Taxon Names and Identifiers
|Reported by:||lowry||Owned by:||cf-conventions@…|
New section to be added to the Convention
6.1.2 Taxon Names and Identifiers A taxon is a named level within a biological classification, such as a class, genus and species. Within the marine environment there are at least half a million taxa. However, CF isn't confined to the marine environment and so the number runs into millions, even billions. When a variable in CF describes a property of a taxon, such as its numeric concentration or abundance one approach would be to incorporate the taxon name into the Standard Name. However, experience with other parameter vocabularies has shown that this can quickly become unsustainable. Consequently, taxonomic names are handled in a similar manner to geographic names using a generic Standard Name for the data variable plus co-ordinate variables to carry the label text. The data variable is labelled using Standard Names of the form 'property_of_taxon_in_medium'. For example, taxon abundance in a water body would be described by the Standard Name 'number_concentration_of_taxon_in_sea_water'. The labelling co-ordinate variables have the Standard Names 'taxon_name' and 'taxon_identifier'. The taxon name included in the data must be taken from a recognised source. Currently, these are the World Register of Marine Species or WoRMS (http://www.marinespecies.org/), which is the preferred resource for the marine environment or the International Taxonomic Information System or ITIS (http://www.itis.gov/) for terrestrial flora and fauna. Note that the only requirement for CF is that the name used is registered in at least one of the named resources. It does not have to be designated as 'valid'. The taxon_identifier from either WoRMS (the aphia ID) or ITIS (the taxonomic serial number or TSN) need to include namespace strings, which are 'aphia:' or 'tsn:'. For example, Calanus finmarchicus is encoded as either 'aphia:104464' or 'tsn:85272'. For the marine domain WoRMS has more complete coverage and so aphia Ids are preferred. Example 6.3 This example shows how the taxonomic information would be encoded for a simple time series of abundance for two taxa. For clarity, a lot of information - such as the time variable has been omitted. dimensions;
time=1000; string80=80; taxon=2;
abundance:standard_name="number_concentration_of_taxon_in_sea_water"; abundance:coordinates="taxon_identifier taxon_name";
data; taxon_name = "Calanus finmarchicus", "Calanus helgolandicus" taxon_label = "aphia:104464", "aphia:104466"
Consequences for Standard Names
The following new Standard Names are required to describe the label variables and to support the bacterial data request that inspired the creation of this ticket. One more has been included in support of the above example. taxon_name The human-readable label for the taxon such as Calanus finmarchicus. The label should be registered in either WoRMS or ITIS and spelled exactly as registered. taxon_identifier The machine-readable identifier for the taxon registration in either WoRMS (the aphia ID) or ITIS (the taxonomic serial number or TSN), including namespace. The namespace strings are 'aphia:' or 'tsn:'. For example, Calanus finmarchicus is encoded as either 'aphia:104464' or 'tsn:85272'. For the marine domain WoRMS has more complete coverage and so aphia Ids are preferred. colony_forming_unit_number_concentration_of_taxon_in_sea_water "Colony Forming Unit" means an estimate of the viable bacterial or fungal numbers determined by counting colonies grown from a sample. "Number concentration" means the number of particles or other specified objects per unit volume. "Taxon" means an organism named in the taxon_name and taxon_identifier variables. number_concentration_of_taxon_in_sea_water "Number concentration" means the number of particles or other specified objects per unit volume. "Taxon" means an organism named in the taxon_name and taxon_identifier variables.