Adding New Taxonomic Names

In Symbiota, if you enter a taxon name that is not present in the taxonomic thesaurus, it will not be indexed in many searches, nor will it count as a species identification for collections statistics purposes.  Entering the name in the data entry form does not automatically add it to the thesaurus (also referred to as taxon tables, taxonomy tables). Nevertheless, we are continuously making an effort to keep the taxonomic names in SCAN up-to-date. Specifically with the LepNet project in mind, we are focused on providing the best taxonomy for Lepidoptera. For most groups of arthropods that occur outside of the United States we have incomplete lists of accepted names and very few groups have synonyms included in the taxonomic thesaurus.  This page provides an update for groups that we have provided additional names from the ITIS Backbone, which is the backbone of our current taxonomy. We periodically harvest names from Catalogue of Life (CoL), but for arthropods there are still many many groups that are not included or updated with full links to synonyms.

We welcome anyone who wants to help complete any part of our taxonomic backbone! To get started, simply send an email to Neil Cobb to get privileges to edit taxonomic tables, then the next time you need to add a name that is not in the table, simply enter the name into the data entry field – there should be a pop-up message prompting the user, asking if they want to add the name to the taxonomic thesaurus. Pretty straightforward – make sure parent taxonomies are entered in the data entry fields, follow the prompts, and the name should be added.

Additionally and more directly, you can either enter a new name directly into the taxonomy tree or enter a list of names through the batch name uploader.

To enter a single taxon name simply go to http://symbiota4.acis.ufl.edu/scan/portal/taxa/admin/taxonomydisplay.php

Click on the green plus sign in the upper right hand corner of the screen. This will bring you to the Add Taxon page.

Fill in the information as needed. Taxon name, authorship, taxon rank (species, genus, etc), parent taxon, locality security status (if the species is endangered and needs locality info hidden), etc. When all the appropriate fields are filled out, click on “Submit New Name”.

Batch Updating Taxonomy in Symbiota

Rather than adding names individually you can batch upload names through the Taxa Upload Form on the  Taxonomic Name Batch Loader page.

The guide below illustrates what is needed for batch taxonomy data uploads, especially with regard to taxonomic synonyms. We emphasize the importance of having the accepted scientific name included your taxonomic data that includes synonymous names. If the accepted name is not present, the synonymous name will be treated as a separate species and not synonymous to any taxa.

  1. Navigate to the Sitemap within your Symbiota Portal. This is typically indicated by a link in the upper-right-hand corner of your screen.
  2. From the sitemap, scroll down to the “Data Management Tools” box – keep in mind that this may not be visible if you lack the appropriate user permissions within your Symbiota Data Portal. You should see an option, under Taxonomy, titled “Batch Upload a Taxonomic Data File”.
  3. From the upload page, you will be prompted to provide a CSV file, preferably compressed in a ZIP archive; this is especially recommended if the CSV file is large (>10MB). While scientific name is the only required field in the CSV, strongly recommended fields include taxon author, family, name of parent taxon name (or hierarchical structure), full accepted name string, full parent name string of next highest parent of each taxon, and name of the taxon rank if taxa higher than species rank are being uploaded.
    1. If the parent taxa is not genus, you need to be explicit with what that parent taxa is.
sciname genus specificEpithet Accepted Name Author Date

 

Apis mellifera Apis mellifera   Linnaeus 1758
Apis mellifica Apis mellifica Apis mellifera Linnaeus 1761
  1. For synonyms, you must create a column with the accepted scientific name; map the data in that column to the acceptedstr field when you do the batch upload. Example above.
    1. If the accepted name field is not present, the synonymous taxa will be treated as a separate species.
  2. After selecting the upload file, it will be necessary to map the input columns to the Symbiota structure. Scientific name, with or without author embedded, must be mapped to “scinameinput”.
  3. Map the data in the columns you provided to the appropriate Symbiota fields. It should be very straightforward. A field containing a genus name will be mapped to the genus field; a field containing the specific epithet will be mapped to specificepithet.
  4. After you have verified your fields are mapped appropriately, you may initiate the loading process. You will be given an opportunity to review your uploaded data before it is committed to the database to ensure its correctness.

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