Taxonomy

Overview

The taxonomic model in Arctos is designed to provide both a controlled table to reduce errors and the flexibility to accommodate each collection’s preferred taxonomic structure and ongoing changes in taxonomic classifications.

“Taxonomy” for the purposes of this document and Arctos in general is “some formal naming system.” Arctos taxonomy is not necessarily hierarchical, it is not limited to biological taxonomies, we follow no organization or committee guidelines, and we make no distinction between taxonomy and nomenclature. We offer no judgements or guidelines regarding acceptability; if all or part of a system of names (and optionally metadata regarding those names) is accepted or endorsed by some user group, it’s acceptable for Arctos. If publication “A new species of critter” declares, however informally, that “Some critter” is a distinct “species” (in the loosest possible sense of the word), then “Some critter” may be a useful taxon in Arctos.

If another publication declares “Some critterrrr” is not a valid taxon, biological distinction, etc., then “Some critterrrr” may still be a useful taxon name to include in Arctos for discovery purposes, even though it’s an obvious misspelling of a name. In short, if a name might be useful in discovering specimens, it should be included in Arctos. Remarks, annotated taxon relationships, taxon status and links to publications should be used to clarify.

Arctos taxonomy consists of two tables:

Informal terms, such as “Sorex sp.” or “Sorex cinereus or Sorex ugyunak” are identifications, not taxonomy. Identifications are, however, generally drawn from and linked to taxonomy in various ways.

Taxon Name

Taxon names are intended to be a formal taxonomic authority and should all be drawn from relevant taxonomic publications. A name is not linked to any particular classification (rather, classifications are linked to taxon names) and may be a homonym or hemihomonym. The name “Diptera” correctly includes classifications for flies and plants, and the taxon has both an Arctos and an Arctos Plants classification. This is not a mistake and should not be “corrected” to any particular point of view. Another example is Ficus gracilis which is both a plant and an animal taxon. Adding the author as non-classification data can ensure that the correct term is selected by users.

Taxon names may be disambiguated at the specimen level via identification publications (“ID sensu”), and at the collection level by choosing and curating a classification. Database rules prevent change of used names. Names may be higher taxon terms, such as “Animalia,” ICZN-type genus-species-subspecies concatenations, ICBN-type genus-species-infraspecific rank-infraspecific epithet concatenations, or nonbiological taxonomy terms (“Granite”). The sole distinguishing feature of this field is that a curator, usually a taxonomist, considers the name to be formal taxonomy.

While single classifications may be hierarchical, taxonomy as a body of  literature is anything but: Most names have a long history of “current family, according to….”, for example, and many refer to multiple concepts, such as plants and animals.

Arctos users with taxonomic authority may create, edit and delete taxonomic names and classifications. Complete instructions are given in the How-to Section of the Handbook.

Name Type

Taxon Names are typed using ttaxon_name_type. Name type is functional; different types of names have different rules and may be used for different purposes. Note that many homonyms exist, so this classification is somewhat arbitrary. For example, “Oar” may refer to a device used to propel a watercraft or a genus of Lepidopteran.

Validation Service

Arctos checks taxon names against various services on creation and edit. This check is a tool, not an authority; all services have significant problems as of this writing. “Valid” names will occasionally be flagged as invalid, and erroneous names will occasionally pass. One of the services contains data from Arctos, so the check is a bit circular. Users remain fully responsible for the content of Arctos taxonomy.

Taxon Term

Taxon Term contains metadata regarding taxon names and a system for organizing such data. Every term may be arranged hierarchically within a classification, and hierarchical terms may optionally be ranked. Terms are further divided as:


Screen Shot 2019-04-13 at 10 15 54 AM ______

Hierarchical Classification Terms

Terms which are organized hierarchically are “classification data” intended to be part of a classification system. These terms may be ranked or unranked but unranked terms may make it difficult for users to find your specimens. Here is the classification for the mollusk Ficus gracilis. _________

Screen Shot 2019-04-13 at 9 30 35 AM _________

Classification Metadata

These are terms which are not part of the classification but clarify and augment the taxon classification. There are currently eight Metadata Term Types which may be completed.

nomenclatural_code is controlled by the code table. Most common values are “ICZN” and “ICNB.” This is a mandatory field.
author_text is the author of ICZN names, or the species author of ICBN names. Always include the author (with or without parenthensis as appropriate) unless no author is given.
infraspecific_author is the author of the infraspecific epithet in ICBN names
taxon-status is controlled by a code table.
source_authority should list the publication, website or other authority for the taxon.
remark is an open field for any comment that will be helpful to Arctos users.
aphiaid is the taxon identification assigned by the World Register of Marine Species
preferred name is completed for “invalid” taxa to identify the synonym that is the valid taxon name. This is especially helpful when there are multiple synonyms listed.

