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

alison.pamment at stfc.ac.uk alison.pamment at stfc.ac.uk
Sat Apr 22 05:15:38 MDT 2017


Dear John, Jim, Paul, Martin, Jonathan, Karl, Roy,

Thank you all for responding again, particularly on the 'surface' question. We are definitely on the right track now. The vast majority of the names can either be accepted or removed from further consideration. I will be preparing the next update to the standard name table on Monday (24th April) when all accepted names will be added. The updated table should appear on the CF website on Tuesday.

There are just a few names that need a little more work (see the last name in section 4, also section 5 (b), (d) and (e)). The numbering of the sections is consistent with my previous email.

2. natural/analogue names

The following three names have been agreed and are accepted for inclusion in the standard name table.

sea_water_ph_natural_analogue_reported_on_total_scale (1)
'sea_water_pH_reported_on_total_scale is the measure of acidity of sea water, defined as the negative logarithm of the concentration of dissolved hydrogen ions plus bisulfate ions in a sea water medium; it can be measured or calculated; when measured the scale is defined according to a series of buffers prepared in artificial seawater containing bisulfate. The quantity may be written as pH(total) = -log([H+](free) + [HSO4-]). In ocean biogeochemistry models, a "natural analogue" is used to simulate the effect on a modelled variable of imposing preindustrial atmospheric carbon dioxide concentrations, even when the model as a whole may be subjected to varying forcings.'

sea_water_ph_abiotic_analogue_reported_on_total_scale (1)
'sea_water_pH_reported_on_total_scale is the measure of acidity of sea water, defined as the negative logarithm of the concentration of dissolved hydrogen ions plus bisulfate ions in a sea water medium; it can be measured or calculated; when measured the scale is defined according to a series of buffers prepared in artificial seawater containing bisulfate. The quantity may be written as pH(total) = -log([H+](free) + [HSO4-]). In ocean biogeochemistry models, an "abiotic analogue" is used to simulate the effect on a modelled variable when biological effects on ocean carbon concentration and alkalinity are ignored.'

sea_water_alkalinity_natural_analogue_expressed_as_mole_equivalent (mol m-3)
'sea_water_alkalinity_expressed_as_mole_equivalent is the total alkalinity equivalent concentration (including carbonate, nitrogen, silicate, and borate components). In ocean biogeochemistry models, a "natural analogue" is used to simulate the effect on a modelled variable of imposing preindustrial atmospheric carbon dioxide concentrations, even when the model as a whole may be subjected to varying forcings.'

N.B. I have taken note of Jim's request to substitute the word 'concentration' for 'activity' in the ph names.

Regarding the sea_water partial pressure names that were added to the standard name table in the last update, Jim suggested removing the sentence 'The partial pressure of a gaseous constituent of air is the pressure which it alone would exert with unchanged temperature and number of moles per unit volume' from the definitions of surface_partial_pressure_of_carbon_dioxide_natural_analogue_in_sea_water and surface_partial_pressure_of_carbon_dioxide_abiotic_analogue_in_sea_water. The previous sentence says 'The partial pressure of a dissolved gas in sea water is the partial pressure in air with which it would be in equilibrium,' so I think it does make sense to then explain what is meant by the partial pressure in air. We have included this text in the two sea water partial pressure names proposed by Beate Geyer which will be published in Monday's update and I would like to keep the definitions of similar names as consistent as possible. The sentence defining partial pressure in air is also included in the definitions of surface_carbon_dioxide_natural_analogue_partial_pressure_difference_between_sea_water_and_air and surface_carbon_dioxide_abiotic_analogue_partial_pressure_difference_between_sea_water_and_air.

3. Carbon13 and carbon14 names

The following two names have been agreed and are accepted for inclusion in the standard name table.

surface_downward_mass_flux_of_carbon13_dioxide_abiotic_analogue_expressed_as_carbon13, kg m-2 s-1
'The surface called "surface" means the lower boundary of the atmosphere. "Downward" indicates a vector component which is positive when directed downward (negative upward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. In ocean biogeochemistry models, an "abiotic analogue" is used to simulate the effect on a modelled variable when biological effects on ocean carbon concentration and alkalinity are ignored. The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. Carbon13 is a stable isotope of carbon having six protons and seven neutrons.'

surface_downward_mass_flux_of_carbon14_dioxide_abiotic_analogue_expressed_as_carbon, kg m-2 s-1
'The surface called "surface" means the lower boundary of the atmosphere. "Downward" indicates a vector component which is positive when directed downward (negative upward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. In ocean biogeochemistry models, an "abiotic analogue" is used to simulate the effect on a modelled variable when biological effects on ocean carbon concentration and alkalinity are ignored. The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. Carbon14 is a radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating.'

