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

[Durack, Paul J.]

Hi folks,

In preparation for the upcoming CMIP6-OMIP experiments we have a number of new standard names we’d like “blessed” for the biogeochemistry and chemistry data request.

I have appended these below. For folks interested, further information and notes are contained in the linked google sheets both indicated below. Many thanks to Alison for taking a first pass at these before sending to the mailing list.

The format below for the new names is:
standard_name_being_requested, units, (google sheet tab(s) and line number(s)).

***
160928 1105 ***@llnl.gov

Biogeochemistry see https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:

mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Oyr, 8; Omon, 63)
mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Oyr, 9; Omon, 64)
mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 13; Omon, 68)
sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Oyr, 27; Omon, 81)
sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr, 29; Omon, 83)
sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr, 30; Omon, 84)
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Oyr, 32; Omon, 86)
mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Oyr, 35; Omon, 89)
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Oyr, 37; Omon, 91)
mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 55; Omon, 108)
mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 56; Omon, 109)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr, 96; Omon, 113)
surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, mol m-3, (Omon, 7)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 8)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Omon, 10)
surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Omon, 11)
surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol m-3, (Omon, 12)
surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 13)
surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 14)
surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 15)
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 16)
surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 17)
surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 18)
surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 19)
surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 20)
surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 21)
surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 22)
surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 24)
surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 25)
surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 26)
surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3, (Omon, 27)
surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Omon, 28)
surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Omon, 30)
surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Omon, 31)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mol m-3, (Omon, 32)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Omon, 33)
surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Omon, 36)
surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3, (Omon, 37)
surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Omon, 38)
surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 39)
surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 40)
surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 41)
surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 43)
surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water, mol m-3, (Omon, 47)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 49)
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 50)
surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water, mol m-3, (Omon, 51)
surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 52)
surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3, (Omon, 53)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 54)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
nitrogen_limitation_of_diatoms, 1, (Omon, 116)
nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
irradiance_limitation_of_diatoms, 1, (Omon, 121)
irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
iron_limitation_of_diatoms, 1, (Omon, 126)
iron_limitation_of_diazotrophs, 1, (Omon, 127)
iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
iron_limitation_of_picophytoplankton, 1, (Omon, 129)
iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-2 s-1, (Omon, 139)
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1, (Omon, 140)
ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2, (Omon, 154)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component, Pa, (Omon, 156)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component, Pa, (Omon, 157)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 170)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 172)


Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG9G0lzIu7o/edit:

mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3; Omon, 4)
mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
***

Cheers,

P

[Jonathan Gregory]

Dear Paul

Thank you for this list. It looks like they conform well to existing patterns
and it must have been a lot of work to compile them!

I have a couple of comments:

* Several pairs of names contrast "abiotic" and "natural", apparently. Am I
right to understand that these are opposites? That's not obvious to me. Not
everything which is "natural" in the Earth system is biotic. In other contexts,
"natural" and "anthropogenic" are opposites. Would it be correct to say
"biotic" instead of "natural" here?

* There are several dimensionless quantities referring to X_limitation_of_Y,
where X is nitrogen, iron or irradiance and Y is a class of organisms. It
would be more informative if you could insert a phrase which indicates what is
limited and/or how this quantity is defined - it must be a ratio, I suppose,
but of what?

I assume that definitions will be needed as well for the stdname table.

Best wishes

Jonathan

[James Orr]

On Thu, 29 Sep 2016, Jonathan Gregory wrote:

> Dear Paul
>
> Thank you for this list. It looks like they conform well to existing patterns
> and it must have been a lot of work to compile them!
>
> I have a couple of comments:
>
> * Several pairs of names contrast "abiotic" and "natural", apparently. Am I
> right to understand that these are opposites? That's not obvious to me. Not
> everything which is "natural" in the Earth system is biotic. In other contexts,
> "natural" and "anthropogenic" are opposites. Would it be correct to say
> "biotic" instead of "natural" here?

