How to use the Taxonomy Browser
Prepared and narrated by Steve Powell, August, 2023
The International Committee on Taxonomy of Viruses website contains several taxonomic resources, one of which is the Taxonomy Browser.
The Taxonomy Browser allows you to search for the current or past taxonomic classification of a given virus species.
To access this feature, click on the Taxonomy Browser link, located on the ICTV website home page.
Next, the taxa representing the most current release, which at the time of this recording is the 2022 release, MSL38, will be listed on the screen.
Also listed are the numbers of each taxon within the release.
Along the top of the screen, you will note the “Taxonomy Search” and the “Taxonomy Browser” help buttons.
The Taxonomy Search help provides information on how to perform a search; whereas the Taxonomy Browser help provides explanations of the meanings of the various symbols that appear in the browser.
Please note that when doing a search, the Taxonomy Browser is only able to search for taxonomic rank names.
In most cases searching for a virus name will produce no results, unless part of the virus name was or is part of a taxonomic rank name.
In addition to the help buttons, there is also a button to download the current MSL.
The “Expand ranks to show” and “Hide ranks above” drop downs, allow you to see or hide the ranks within the various taxa.
As an example, suppose that we want to see the orders within the realms, kingdoms, and classes that are listed.
To do this, select “order” from the “Expand ranks” drop down, and then click the “Go” button.
When we do that, the ranks above that of order will expand down.
If the screen gets too cluttered, you can also hide higher ranks by selecting the rank from the “Hide ranks” drop down and then clicking the “Go” button.
For example, if we select “class”, click the “Go” button, then all of the ranks above class will be hidden.
Suppose now that you have a virus species name and you want to know whether it is the current species name and what the species current taxonomic classification is.
You can either search the current MSL or do a search on the Taxonomy Browser.
As an example, let’s search for Yellow fever virus. First, we will search in the current MSL.
Download the current MSL by clicking on the “Download Current Taxonomy Spreadsheet” button at the top of the screen.
Once the MSL has been downloaded, do a search for Yellow fever virus in the spreadsheet.
We see that the MSL search does not find the species, so we conclude that the name is not current.
Since we were unable to find Yellow fever virus in the current MSL, go to the Taxonomy Browser and enter “Yellow fever virus”, and click in the check box located just below the search window to search through all ICTV MSL releases.
Then click the “Search” button.
From the search results, we see that the most recent MSL in which the species name Yellow fever virus appears is the 2021 release.
Click the “View” button.
This will automatically open the 2021 MSL release, MSL37, and the browser will scroll down to the species.
As we see here.
When you hover over the row, you will see the words “click for details” appear.
Clicking on this will take you to the Taxon Details page, which provides the history of this taxon.
At the top of the screen is the lineage for the species as it appears in the 2021 MSL release.
Just under that are all the taxa changes for the species starting with the most recent change .
The most recent change is that Yellow fever virus was renamed Orthoflavivirus flavi in the 2022 MSL release, MSL38.
There are no changes listed for the 2021 MSL release, MSL37.
However, in the 2020 MSL release, MSL36, the species was removed as Type Species, since Type Species were abolished in 2020.
Scrolling down further in the Taxon Details shows all of the changes for this species going back to 1971.
You will note that for each taxon change, there is a URL for the proposal for the change.
Clicking on this will download the zipped files, which consist of a Word document and an Excel worksheet.
The Word document is the actual proposal, and the Excel worksheet shows the change.
Returning to the Taxon Details page, just below the proposal URL, are buttons which allow you to export the taxon lineage to be either copied to the clipboard or downloaded.
The export settings at the top of the screen provide formatting options.
We hope that this video has been helpful.
For additional How-To videos, please see the ICTV website under “Help”.