4. When is a surface not a surface?

I am really pleased that the discussion of this issue has been resolved to everyone's satisfaction. Thank you all for the constructive comments and patience during this process. It seems we are all now agreed that separate 'sea_surface' standard names are not needed for the OMIP names because the long_name and CMIP short names can be used to distinguish between 2D and 3D fields in the metadata.

As a result of this decision, many of the quantities proposed for OMIP can make use of existing standard names. These are listed below:

surface_mole_concentration_of_carbonate_abiotic_analogue_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_carbonate_abiotic_analogue_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water
surface_sea_water_ph_abiotic_analogue_reported_on_total_scale -> use name sea_water_ph_abiotic_analogue_reported_on_total_scale which will be added in next update to standard name table

surface_mole_concentration_of_carbonate_natural_analogue_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_carbonate_natural_analogue_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water
surface_sea_water_ph_natural_analogue_reported_on_total_scale -> use name sea_water_ph_natural_analogue_reported_on_total_scale which will be added in next update to standard name table
surface_sea_water_alkalinity_natural_analogue_expressed_as_mole_equivalent -> use name sea_water_alkalinity_natural_analogue_expressed_as_mole_equivalent which will be added in next update to standard name table

surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water -> use existing name mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water
surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water -> use existing name mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water -> use existing name 
mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water
surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water -> use existing name mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water

surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water

surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water
surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water
surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water
surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water
surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water
surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water -> use existing name mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water

surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water -> use existing name 
mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water

surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water -> use existing name mole_concentration_of_dissolved_organic_carbon_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_carbon_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_calcite_expressed_as_carbon_in_sea_water

surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water -> use existing name mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water
surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water -> use existing name mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
surface_mole_concentration_of_dissolved_iron_in_sea_water -> use existing name mole_concentration_of_dissolved_iron_in_sea_water
surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water -> use existing name mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water
surface_mole_concentration_of_dimethyl_sulfide_in_sea_water -> use existing name mole_concentration_of_dimethyl_sulfide_in_sea_water
surface_mole_concentration_of_ammonium_in_sea_water -> use existing name mole_concentration_of_ammonium_in_sea_water
surface_mole_concentration_of_nitrate_in_sea_water -> use existing name mole_concentration_of_nitrate_in_sea_water
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water -> use existing name 
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation -> use existing name mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation

surface_sea_water_ph_reported_on_total_scale -> use existing name sea_water_ph_reported_on_total_scale
surface_sea_water_alkalinity_expressed_as_mole_equivalent -> use existing name sea_water_alkalinity_expressed_as_mole_equivalent

I have now removed these surface names from the list of OMIP proposals.

There is just one proposed 'surface' name, surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water (mol m-3), for which no generic (3D) name currently exists. We therefore do need a new name for this:
mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water (mol m-3)
'Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A.'

This name follows the syntax of many existing ones and does not need any novel terms to be defined, therefore it is accepted for publication in the standard name table and will be added on 24th April. 'Particulate organic matter' is a well established term in existing sea water standard names, but lacks a definition. If we can agree such a definition (see section 5b below) it can be added to this new name in the May update, as well as to the twelve existing names.

5. Miscellaneous names

a. We have agreed to use the existing name surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon instead of the proposed name surface_downward_mass_flux_of_carbon_dioxide. I have removed this one from the list of OMIP proposals.

b. surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water and
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water

Following the discussion in section 4 we can use the existing 3D names for these quantities:
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water -> use existing name mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water -> use existing name mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water

I have removed the surface names from the list of OMIP proposals.

