Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

[John Dunne - NOAA Federal]

I like the idea of appending "growth" to those limitation names - makes
sense.

On Thu, Oct 20, 2016 at 1:06 PM, Jonathan Gregory  wrote:

> Dear John and Alison
>
> I think the definition of limitation is fine for the names. However I do
> still
> have a slight concern that "limitation" alone is not a very
> self-explanatory
> term for the non-expert. Would it be possible and acceptable to say
> growth_limitation instead? Another possible way to make the names easier to
> parse might be to use due_to e.g.
>   solar_irradiance_limitation_of_miscellaneous_phytoplankton
> could be
>   growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance
> Would that still be comprehensible to an expert?
>
> > I think we're agreed that the abiotic names are needed, and if I've
> understood correctly we seem to have agreed to stick with
> due_to_abiotic_component because it works for all the names where it's
> used, including ph names. Is that right?
>
> I think so. Apart from the pH names, we could say abiotic_carbon, I think,
> which is a bit neater - I don't know whether it's preferable for an expert.
>
> Best wishes
>
> Jonathan
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Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

[Jonathan Gregory]

Dear John and Alison

I think the definition of limitation is fine for the names. However I do still
have a slight concern that "limitation" alone is not a very self-explanatory
term for the non-expert. Would it be possible and acceptable to say
growth_limitation instead? Another possible way to make the names easier to
parse might be to use due_to e.g.
  solar_irradiance_limitation_of_miscellaneous_phytoplankton
could be
  growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance
Would that still be comprehensible to an expert?

> I think we're agreed that the abiotic names are needed, and if I've 
> understood correctly we seem to have agreed to stick with 
> due_to_abiotic_component because it works for all the names where it's used, 
> including ph names. Is that right?

I think so. Apart from the pH names, we could say abiotic_carbon, I think,
which is a bit neater - I don't know whether it's preferable for an expert.

Best wishes

Jonathan
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Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

[Jonathan Gregory]

Dear Alison

I agree with you and Roy about the below. I think that it would be much better
to specify the depth of measurement, unless they really have the same
unavoidable vagueness of SST and SSS. In the case of those quantities, we
followed the existing universally used terminology rather than defining our
own, as we often do for clarity - perhaps that was a mistake!

Best wishes

Jonathan

> d. Surface concentration names
> There are a lot of these: 42 surface_mole_concentration names (units of mol 
> m-3), 6 surface_mass_concentration names (kg m-3) and I'm also including 2 
> surface_sea_water_alkalinity (mol m-3) names and 3 surface_sea_water_ph names 
> in this section. 
> 
> My concern about these proposals is that the names and units are not 
> consistent. In CF standard names, "surface" means the lower boundary of the 
> atmosphere. It has no depth, so it is not meaningful to regard it as having a 
> mass or a volume. For this reason we can't assign units of kg m-3 or mol m-3 
> to a 'surface' name. I assume that all these quantities are in fact "near 
> surface" values, i.e. representative of the top model layer, in which case 
> there are two possible ways to deal with this.
> 
> The first solution is simply to remove 'surface' from all these names and 
> instead use a vertical coordinate or scalar coordinate and coordinate bounds 
> to indicate the location and thickness of the layer. This has the advantage 
> that many of the required names actually already exist, without the need to 
> introduce separate surface names. E.g, instead of adding a new name 
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, you 
> could use the existing name 
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water accompanied by 
> suitable coordinate information to describe your quantity.
> 
> The second solution, if you do feel that it is necessary to have distinct 
> standard names for all these near-surface quantities, would be to follow the 
> approach used in some existing sea_surface names such as 
> sea_surface_temperature and sea_surface_salinity. The names would then be 
> 'sea_surface' names and there would be an accompanying sentence in the 
> definition to explain what that means, i.e. that it refers to water close to 
> the surface. You would still also need to include the coordinate information 
> and coordinate bounds to fully describe your data. With this approach the 
> proposed name 
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water would 
> become sea_surface_mole_concentration_of_dissolved_inorganic_carbon.
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Re: [CF-metadata] New standard names for NEMO ocean model output

[alison.pamment]

Dear Kevin,

Thank you for your proposals and apologies for the delay in responding. Your 
proposals have all been added to the CEDA vocabulary editor and can be viewed 
at the following link: 
http://cfeditor.ceda.ac.uk/proposals/1?status=active==Marsh+and+display=Filter.

