[CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

From: Jonathan Gregory <j.m.gregory>
Date: Mon, 25 Mar 2013 09:00:03 +0000

Dear all

I agree with Philip that cfu should be spelled out. I was also going to make
the same point about Roy's proposal being different from our treatment of
chemical species, which are encoded in the standard name; this system seems to
be working. One reason for keeping this approach was the "green dog" problem.
That particular phrase is actually Roy's, if I remember correctly. That is, we
wish to prevent nonsensical constructions, by approving each name which makes
(chemical) sense individually.

However Roy argues that there is an order of magnitude more biological species
to deal with than chemical. I don't think that keeping the same approach
(encoding in the standard name) would break the system, but it would make the
standard name table very large. Perhaps more importantly, if there were so
many species, I expect that data-writers would simply assume that each of the
possible combinations of pattern and species did already exist in the standard
name table, without bothering to check or have them approved. That would defeat
the object of the system of individual approval.

We don't have to follow the chemical approach. For named geographical
regions and surface area types (vegetation types etc.) we use string-valued
coordinate variables, rather like Roy proposes here. To follow that approach
we would need a new table, subsidiary to the standard name table, containing
a list of controlled names of biological species. We would use the same
approval process to add names to this list as we do for the standard name
table. (This is what we do for geographical regions and area types.) We would
then have a standard_name such as
  number_concentration_of_biological_species_in_sea_water
whose definition would note that a data variable with this standard_name must
have a string-valued auxiliary coordinate variable of biological_species
containing a valid name from the biological species table. If there is just
one species, the auxiliary coordinate variable wouldn't need a dimension,
but this construction would also allow a single data variable to contain data
for several species, by having a dimension of size greater than one.

Cheers

Jonathan
Received on Mon Mar 25 2013 - 03:00:03 GMT