Dear All,
I am currently working on a Trac ticket submission for handling of taxonomic
data in CF and thought I'd run an example past the list to make sure I've got
it right.
Jonathan suggested using a container variable analogous to geographic regions.
My interpretation of this would result in a simple time series (excluding
ancillary variables and most parameter attributes for clarity) for two taxa
being structured as follows:
dimensions;
INSTANCE = 1 ;
MAXT = 1000 ;
STRING80 = 80;
LABEL = 2;
variables;
float abundance(INSTANCE, MAXT, LABEL);
abundance:standard_name="number_concentration_of_taxon_in_sea_water";
abundance:co-ordinates="taxon_name";
double time (INSTANCE, MAXT);
char taxon_name (INSTANCE, LABEL, STRING80);
taxon_name:standard_name="taxon_name" /*Standard Name yet to
be proposed*/;
char taxon_identifier (INSTANCE, LABEL, STRING80);
taxon_identifier: standard_name="taxon_identifier";
Note that I have included a taxon_identifier (populated using aphiaID, ITIS
TSN, LSID) in addition to a taxon name because homonyms do exist and this is
the only way of distinguishing them. It also provides some degree of
protection against spelling errors, which are a persistent problem with
taxonomic names.
My instinctive encoding would have been:
dimensions;
INSTANCE = 1 ;
MAXT = 1000 ;
variables;
float abundance1(INSTANCE, MAXT);
abundance:standard_name="number_concentration_of_taxon_in_sea_water";
abundance:taxon_name="taxon#1 name";
abundance:taxon_identifier="aphiaid:taxon#1 aphia identifier";
float abundance2(INSTANCE, MAXT);
abundance:standard_name="number_concentration_of_taxon_in_sea_water";
abundance:taxon_name="taxon#2 name";
abundance:taxon_identifier="aphiaid:taxon#2 aphia identifier";
double time (INSTANCE, MAXT);
However, having thought it through I'm coming around to preferring Jonathan's
encoding as it's much more powerful and allows different taxa lists to co-exist
within a single NetCDF container. Does anybody disagree with this? If not, is
there anything that needs to be changed in my example - e.g. should
taxon_identifier also be specified as a co-ordinate?
Cheers, Roy.
Please note that I now work part-time from Tuesday to Thursday. E-mail
response on other days is possible but not guaranteed!
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