Please see below for my detailed comments on each name.

1. bottom_pressure_equivalent_height (m) 
'Difference between the sea level height and the ocean steric height.' 

Units of m are fine. Thinking first about the definition, in CF standard names 
we always use 'sea level' to mean mean sea level and 'steric' is defined in sea 
level change names as 'Global average steric sea level change is caused by 
changes in sea water density due to changes in temperature (thermosteric) and 
salinity (halosteric).' From this I would understand your quantity to be the 
difference between mean sea level and the local sea level due to the 
temperature and salinity of the water column. Is that correct?
If so, then as a non-ocean expert I find the name rather confusing and I'd 
prefer something more explicit, e.g., 
difference_of_ocean_steric_height_from_sea_level and we'd add a sentence to the 
definition explaining that 'steric height' refers to temperature and salinity 
effects on the density of the water column. Does that sound OK?

2. ocean_turbocline_depth (m) 
'The turbocline depth is similar to the mixed layer depth but is estimated in 
models as the depth at which the vertical eddy diffusivity coefficient 
(resulting from the vertical physics alone) fall below a given value defined 
locally.

I think the name and units look fine. If you wanted to also be able to specify 
what value of the vertical eddy diffusivity coefficient was used to calculate 
the turbocline depth, it could be specified in a scalar coordinate variable and 
I'd suggest adding some words to the definition along those lines:
'The turbocline depth is similar to the mixed layer depth but is estimated in 
models as the depth at which the vertical eddy diffusivity coefficient 
(resulting from the vertical physics alone) fall below a given value defined 
locally. A coordinate variable or scalar coordinate variable with standard name 
ocean_vertical_diffusivity can be specified to indicate the value of the 
coefficient that was used to calculate the turbocline depth.'

ocean_vertical_diffusivity already exists as a standard name and is defined as 
' "Vertical diffusivity" means the vertical component of diffusivity due to 
motion which is not resolved on the grid scale of the model.'

OK?

3. ocean_steric_height (m)
'The steric measures the height by which a column of water with standard 
temperature T=0°C and salinity S=35.0 expands if its temperature and salinity 
are changed to the observed values.'

To make this name consistent with proposals 4 and 5 below, I'd call this one 
ocean_steric_thickness because it's really referring to changes in the 
thickness of the water column rather than a height above any particular 
surface. Then the definition could read:
'The quantity with standard name ocean_steric_thickness is a measure of the 
change in thickness that would be undergone by a column of water of standard 
temperature T=0°C and practical salinity S=35.0 if its temperature and salinity 
were changed to the locally observed values. Thickness is the extent of a 
vertical column or layer.'

OK?

4.  ocean_steric_thickness_due_to_salinity (m)
'Contribution of the salinity of the water column to the Ocean steric height.'

In an off list discussion prior to the submission of these names I suggested 
'due_to_salinity' for this name, but I am now having a rethink because most 
often we use the phrase 'due_to' to refer to some process in the model (e.g. 
due_to_convection) which isn't quite the case here. Also, when reading through 
our existing steric sea level change names the definitions refer to 
thermosteric and halosteric components, which do apply to this case. Hence, I'd 
suggest changing the name to ocean_halosteric_thickness which also has the 
advantage of being shorter. Then the definition could read:
'The quantity with standard name ocean_halosteric_thickness is a measure of the 
change in thickness that would be undergone by a column of water of standard 
temperature T=0°C and practical salinity S=35.0 if its salinity were changed to 
the locally observed value. Thickness is the extent of a vertical column or 
layer. There are also standard names for ocean_steric_thickness and 
ocean_halosteric_thickness.'

OK?

5. ocean_steric_thickness_due_to_temperature (m)
'Contribution of the temperature of the water column to the Ocean steric 
height.'
As per my comments on proposal 4, I suggest changing this name to 
'ocean_thermosteric_thickness' and then the definition would be:
'The quantity with standard name ocean_thermosteric_thickness is a measure of 
the change in thickness that would be undergone by a column of water of 
standard temperature T=0°C and practical