Taxonomy

SCAN Taxonomy Recommended Practices - Updated July, 2013

 

Compiled by Nico M. Franz, Arizona State University (http://franz.lab.asu.edu/contact.html)

 

1. Overview and Disclaimer

This page introduces conventions for handling the SCAN Taxonomy, with particular emphasis on collaborative day-to-day management of valid names, synonyms, and classification rearrangements. At present we will limit the topics to taxomomy management within the Symbiota software platform. At a later stage we will also treat remote taxonomy and identification functions provided by the Filtered Push system.  You must be registered with SCAN and have editorial priviledges (see below) in order to see the screens referenced in this guide.

Disclaimer - Symbiota is an evolving software, which means that the specific look of the herein displayed screenshots (taken in July, 2013) may soon become outdated. Hopefully the underlying content and practices will remain stable. Please send comments regarding errors and improvements to Nico Franz (contact information above).

2. Taxonomy / Specimen Interaction

Symbiota maintains two separate yet interacting "trunks" for managing (1) taxonomy and (2) specimens. The overlap occurs primarily in the Edit Existing Occurrence Records interface, under the Latest Identification field. This field is linked to the Taxonomic Thesaurus, with the following important implications:

1. If the Scientific Name for a newly entered specimen (record) is present in the Taxonomic Thesaurus (as is the case here for Artipus floridanus), then Symbiota will auto-locate this name in the Thesaurus as the initial letters are typed (red rectangle), and auto-complete the Author name and year (Horn, 1876) and Family name (Curculionidae) once the cursor is moved to the Author field (green rectangle). By "activating" the record-to-Thesaurus link we can subsequently search for the record making full use of the hierarchical and synonymy information stored in the Taxonomic Thesaurus.

2. If the name for a newly entered specimen is not present in the Thesaurus, then we will not have the aforementioned search capabilities. This is also true for batch-imported records that still require proper linkage between the record's name and the Thesaurus' name. Two options remain: (1) to proceed with a name that is not contained in the Thesaurus (a corresponding warning message will appear, though the entry remains acceptable), or (2) to navigate to the Thesaurus and add/edit the new name properly, and prior to completing the specimen record entry. The second option is strongly preferred.

3. History and Current State

The initial SCAN Taxonomy was imported in March, 2012, via ITIS. This was a pragmatic choice - the input taxonomy was known to by incomplete and/or outdated, but was readily available in a hierarchical format facilitating batch import. This way nobody had to manually names such as Hexapoda, Insecta, Pterygota, etc.

Implication - the Taxonomic Thesaurus is slightly to profoundly incomplete or outdated, even for many North American arthropod taxa! This partly is a reflection of "where we are" in terms of providing comprehensive classifications for arthropods in a structured digital format. The Thesaurus therefore requires constant and collaborative curation by SCAN members.

4. Who Can Edit, and How?

As we are still in the developing phase of the Thesaurus, anybody with SCAN login access and pertinent interests and/or tasks (as assigned by their home collection) can assume the role of a SCAN Taxonomy Editor. This role requires a separate permission, granted by a Super Administrator. If you would like to acquire this permission please e-mail Nico Franz (contact information above). Our stated objective up to this point is to maintain a single Thesaurus; however other Symbiota portals such as SEINet maintain multiple alternative taxonomies.

Note - in the near future SCAN members can be assigned taxon-specific editing rights and responsibilities. A log of expert edits in the Thesaurus is also desirable (similar to the collection management edits log).


5. Navigating the Taxonomic Tree Viewer

The Taxonomic Tree Viewer is the main interface for navigating and editing the Thesaurus. It can be accessed via Sitemap: Taxonomy. Any entry into the hierarchy of the Thesaurus starts with searching for, and then selecting, a particular name in the "intelligent" search window (in this case: "Artipus"). Species epithets ("floridanus") and not yet entered names ("Belus") will produce no match.

Once a name is selected, together with Display Taxon Tree, the corresponding Thesaurus hierarchy above and below the chosen rank will appear, as follows:


6. Adding and Editing Names

Clicking on a specific name will produce a more detailed panel with (1) an Editor window and (2) a Taxonomic Status window. The former summarizes information about orthography, authorship, rank, and the source from where this information was taken.

Clicking on the Pen Icon will switch from a summary view to the editing panel where the existing information can be corrected, edited, and the changes confirmed. In this example, a source "O'Brien, C.W., Wibmer, G.J. 1982." was added to indicate a suitable "circumscription" or concept of Artipus Sahlberg. New taxa are added by clicking the green Plus Icon. If a new species and new genus need to be added, then the parent (genus) name must be created first, since no child (species) name can be entered without a parent. Lastly, the green curved Arrow Icon returns to the hierachy.

Note - ideally all names in the Thesaurus have their authors and year specified (in parentheses if not the the original genus/species combination), and separated by a comma. Sources are also desirable; and multiple sources may be used depending on the taxon and hierarchical focus (species level, higher classification). In the near future Symbiota will have a references module to facilitate this process. "ITIS. 2012." is the default (see above) if there is no other source given, though in most cases nothing is filled in under Source.


7. Editing Taxonomic Placement and Nomenclatural Status

The Taxonomic Status window allows viewing and, using the Pen Icon, editing of (1) the hierarchical placement - i.e. specification of the immediate parent - for a taxonomic name, and (2) establishment of synonymies. Each action follows a particular workflow shown here by example.

Assuming that a fully nested and synonymy-rich Thesaurus is desirable for SCAN, the genus name "Mesagroicus" presents at least two problems (both due to the imperfect ITIS source): (1) its Parent Taxon is listed as Curculionidae, when (according to e.g. Alonso-Zarazaga & Lyal, 1999 - a standard reference for the mid-level weevil classification of weevils) the genus should be placed immediately under the tribe Naupactini, in the subfamily Entiminae [in this case the tribe and subfamily names are present in the Thesaurus and need not be entered anew]. (2) Mesagroicus Gistel, 1856, has a junior synonym Lepidocricus Pierce, 1910, that is absent from the Thesaurus' Synonymy list. Both issues are readily resolved.

1. By replacing Mesagroicus' immediate parent with Naupactini (which in turn has its immediate parent listed as Entiminae thanks to a previous edit), we can shift the genus into its proper tribe.

2. Symbiota handles names "by default" as Accepted. [although names can be added anew and immediately listed as synoyms of another valid name] This means that a name is demoted from valid status into synonymy in the following sequence: (1) both names are in the Thesaurus and handled as "Accepted"; (2) the Taxonomic Status window of the the name to be demoted is accessed, and its Synonymy section isedited. (3) There the valid name is entered, and (4) Change Status to Not Accepted is clicked. In our example, Lepidocricus Pierce, 1910, is now a synonym of Mesagroicus Schoenherr, 1840.

Symbiota allows for establishing multiple ("pro parte") synonymy relationships, and naturally a relationship between a valid name and a synonym is reversible.

Once these changes are made, the Thesaurus hierarchy shows Mesagroicus placed in the tribe Naupactini, with Lepidocricus shown in brackets as a junior synonym. Now pertinent specimens of Mesagroicus can be searched via either the terms "Naupactini" or "Lepidocricus", which was not possible previously.


8. Insufficiently Identified Specimens

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