The Display Name and Scientific Name are autogenerated by Arctos. ______

Screen Shot 2019-08-05 at 10 30 08 AM ______

Common Names

Common Names are intended to help users find what they are looking for, and not to propagate any standard or system. A taxon may have several common names, in several languages and using several types of characters, or nothing. 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”).

Common Names are added to the taxon record as classification metadata.

Taxon Relations

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. ______

Screen Shot 2019-04-13 at 9 45 24 AM ______

The taxon status is used to clarify which synonym is preferred by entering “valid” for the accepted or preferred name and “invalid” for the unaccepted name.

Taxon Relation Authority

Taxon Relation Authority is an open text field, and it may be null. Presumably the 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 should have the Taxon Status of “valid.” The other synonyms should have the Taxon Status “invalid.”

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.

Publications

Taxon names may be linked to any number of Publications. These publications should directly support the name.

Taxon Classification Sources

There are several local sources of taxonomic data that can be used by a collection for specimen identification. Each collection selects any number of sources and specifies an order of preference; the classification(s) from the first encountered source with relevant data are used in their records for specimen identification. Taxon names and classifications of “Local” sources are added, deleted and modified via Arctos. A controlled vocabulary is required for local data.

Collections may elect to use an independent taxonomic database that suits their specimens. They remain responsible to curate the taxa.

Through GlobalNames webservice, Arctos users can access multiple remote classifications for taxa. These are automatically maintained and cannot be edited by Arctos users. They are provided as a resource and Arctos users frequently clone them into the local source used by the collection. Arctos users may wish to collaborate with the remote sources to edit taxa before they are pushed to GlobalNames and then to Arctos.

Usage of Sources

Taxonomy in general does not scale well; there are very many homonyms (intra-Code shared names; “Echidna” may refer to mammals, reptiles, fish, etc.) and hemihomonyms (cross-Code shared names; Adesmia muricata is a beetle and a legume). These are simply ignored in many taxonomy resources, but this situation is not possible in Arctos which may for example hold type material for both Echidna-the-mammal and Echidna-the-eel. We recommend taxonomy be managed at about the same scales as which it’s created, and the ability of a collection to prefer multiple Sources provides a mechanism by which to do so. This approach also provides a mechanism by which taxonomists may curate only those names which are of special importance to them, and share those with other collections. For example, if:

then all three collections might prefer

  1. Shrews by UserA
  2. Bats of North America (UserB)
  3. Arctos (a legacy ICZN-centric mess of ~1.8 million inconsistently-classified names)

and for those collections, a shrew would draw classification data from Shrews by UserA, a bat would draw from Bats of North America (UserB), and a moose would fall back to Arctos for classification data.

Shrews by UserA might be managed in local software and periodically exported to Arctos, Bats of North America (UserB) might be managed in a specialized part of Arctos (eg, the hierarchical editor), and Arctos is managed by many users via the Arctos single-record classification editor.

If CollectionD, who has their own shrew expert who doesn’t entirely agree with UserA, comes along, they can simply manage the conflicting data (perhaps a single genus) in “Myosorex by CollectionD” using the tool of their choice, and prefer

  1. Myosorex by CollectionD
  2. Shrews by UserA
  3. Bats of North America (UserB)
  4. Arctos

which will result in a Myosorex drawing from Myosorex by CollectionD, a Sorex drawing from Shrews by UserA, a bat from Bats of North America (UserB), and so on.

Managing Sources

Arctos taxonomy may be managed in about any tool, but “saves” will ultimately need to go through one of three pathways.

  1. The built-in “single record edit screen” may be used to alter any aspect of a single classification. The Arctos data model - and therefore the tool built directly upon it - are not interested in consistency, but rather in being capable of losslessly accepting any data which might be considered “taxonomy.” It is near-inevitable that edits using this tool will produce increasingly inconsistent data. This may be a valuable trait when managing particularly heterogeneous data, but is best avoided when consistency between records (e.g., if all Canis should be children of Canidae) is desirable.

  2. The classification bulkloader is essentially a “flat” file format, but tools which write to it need not be entirely flat. (The Arctos hierarchical tools ultimately converts to this format, for example.) Most (perhaps all) checklists or exports from tools should be capable of being munged into this format. This makes it possible to manage taxonomy in a desktop tool (including something as simple as a spreadsheet) and periodically save to a Source in Arctos, or to push products of virtually any tool to an Arctos source.

