How to use Find the Species

The International Committee on Taxonomy of Viruses website contains several taxonomic resources, one of which is Find the Species tool. 

Which is a tool that provides the current taxon name (species or higher taxonomic rank) for a virus when you enter a full or partial name into the search box.   

It can be located on the home page under “Official Taxonomic Resouces” 

Or by hovering over the taxonomy drop down and selecting “Find the Species” 

After clicking the tab, the website is directed to the Find the species page. At the top you can find the explanation of what Find the Species is. 

Under this, you can find a detailed list of instructions that explain each component of find the species and how it is used. 

Searches can be done by a specific search strategy. These strategies can be found and selected on the left of the search bar with the drop-down arrow. 

They are as follows: “exact match” which finds a species using the exact word or phrase that is entered, “all words” which will find a species that includes all the words of your search in any order, “any words” which finds the species of your search by querying matches that have any mention of any word or phrase of the search. Lastly, “contains” which adds wild cards on both ends of your search to find matches to part of a name. 

The Find the Species tool uses the ICTV Master Species List, the Virus Metadata Resource, and NCBI data base to match searches to ICTV virus taxonomy, exemplar virus information, and name types, respectively. 

In this example we will search for the species name of “The SARS Covid Virus” by its common name “covid” and select “Exact match”  

“Exact Match” outputs results of your query in the order entered that matches exactly to a word or phrase in our virus database but is not case sensitive. 

Searching “covid’ results in one hit to a current ICTV taxa from the 39^th master species list. This hit was matched based off the matching name “COVID-19 virus” from NCBI and severe acute respiratory syndrome related coronavirus as its previous species name. 

When the species name is clicked on Find the Species, the page is redirected to the taxon details page. Which details the entire taxon history of the species, starting with the most recent release of the Master Species List that has the species name that was searched. In this case, that is the 39^th MSL.  

Hits are numbered starting with #1. The official species is presented in bold with a hierarchal taxon starting with family, subfamily, genus, and subgenus.  

The Exemplar virus accession number can be selected to access a complete genome and information about the virus. This link will be redirected to the NCBI website. 

In the next example, Herpes Simplex Virus is searched using the “all words” strategy. All words will only find hits that include every word (in any order) to obtain a match. 

This time matches from the 39^th Master Species List were queried from any mention of “herpes simplex virus” which resulted in 4 different hits to current ICTV taxa. Conversely to the first search, this search found 2 matches from NCBI that had no valid taxon match from ICTV. 

Further on, searching “Herpes Simplex Virus” using the “any words” strategy would return hits including any word present in the query (in any order) to obtain a match. 

Consequently, any mention of “herpes,” “simplex,” or “virus” is returned. Which would explain the 5644 results. The word virus having primary use in the databases returned thousands of results. 

A key difference from the previous examples is that this search returns hits to abolished ICTV taxa that was abolished once new data no longer supported the existence of a particular taxon. 

The final example for this how-to video is the use of the “contains’ strategy that uses your query and adds a wild card character to both ends of your text to look for partial matches. 

This time I will search “immuno” to potentially find the species for the human immunodeficiency virus. As shown, using only a portion of the common name resulted in successfully locating the correct species for both human immunodeficiency viruses. 

If used correctly, Find the species tool could be helpful for locating the current taxon of viruses by a full or partial name in the search bar.