Jim, thank you for clarifying the difference between 'organic_detritus' and 'particulate_organic_matter'. I looked at the way we define particulate_organic_matter for atmosphere names - we say 'the term "particulate_organic_matter_dry_aerosol" means all particulate organic matter dry aerosol except elemental carbon.' Would a similar definition apply to sea water names, e.g, could we say 'the term "particulate organic matter" means all particulate organic matter except elemental carbon'? If we can agree an appropriate definition I can add it to the twelve existing particulate_organic_matter in sea water names.

c. tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-3 s-1

John, thank you for clarifying the meaning of 'nitrogen' in this name. I have borrowed some of the definition of 'nitrogen' in atmosphere deposition names to come up with the following text:
' "tendency_of_X" means derivative of X with respect to time. "Content" indicates a quantity per unit area. "Nitrogen" summarizes all chemical species containing nitrogen atoms. The list of individual species that are included in this quantity can vary between models. Where possible, the data variable should be accompanied by a complete description of the species represented, for example, by using a comment attribute. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase.'

This name is accepted for publication in the standard name table and will be added in the update of 24th April.

d. tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1

Jim, thank you for providing a definition for remineralization. Adding this to our usual definition text we have:
' "tendency_of_X" means derivative of X with respect to time. Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Remineralization is the degradation of organic matter into inorganic forms of carbon, nitrogen, phosphorus and other micronutrients, which consumes oxygen and releases energy.'

This name is accepted for publication in the standard name table. I will include it in the update of the 24th. If we can agree a definition of particulate_organic_matter, as discussed in (b), I can add that in the May update of the table.

e. mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite (mol m-3) and mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite (mol m-3)

Jim, thank you for your detailed explanation of the chemistry behind these names. I agree that these are new quantities and that they do need standard names. For consistency with many existing names I'd rather we said 'in_sea_water' than 'for_sea_water'. To avoid repeating 'in' too many times we could then say 'at_equilibrium' which is also more consistent with existing 'at_saturation' names. Also, I think the 'in_sea_water' really belongs at the end because then it's clear that the equilibrium is between the carbonate and the aragonite/calcite and that sea water is the medium.  I've used your explanation in the suggested definitions.

mole_concentration_of_carbonate_expressed_as_carbon_at_equilibrium_with_pure_calcite_in_sea_water
'Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. The chemical formula of the carbonate anion is CO3 with an electrical charge of minus two. Calcite is a mineral that is a polymorph of calcium carbonate. The chemical formula of calcite is CaCO3. At a given salinity, the thermodynamic equilibrium is that between dissolved carbonate ion and solid calcite. Standard names also exist for aragonite, another polymorph of calcium carbonate.'

mole_concentration_of_carbonate_expressed_as_carbon_at_equilibrium_with_pure_aragonite_in_sea_water
'Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. The chemical formula of the carbonate anion is CO3 with an electrical charge of minus two. Aragonite is a mineral that is a polymorph of calcium carbonate. The chemical formula of aragonite is CaCO3. At a given salinity, the thermodynamic equilibrium is that between dissolved carbonate ion and solid aragonite. Standard names also exist for calcite, another polymorph of calcium carbonate.'

Do these look okay? These two names are still under discussion.

Two corresponding 'surface' names were also proposed:
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite.

Following the discussion in section 4, I have now removed these from the list. Once agreed, the 3D names can be used for all quantities.

Best wishes,
Alison

-----
Alison Pamment                                                       Tel: +44 1235 778065
Centre for Environmental Data Analysis         Email: alison.pamment at stfc.ac.uk
STFC Rutherford Appleton Laboratory     
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