  3. The hierarchical classification bulkloader is a parent-child file format, into which most hierarchical data should be transformable. The built-in hierarchical taxonomy editor can import from and export to this format, and using this format rather than the flatter CSV option in eg, spreadsheets greatly reduces the possibility of introducing inconsistencies.

Examples of model taxa

The taxonomic model in Arctos conveys more than just the classification of each taxon. As displayed in the examples below, each taxon entry integrates media and the geolocation of specimens in Arctos identified with that taxon name. This can be a highly useful tool for researchers and the general public. Here are links to various taxa that show these features.

https://arctos.database.museum/name/Canis%20lupus
http://arctos.database.museum/name/Amazona%20amazonica
http://arctos.database.museum/name/Chamaesaracha%20sordida
http://arctos.database.museum/name/Thera%20otisi https://arctos.database.museum/name/Achatinella%20lorata
http://arctos.database.museum/name/Mus%20musculus

Taxonomic Concepts

Despite their ubiquitous use in biology, taxonomic names on their own can be ambiguous identifiers for communicating the taxonomic concept intended by a taxonomist, where “taxonomic concept” refers to an understanding of the range of variation in a taxon, and its boundaries, i.e., a taxon’s circumscription. As taxa are revised, and sometimes merged with or split from other taxa, the circumscription associated with an unchanging type specimen’s name may change greatly. In order to overcome this ambiguity, it is recommended that the usage of a name is always specified: name X according to publication Y; this is the ‘taxon concept’ of biodiversity informatics (Franz, N., Peet, R. K., and Weakley, A. 2008. On the use of taxonomic concepts in support of biodiversity research and taxonomy. In The New Taxonomy ed. Q. D. Wheeler).

Since 2020, the Arctos data model allows for i) associating taxon concepts with names, ii) mapping taxon concepts to other taxon concepts (using terms from set theory), and iii) giving a taxonomic concept in an identification as well as just a name.

Managing taxon concepts

To create a concept:

  1. First make sure the publication that is the ‘according to’ for a taxon concept exists in Arctos,
  2. In a taxonomy page for a name, click on [Manage Concepts],
  3. Enter the author’s name and hit RETURN, and choose from the available publications in the pop-up window,
  4. Enter the taxon author as used in the publication (e.g., “L.”),
  5. Click the generate label button, to automatically create a taxon concept label of the form <i>name</i> author <i>sensu</i> ref,
  6. Click the create taxon concept button to accept the label and create the concept linking a name with a publication.

(Delete and recreate a taxon concept to edit it)

To create a mapping between two concepts:

  1. In the same [Manage Concepts] page, find the concept_label for the concept you want to map,
  2. Pick the publication that documents this mapping,
  3. Choose the RCC-5 set mapping relationship,
  4. Pick the concept label for the other taxon concept,
  5. Hit create.

(Delete and recreate a taxon concept mapping to edit it)

Editors

Built-in single-record editor

The single-record editor has limited control of data within a record, and no control of consistency across records. We do not recommend using this tool if those attributes are important.

Built-in hierarchical editor

Arctos provides a hierarchical editor which is capable of producing consistent data. Import and export tools are built into Arctos.

CSV

Arctos provides a full-features CSV upload option. Data may be managed in anything which will export CSV, and that CSV may be imported into Arctos.

FAQ

Q: Why not hierarchies/thesauri/some other model?

A: The taxonomy model is primarily designed for flexibility, an idea somewhat incompatible with more-structured data. This model is designed to work with changes, uncertainty, unranked terms, and even nonbiological taxonomies, and to communicate with services such as globalnames.

Q: Why does the editing interface not ….. ?

A: The editing interfaces are designed to get us by until someone does a better job, and are a reflection of the model in being very generic (and therefore also very limited and scary in terms of multi-record updates). We hope that most taxonomy will eventually be managed in remote, limited-scope applications (that is, applications that do not have to worry about historical names and homonyms and all the other reality that is taxonomy at the scale of Arctos) rather than in Arctos (which can now leverage any number of those services to compile a complete picture).

Q: How does the model assert “acceptedness”?

A: All names exist because someone with the proper credentials loaded them, and presumably because there exists “appropriate” (a term which varies by discipline, tradition, and time) literature creating or supporting them. Collections choose a classification, which asserts “classification according to this collection.” Many classifications are historic and no longer accepted but may be helpful in searching for specimens. They should be marked “invalid” and linked to the currently valid taxon.

For further instructions, consult the following “How to” documents.