Hi Jonathan,

For the biogeochemistry in OMIP, we've agreed on using the terms
'abiotic' and 'natural', neither synonyms nor antonyms for our purposes.
The OMIP-BGC simulations will be run with 2 parallel simulations (or
parallel tracers in the same simulation):

* 'natural' means it will be maintained at same the CMIP6 preindustrial
CO2 level throughout the simulation, while the

* 'total' simulation will have varying atmospheric CO2, but the same
climate (e.g., forced in the OMIP ocean only run).

The difference between the total and natural carbon tracers in the two
will give us the anthropogenic carbon. The ocean's natural carbon cycle
is considered in OMIP to change with climate change even though its
simulated atmospheric CO2 is held constant.

Regarding 'abiotic', the natural and the total simulation include both
abiotic and biotic processes. To distinguish the two we also include an
abiotic carbon tracer. Furthermore, we use a simplified abiotic
approach to model C-14 in the ocean, e.g., to provide deep-ocean
ventilation ages.

Jim

--
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: ***@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

[Jonathan Gregory]

Dear Jim

Thanks for explaining. So "natural" is the opposite of "anthropogenic", in
a restricted sense. It includes the effect of anthropogenic climate change,
but not the anthropogenic emissions of CO2. Is that right? I think this is
potentially confusing in the context of CF, which has to cover a wide range of
applications. It is not hard to imagine people wanting to use natural in the
sense of *completely* unaffected by anthropogenic influence. (Obviously I'm
not commenting on the terminology used in OMIP - I'm sure that's clear in
that context.) I wonder if for CF we could think of something more explicit.

Actually I'm unclear quite what is meant by due_to_natural_component (in
several names). Component of what? Could you explain a bit more?

Also, what does sea_water_ph_reported_on_total_scale_due_to_X mean? Is it
perhaps a *change* in pH?

Best wishes

Jonathan

> For the biogeochemistry in OMIP, we've agreed on using the terms
> 'abiotic' and 'natural', neither synonyms nor antonyms for our
> purposes. The OMIP-BGC simulations will be run with 2 parallel
> simulations (or parallel tracers in the same simulation):
>
> * 'natural' means it will be maintained at same the CMIP6
> preindustrial CO2 level throughout the simulation, while the
>
> * 'total' simulation will have varying atmospheric CO2, but the same
> climate (e.g., forced in the OMIP ocean only run).
>
> The difference between the total and natural carbon tracers in the
> two will give us the anthropogenic carbon. The ocean's natural
> carbon cycle is considered in OMIP to change with climate change
> even though its simulated atmospheric CO2 is held constant.
>
> Regarding 'abiotic', the natural and the total simulation include
> both abiotic and biotic processes. To distinguish the two we also
> include an abiotic carbon tracer. Furthermore, we use a simplified
> abiotic approach to model C-14 in the ocean, e.g., to provide
> deep-ocean ventilation ages.

[John Dunne - NOAA Federal]

Hi Jonathan,

With respect to the limitation terms, we currently have the definitations
explained in the "Resolved Comment" column as "Ratio of
realizable miscellaneous other phytoplankton growth rate under low nitrogen
stress to theoretical rate without such limitation"... Is this the scope of
description for which you were looking? Are you suggesting
this description should be the long name instead of the comment?

Cheers, John


On Thu, Sep 29, 2016 at 11:06 AM, Jonathan Gregory <
***@reading.ac.uk> wrote:

> Dear Jim
>
> Thanks for explaining. So "natural" is the opposite of "anthropogenic", in
> a restricted sense. It includes the effect of anthropogenic climate change,
> but not the anthropogenic emissions of CO2. Is that right? I think this is
> potentially confusing in the context of CF, which has to cover a wide
> range of
> applications. It is not hard to imagine people wanting to use natural in
> the
> sense of *completely* unaffected by anthropogenic influence. (Obviously I'm
> not commenting on the terminology used in OMIP - I'm sure that's clear in
> that context.) I wonder if for CF we could think of something more
> explicit.
>
> Actually I'm unclear quite what is meant by due_to_natural_component (in
> several names). Component of what? Could you explain a bit more?
>
> Also, what does sea_water_ph_reported_on_total_scale_due_to_X mean? Is it
> perhaps a *change* in pH?
>
> Best wishes
>
> Jonathan
>
> > For the biogeochemistry in OMIP, we've agreed on using the terms
> > 'abiotic' and 'natural', neither synonyms nor antonyms for our
> > purposes. The OMIP-BGC simulations will be run with 2 parallel
> > simulations (or parallel tracers in the same simulation):
> >
> > * 'natural' means it will be maintained at same the CMIP6
> > preindustrial CO2 level throughout the simulation, while the
> >
> > * 'total' simulation will have varying atmospheric CO2, but the same
> > climate (e.g., forced in the OMIP ocean only run).
> >
> > The difference between the total and natural carbon tracers in the
> > two will give us the anthropogenic carbon. The ocean's natural
> > carbon cycle is considered in OMIP to change with climate change
> > even though its simulated atmospheric CO2 is held constant.
> >
> > Regarding 'abiotic', the natural and the total simulation include
> > both abiotic and biotic processes. To distinguish the two we also
> > include an abiotic carbon tracer. Furthermore, we use a simplified
> > abiotic approach to model C-14 in the ocean, e.g., to provide
> > deep-ocean ventilation ages.
> _______________________________________________
> CF-metadata mailing list
> CF-***@cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>

[James Orr]

> Thanks for explaining. So "natural" is the opposite of "anthropogenic", in
> a restricted sense. It includes the effect of anthropogenic climate change,
> but not the anthropogenic emissions of CO2. Is that right?

Yes, exactly.

> I think this is potentially confusing in the context of CF, which has
> to cover a wide range of applications. It is not hard to imagine
> people wanting to use natural in the sense of *completely* unaffected
> by anthropogenic influence. (Obviously I'm not commenting on the
> terminology used in OMIP - I'm sure that's clear in that context.) I
> wonder if for CF we could think of something more explicit.
>
> Actually I'm unclear quite what is meant by due_to_natural_component
> (in several names). Component of what? Could you explain a bit more?

You are right that this may be confusing. In ocean biogemchemical
modeling, anthropogenic CO2 (or anthropogenic dissolved inorganic carbon
in the ocean) is always defined as due only to the increase in
atmospheric CO2 since the onset of the industrial era. Natural CO2 is
everything else, i.e., referring to the idealized unperturbed natural
state AND its changes due to changes climate. So for ocean
biogeochemical community there is less room for ambiguity. These terms
are also defined in the OMIP-BGC protocols paper (in the CMIP6 special
issue):

http://www.geosci-model-dev-discuss.net/gmd-2016-155/

For others, what would you have in mind? One possibility would be to
change part of the name "*_due_to_natural_component"
"*_for_the_natural_component_and_its_changes_due_to_changing_climate"
but that makes for some awfully long names.

> Also, what does sea_water_ph_reported_on_total_scale_due_to_X mean? Is it
> perhaps a *change* in pH?

No it is not a change in pH, but the pH itself. I see the problem
though, e.g., with the following 2 full names:

* surface_sea_water_ph_reported_on_total_scale_due_to_natural_component
* sea_water_ph_reported_on_total_scale_due_to_abiotic_component

What about just changing the "due_to" to "for_the"

Jim


>> For the biogeochemistry in OMIP, we've agreed on using the terms
>> 'abiotic' and 'natural', neither synonyms nor antonyms for our
>> purposes. The OMIP-BGC simulations will be run with 2 parallel
>> simulations (or parallel tracers in the same simulation):
>>
>> * 'natural' means it will be maintained at same the CMIP6
>> preindustrial CO2 level throughout the simulation, while the
>>
>> * 'total' simulation will have varying atmospheric CO2, but the same
>> climate (e.g., forced in the OMIP ocean only run).
>>
>> The difference between the total and natural carbon tracers in the
>> two will give us the anthropogenic carbon. The ocean's natural
>> carbon cycle is considered in OMIP to change with climate change
>> even though its simulated atmospheric CO2 is held constant.
>>
>> Regarding 'abiotic', the natural and the total simulation include
>> both abiotic and biotic processes. To distinguish the two we also
>> include an abiotic carbon tracer. Furthermore, we use a simplified
>> abiotic approach to model C-14 in the ocean, e.g., to provide
>> deep-ocean ventilation ages.