> -----Original Message-----
> From: CF-metadata [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of
> James Orr
> Sent: 11 April 2017 12:00
> To: Durack, Paul J.
> Cc: cf-metadata at cgd.ucar.edu
> Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and
> chemistry
> 
> Paul,
> 
> > So, use a single standard_name (for the identical quantity), and keep
> > the second 2D (CMOR) variable (as is the status of the current CMIP6
> > data request). I believe this solution would solve many of the 51
> > “surface” variables that Alison highlighted, as these requests could
> > be dropped in favor of their 3D (existing) names.
> 
> Your suggestion is excellent.  Using the same standard-name but a
> different "CMIP name" to indicate the surface variable would be a
> fine solution.
> 
> > As an aside, the “depth0m” current CMOR_dimension is not correct
> > either. I assume these variables will be reported for the top ocean
> > level, which in CMIP5 was 0-10m reported as 5m for many models, and
> > for CMIP6 will be varied across the model suite. Jim/John, should this
> > be clarified? Martin, would you care to comment here?
> 
> Yes, for these "sea surface" variables, we mean the top layer of the
> ocean model.  In CMIP6, the thickness of that layer will indeed vary
> among ocean models. Any ideas for clarification are welcome although
> most ocean modelers should not need it.
> 
> Best,
> 
> Jim
> 
> On Thu, 6 Apr 2017, Durack, Paul J. wrote:
> 
> > To answer the “surface” question raised by Alison, and posed by Jim (the
> bottom of this email) - apologies for the tardy response.
> >
> > The analogue in the physical domain are the tos and sos variables which are
> the “surface” (or more correctly top model level) 2D equivalents of their
> counterpart 3D variables thetao and so.
> >
> > In this instance, we could have two variables with the same standard_name
> and differing “CMIP name”, so for example:
> >
> > The originally proposed variables and standard_names (see biogeochemistry
> sheet: https://goo.gl/Fyr6QW)
> >
> > dissicos – CF_standard_name:
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water;
> CMOR_dimensions: longitude latitude time depth0m (Omon line 7)
> > dissic – CF_standard_name:
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water;
> CMOR_dimensions: longitude latitude olevel time (Omon line 60)
> >
> > Could be finalized as:
> >
> > dissicos – CF_standard_name:
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water;
> CMOR_dimensions: longitude latitude time depth0m
> > dissic – CF_standard_name:
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water;
> CMOR_dimensions: longitude latitude olevel time
> >
> > So, use a single standard_name (for the identical quantity), and keep the
> second 2D (CMOR) variable (as is the status of the current CMIP6 data
> request). I believe this solution would solve many of the 51 “surface” variables
> that Alison highlighted, as these requests could be dropped in favor of their 3D
> (existing) names.
> >
> >
> > As an aside, the “depth0m” current CMOR_dimension is not correct either. I
> assume these variables will be reported for the top ocean level, which in CMIP5
> was 0-10m reported as 5m for many models, and for CMIP6 will be varied
> across the model suite. Jim/John, should this be clarified? Martin, would you
> care to comment here?
> >
> >
> > Cheers,
> >
> > P
> >
> > On 4/6/17, 10:51 AM, "CF-metadata on behalf of martin.juckes at stfc.ac.uk"
> <cf-metadata-bounces at cgd.ucar.edu on behalf of martin.juckes at stfc.ac.uk>
> wrote:
> >
> >    Hello All,
> >
> >    I'd like to support Alison on point 4 (see
> http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2017/059357.html ),
> regarding the proposal for new standard names for near surface tracer fields.
> >
> >    The statement 'The surface called "surface" means the lower boundary of
> the atmosphere' occurs in many standard name definitions: introducing a new
> set of names in which "surface" means "near surface" introduces an
> unnecessary ambiguity.
> >
> >    I also note that some of these variables have already been requested in
> CMIP5, using the approach described by Karl.
> >
> >    regards,
> >    Martin
> >
> > On 3/31/17, 9:04 AM, "CF-metadata on behalf of Jonathan Gregory" <cf-
> metadata-bounces at cgd.ucar.edu on behalf of j.m.gregory at reading.ac.uk>
> wrote:
> >
> >    Dear Alison
> >
> >    I second Jim Orr's vote of thanks to you for your great efforts on these
> names
> >    and several other sets recently.
> >
> >    I accept your recommendation not to introduce new names for surface con-
> >    centrations if these aren't really *at* the surface. I agree that it's
> >    consistent with other cases, such as near-surface air temperature, to use
> >    a coordinate instead. My reply to Karl was about the case when the quantity
> >    is truly *at* the surface, in which case there are many equivalent choices
> >    of coord, and that's not convenient. It's more informative too to include a
> >    coordinate value.
> >
> >    I don't think will be a problem for analysts in finding the data because, as
> >    Karl said, the 2D and 3D versions would have different CMIP6 quantity
> names
