ITIS Species Codes
Species and Call Type Names
When exporting data from PAMGuard to Tethys, some PAMGuard records will require additional information indicating what type of animal or phenomena were detected. If a specific call-type was detected, e.g. “Clicks” or “Whistles”, these should be noted as well.
Species Names
Tethys uses the Integrated Taxonomic Information System (ITIS) to encode species names as taxonomic serial numbers (TSNs), unique numeric identifiers for species. These data conform with several international coding systems which are described on the ITIS standards page.
It is not uncommon to be unable to describe a call to the genus level. In such cases, one can use a higher taxonomic level. For example, beaked whale echolocation clicks are distinctive from the clicks of other toothed whales as their pulses have a frequency-modulated component. While they can frequently be associated with the family Hyperodontidae, it is not always possible to associate a click to a specific species as many of the at least twenty-two species remain understudied. In such a case, we would use the TSN for Hyperodontidae, 770799. While not currently supported by PAMGuard, each species identifier has an optional Group attribute that can be used in an ad-hoc manner to provide additional information. This can be used to add population markers, tentative genus groups, etc.
ITIS does not describe abiotic sounds, Tethys records such sounds as follows:
- For anthropogenic signals, the Tethys convention is to use Homo sapiens, TSN 180092, for the species code and describe the human-generated signal via a call type, e.g. ship, mid-frequency active sonar, etc.
- Tethys reserves the TSN -10 for geophonic signals. The call type is used to describe the source. Examples include ambient sound, earthquake, rain, etc. Note that negative TSNs are not part of the ITIS standard.
Note that in general, you do not have to worry about remembering TSNs. Tethys uses TSNs internally, but will translate TSNs to/from Latin names or user-defined abbreviations both when querying and presenting results.
Call types
Some detectors identify specific call types. When this is the case, users will need to specify the call type name. While species names are standardized in Tethys, call names do not have a well-defined standard and experts frequently use different names for the same type of call. Consequently, Tethys does not provide a standard coding for call types and users are free to choose the call type names with which they feel most comfortable.
That said, the authors of Tethys do however provide a list of recommend call types for many species. These recommendations can be accessed in the supplemental information of the open access article “Management of acoustic metadata for bioacoustics,” Roch et al. (2016), (DOI:10.1016/j.ecoinf.2015.12.002).
Export dialog
During export of records that are species-specific, a dialog will appear that lists the types of events that were found by PAMGuard modules. This dialog permits users to specify how the ad-hoc species species/call encoding scheme used by PAMGuard modules can be systematically translated to the TSNs and call types are stored in Tethys.
PAMGuard events typically are a short name that represents the species and/or potentially a call. Knowledge of the PAMGuard modules that were run and the data on which they executed will let a user infer what should be recorded. The dialog below shows a sample set of events produced by one or more PAMGuard modules using the names: HP, DO, SON, KW, UNK, and PHP:
The dialog above was produced from detections on data that were recorded near the mouth of the River Tay in Scotland. Consequently, we can infer that the harbour porpoise that is denoted by “HP” is Phocena phocena, the only harbour porpoise endemic to Scottish waters.
An ITIS code and call/sound type can be associated with each event. The dialog lists:
Name - The ad-hoc name given by the PAMGuard module. This may not be changed.
ITIS code -This is the ITIS TSN that is associated with PAMGuard event code. Click on Find to inovke the TSN search dialog whose behavior is described in the next section.
If you happen to know the TSN, you can enter it directly. Pressing Find after typing the TNS will populate the Latin and English vernauclar names so that you may verify your TSN was entered correctly.
Call / sound type - This will default to the code provided by the module but should be updated to specify an appropriate call type or left blank to indicate that the detection is not related to a specific call type. In the case of a porpoise detector, the likely call type would be “Clicks”. We should double check that no Call element is generated when this is blank.
Once all species names and call/sound types have been identified, press the Okay button.
Searching for ITIS Taxonomic Serial Numbers (TSNs)
As noted above, pressing Find without typing a TSN will bring up a search dialog:
The top of this dialog has a search box where one can enter either a Latin name or the common name for a species. The Tethys server will search for all species that match the search-box contents. For many species, there are common name entries in languages other than English, and these are searched as well.
Once you press the search button, a list will appear with all matches for your search term. If there are too many, a scroll bar will permit you to look through the list. Select the entry that you wish and press OK. The TSN on the species dialog will be populated along with the Latin name and common names from the ITIS database.