[a***@stfc.ac.uk]

Dear Paul, Jim and Jonathan,

Thank you for all the proposals for OMIP biogeochemistry and chemistry names and the discussion that has already begun on these.

I have created entries for all the proposed names in the CEDA vocabulary editor, available here: http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter.
At the moment, the names themselves are all shown as originally proposed and I have added standard definition text for consistency with existing names. Please use the link to view the full list of names and definitions as it is easier than reproducing it all in an email to the list.

I think a number of the names look fine and could be published in their current form (see item 1 below). Paul and Jim, please can you check the definitions that I'm suggesting for these names and let me know if you're happy with them? (Comments from others are of course welcome).

For the groups of names where some discussion is still required my comments are in item 2.

1. Names that I think can be approved, subject to checking of the definitions.

mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1
ocean_mass_content_of_dissolved_organic_carbon, kg m-2
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2
mole_concentration_of_cfc11_in_sea_water, mol m-3
mole_concentration_of_cfc12_in_sea_water, mol m-3
surface_downward_mole_flux_of_cfc11, mol m-2 s-1
surface_downward_mole_flux_of_cfc12, mol m-2 s-1

2. Names requiring further discussion.

a. Phosphorus names
Sorry that I didn't notice it when previewing the names, but I have realized that 'phosphorus' is misspelled in the proposals, i.e., it should be 'phosphorus', not 'phosphorous'. Subject to this correction and checking of the definitions, I think the following names can be approved.
mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1

I will also correct the spelling in three further phosphorus names which remain under discussion due to other issues:
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water, mol m-3
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water, mol m-3

b. Definitions relating to new chemical species
It is usual to include a sentence in the definition when a standard name refers to a chemical species. There are three new species/isotopes in the current set of proposals. I suggest adding a single sentence to the definitions of the relevant names as follows:

carbon13: ' "carbon13" means the naturally occurring isotope of carbon having six protons and seven neutrons.'
carbon14: ' "carbon14" means the radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating.'
sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'

OK?

c. tendency_of_ocean_mole_content_of_[in]organic_carbon names

My question here refers to the following five proposals:
tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1

We have a couple of existing names for tendencies of inorganic carbon content, both of which are for dissolved_inorganic_carbon. Am I correct in thinking that your names also refer to dissolved amounts? If so, we should include it, e.g. tendency_of_ocean_mole_content_of_inorganic_carbon should be tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon, and so on.

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.

Either solution would be consistent with the proposed units and I'd be happy with either. Please let me know how you prefer to proceed.

As a final point in this section, the three proposed surface_sea_water_ph names are dimensionless, but I imagine that these too are really intended to represent the top model layer, in which case we should either drop 'surface' or change them to 'sea_surface' names too.

e. Limitation names
Jonathan has already raised the question of what 'limitation' means and also what measure of the various phytoplankton populations is being limited. This is a new concept in standard names so it's important to get the definitions right.

John Dunne replied to Jonathan:
> With respect to the limitation terms, we currently have the definitions explained in the "Resolved Comment" column as "Ratio of realizable miscellaneous other
> phytoplankton growth rate under low nitrogen stress to theoretical rate without such limitation".

So from this, my understanding is that nitrogen and iron are nutrients whose availability promotes the growth of phytoplankton, presumably by being absorbed somehow into the organic matter, while solar irradiance is clearly the energy source essential to the photosynthesis reaction. John's reply talks about growth rate, so I assume that means the growth rate of the population of a particular species (as opposed to the growth rate of individuals of that species).