> >    (the ones like tas and thetao) and reside in different files for CMIP6.
> >
> >    Best wishes
> >
> >    Jonathan
> >
> >    > >4. When is a surface not a surface?
> >    > >
> >    > >There are 3 proposed names for surface fluxes. Such names clearly
> >    > >refer to conditions at the air/sea interface and it is correct to
> >    > >label them as surface quantities. Those names are excluded from
> >    > >the discussion in this section.
> >    > >
> >    > >There are 51 proposed names referring to
> >    > >'surface_mole_concentration', 'surface_mass_concentration',
> >    > >'surface_sea_water_ph' and 'surface_sea_water_alkalinity'. These
> >    > >are the names I want to discuss here. We have already had some
> >    > >discussion of these names on the mailing list and there has been
> >    > >some further on and off-list discussion over the last couple of
> >    > >days. So far we have not arrived at consensus, but it is important
> >    > >that we try to do so now to allow the majority of the remaining
> >    > >OMIP names to be accepted. I will attempt to summarize the
> >    > >discussion and then make a recommendation as to how I think we
> >    > >should proceed.
> >    > >
> >    > >The reason for the discussion is that the surface concentration
> >    > >and alkalinity names have all been proposed with units of mol m-3
> >    > >or kg m-3, which indicates that the named quantities are intended
> >    > >to represent 'near surface' layer concentrations, i.e., the top
> >    > >one or two levels in an ocean model. Although the ph names are
> >    > >dimensionless it is clear that these also are intended to
> >    > >represent a near surface layer. In CF standard names it is
> >    > >inappropriate to refer to these layer quantities simply as
> >    > >'surface' quantities because the term 'surface' is defined as 'the
> >    > >lower boundary of the atmosphere', i.e. it is the exact interface
> >    > >between air and sea which therefore has no thickness or volume and
> >    > >is therefore unsuitable for use with units of m-3.
> >    > >
> >    > >At an earlier point in the discussion
> >    > >(http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/059044.html)
> >    > >I mentioned that we have a small number of existing sea_surface
> >    > >names - these are near surface layer quantities and nearly all
> >    > >relate to specific definitions of sea surface temperature, e.g.,
> >    > >sea_surface_skin_temperature is defined as 'the temperature within
> >    > >the conductive diffusion-dominated sub-layer at a depth of
> >    > >approximately 10 - 20 micrometers below the air-sea interface'.
> >    > >The only generic quantity is sea_surface_temperature which is a
> >    > >deliberately vague term to cover different definitions of SST that
> >    > >have been used historically, for example, when making temperature
> >    > >measurements using the water in a ship's engine intake or by
> >    > >lowering a bucket over the side. These are all in some sense 'near
> >    > >surface' values but the depth of measurement can vary widely and
> >    > >in some cases may not even be recorded. I did toy with the idea
> >    > >that for OMIP we could have 'sea_surface' names for near-surface
> >    > >quantities because this would at least be consistent with the m-3
> >    > >in the units. However, I don't think this is the most satisfactory
> >    > >approach because the OMIP quantities can perfectly well be
> >    > >described by using standard names that can apply to quantities at
> >    > >any depth in conjunction with coordinate variables and coordinate
> >    > >bounds to state the actual depth and thickness of the surface
> >    > >layer. Even if we did introduce sea_surface names for OMIP it
> >    > >would still be necessary to supply the coordinate information in
> >    > >other metadata attributes to fully describe the location of the
> >    > >data, so it wouldn't do anything to reduce the amount of metadata
> >    > >that would need to be provided. Not to supply this metadata would
> >    > >render the data far less useful. Furthermore, other contributors
> >    > >to the discussion (Roy, Jonathan) have clearly expressed the view
> >    > >that we should not generalise the rather specialised
> >    > >sea_surface_temperature approach to other variables.
> >    > >
> >    > >In his most recent post, Jim has said that many fields will be
> >    > >output as 2D quantities in order to reduce the amount of data
> >    > >generated for OMIP. Karl has already explained that from a CMIP6
> >    > >viewpoint this is perfectly consistent with using standard names
> >    > >that could equally well apply to 3D quantities. It is also
> >    > >consistent with usual practice in CF. There is no limitation on
> >    > >the number of data variables in a CF-NetCDF file that can have the
> >    > >same standard name and they do not all have to have the same
> >    > >dimensions, so it's even possible to have 2D and 3D fields with
> >    > >the same standard name in the same file. The important point for
> >    > >data users is not to rely solely on the standard name to decide
> >    > >how to treat a variable, but also to examine many other metadata
