may find the name that they are using and its accepted synonym, or they may use a query which returns records from unaccepted synonyms.

Any number of taxa may be synonymous, but only one of these should have the value “accepted synonym of,” and it should have this value for each of its synonyms. Accepted synonyms should have a Valid Catalog Term flag of “yes.” The other synonyms should have the value “synonym of,” for each synonym, and their Valid Catalog Term flag should be “no.”

Named hybrids have a unique relationship to their parent taxa, and this is expressed by “hybrid offspring of.” Each named hybrid should have two such relationships.

Taxon relations may also represent hierarchical relationships between taxa. So far, this is included only for the purpose of constructing botanical trinomens with author text for both the species and the infraspecific category. For example, Trichophorum pumilum (M. Vahl) Schinz & Thell var.Rollandii (Fern.) Hult. would be constructed from the “parent” binomen, Trichophorum pumilum (M. Vahl) Schinz & Thell plus the infraspecific rank, “subspecies,” and author text from the “child” trinomen, Trichophorum pumilum var. Rollandii (Fern.) Hult.

Taxonomy Rules: A complicated set of rules about how names may be created or updated exist in the form of a programmed trigger. This documentation is intended as a readable summary. Actual rules are in the Arctos code repository. These rules attempts to reflect standards created by the various taxonomic organizations.

• Terms of rank tribe and above must be Proper Case A-Z strings.
• Where nomenclatural_code is ICBN
  • Genus must be Proper Case, but may start with a multiplication sign and contain a dash.
  • Species must be lowercase letters, but may start with a multiplication sign and contain a dash.
  • Subspecies (the field name, not necessarily the infraspecific rank) must be lowercase letters, but may start with a multiplication sign and contain a dash.
• Where nomenclatural_code is ICZN
  • Genus must be Proper Case.
  • Species must be lowercase letters, except the second character may be a hyphen.
  • Subspecies must be lowercase letters, except the second character may be a hyphen.
  • Infraspecific Rank may not be given.
• Records with Genus must have Family to be Accepted.
• Records with Family must have Order to be Accepted.
• Records with Order must have Class to be Accepted
• Records with Class must have Phylum to be Accepted.
• Records with Phylum must have Kingdom to be Accepted.
• Records with Nomenclatural Code of “noncompliant” do not have to adhere to most of these rules.
• Records with Nomenclatural Code values of  “noncompliant” or “unknown” must have their Valid Catalog Term set to “no.”