> >    > >attributes such as coordinate variables, coordinate bounds and
> >    > >cell_methods. This is the always the correct way to work with CF
> >    > >metadata. Indeed, I would argue that the most 'standard' way to
> >    > >record the OMIP near-surface data in your files is to follow the
> >    > >practice I described earlier: use standard names that can apply to
> >    > >any depth and supply coordinate variables and coordinate bounds to
> >    > >state the actual depth and thickness of the surface layer. I think
> >    > >users of the data are more likely to discover data named in this
> >    > >way than if we introduce special sea_surface names for some
> >    > >quantities. Also, this approach significantly reduces the number
> >    > >of new standard names needed for OMIP. For example, the proposed
> >    > >name
> [sea_]surface_mole_concentration_of_carbonate_expressed_as_carbon_in_se
> a_water
> >    > >could be dropped in favour of using the existing name
> >    > >mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water.
> >    > >Again, it is standard practice in the CF community to avoid adding
> >    > >new standard names that are not strictly necessary.
> >    > >
> >    > >Based on the above arguments I recommend that we follow the second
> approach
> >    > >and don't introduce separate sea_surface names. Please can those
> >    > >of you who have been engaged in this discussion indicate whether
> >    > >you are in agreement. If we can get consensus, or at least a clear
> >    > >majority on which approach to use, then many of the outstanding
> >    > >names can be accepted very quickly. If we are unable to reach a
> >    > >decision through this discussion, then I will need to call on the
> >    > >CF committee to vote on their preferred approach. The committee's
> >    > >decision will be final. This is in accordance with usual CF
> >    > >procedures.
> >    >
> >    > It would be great if we could come to an agreement on this issue by
> >    > ourselves, without having to bother the CF committee.
> >    >
> >    > If we adopt the idea to use the same name for variables whether they
> >    > are 3-D (full water column) or 2-D (sea surface only), that could
> >    > confuse typical users of the CMIP6 data. For CMIP5, users searched
> >    > for available data files based on variable names along with other
> >    > criteria in the CMIP5 Data Reference Syntax (DRS), which includes
> >    > keywords for Institute, Model, Experiment, Frequency, Realm, MIP
> >    > Table, Ensemble, Version, Variable, and Temporal Subset.  No keyword
> >    > currently exists for spatial dimensions. So removing "sea surface"
> >    > from the variable names would not be optimal unless a new keyword
> >    > such as "Spatial Domain" could be added to the CMIP6 DRS.
> >    >
> >    > Paul, is this something that could be considered for CMIP6?
> >    > Otherwise, I would prefer to keep the "sea surface" prefix, as
> >    > previously adopted for the physical variables, 'sea surface
> >    > temperature' and 'sea surface salinity' (tos, sos).
> >    >
> >    > As for having 2 variables in the same file with the same name but
> >    > different shapes or dimensions, that would be confusing, both to
> >    > users and to software that is often used to analyze model output.
> >    > Would CMIP6 even allow such a practice. In any case, because the
> >    > Temporal frequency of the 2 variables would differ, that solution
> >    > does not seem practical.
> >    _______________________________________________
> >    CF-metadata mailing list
> >    CF-metadata at cgd.ucar.edu
> >    http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
> >
> > On 3/29/17, 7:08 AM, "James Orr" <James.Orr at lsce.ipsl.fr> wrote:
> >
> >    If we adopt the idea to use the same name for variables whether they are 3-
> D
> >    (full water column) or 2-D (sea surface only), that could confuse typical
> users
> >    of the CMIP6 data. For CMIP5, users searched for available data files based
> on
> >    variable names along with other criteria in the CMIP5 Data Reference
> Syntax
> >    (DRS), which includes keywords for Institute, Model, Experiment, Frequency,
> >    Realm, MIP Table, Ensemble, Version, Variable, and Temporal Subset.  No
> keyword
> >    currently exists for spatial dimensions. So removing "sea surface" from the
> >    variable names would not be optimal unless a new keyword such as "Spatial
> >    Domain" could be added to the CMIP6 DRS.
> >
> >    Paul, is this something that could be considered for CMIP6?  Otherwise, I
> would
> >    prefer to keep the "sea surface" prefix, as previously adopted for the
> physical
> >    variables, 'sea surface temperature' and 'sea surface salinity' (tos, sos).
> >
> >
> 
> --
> LSCE/IPSL, Laboratoire des Sciences du Climat et de l'Environnement
> CEA-CNRS-UVSQ
> 
> LSCE/IPSL, CEA Saclay           http://www.ipsl.jussieu.fr/~jomce
> Bat. 712 - Orme                 mailto:  James.Orr at lsce.ipsl.fr
> Point courrier 132
> F-91191 Gif-sur-Yvette Cedex    Phone:   (33) (0)1 69 08 39 73
> FRANCE                          Fax:     (33) (0)1 69 08 30 73


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