Based on this I've attempted a couple of example definitions. If we can agree these, then I can go ahead and add the appropriate sentences to all the limitation names.
nitrogen_limitation_of_diatoms (canonical units: 1)
'Diatoms are single-celled phytoplankton with an external skeleton made of silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. Nitrogen is a nutrient essential to the growth of phytoplankton populations. "Nitrogen limitation" means the ratio of the growth rate of a species population in the environment (where there is a finite availability of nitrogen) to the theoretical growth rate if there were no such limit on nitrogen availability.'

N.B. For the irradiance names, I suggest we make them 'solar_irradiance' to be absolutely clear.
solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical units:1)
'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton that are not diatoms, diazotrophs, calcareous phytoplankton, picophytoplankton or other separately named components of the phytoplankton population. "Irradiance" means the power per unit area (called radiative flux in other standard names), the area being normal to the direction of flow of the radiant energy. Solar irradiance is essential to the photosynthesis reaction and its presence promotes the growth of phytoplankton populations. "Solar irradiance limitation" means the ratio of the growth rate of a species population in the environment (where the amount of sunlight reaching a location may be limited) to the theoretical growth rate if there were no such limit on solar irradiance.'

Comments and suggestions for improvement are welcome!

f. Natural/abiotic component names
Thank you for the useful discussion that has already taken place about the 22 proposed natural_component and abiotic_component names. I hadn't previously understood the details of how the OMIP experiments will be run.

Reading through the discussion, I agree with Jonathan that the natural_component names seem to be describing the forcing conditions for the model, rather than being a separate set of diagnostics that represent the effects of some process within the model. Hence I agree that it isn't necessary to define separate standard names with due_to_natural_component and I'd advocate leaving them out. Is that OK?

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?

Best wishes,
Alison

------
Alison Pamment Tel: [phone]
Centre for Environmental Data Analysis Email: ***@stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


From: Durack, Paul J. [mailto:***@llnl.gov]
Sent: 28 September 2016 19:12
To: cf-***@cgd.ucar.edu
Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu
Subject: New standard names for OMIP biogeochemistry and chemistry

Hi folks,

In preparation for the upcoming CMIP6-OMIP experiments we have a number of new standard names we'd like "blessed" for the biogeochemistry and chemistry data request.

I have appended these below. For folks interested, further information and notes are contained in the linked google sheets both indicated below. Many thanks to Alison for taking a first pass at these before sending to the mailing list.

The format below for the new names is:
standard_name_being_requested, units, (google sheet tab(s) and line number(s)).

***
160928 1105 ***@llnl.gov

Biogeochemistry see https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:

mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Oyr, 8; Omon, 63)
mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Oyr, 9; Omon, 64)
mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 13; Omon, 68)
sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Oyr, 27; Omon, 81)
sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr, 29; Omon, 83)
sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr, 30; Omon, 84)
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Oyr, 32; Omon, 86)
mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Oyr, 35; Omon, 89)
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Oyr, 37; Omon, 91)
mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 55; Omon, 108)
mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 56; Omon, 109)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr, 96; Omon, 113)
surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, mol m-3, (Omon, 7)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 8)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Omon, 10)
surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Omon, 11)
surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol m-3, (Omon, 12)
surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 13)
surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 14)
surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 15)
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 16)
surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 17)
surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 18)
surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 19)
surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 20)
surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 21)
surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 22)
surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 24)
surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 25)
surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 26)
surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3, (Omon, 27)
surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Omon, 28)
surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Omon, 30)
surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Omon, 31)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mol m-3, (Omon, 32)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Omon, 33)
surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Omon, 36)
surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3, (Omon, 37)
surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Omon, 38)
surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 39)
surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 40)
surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 41)
surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 43)
surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water, mol m-3, (Omon, 47)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 49)
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 50)
surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water, mol m-3, (Omon, 51)
surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 52)
surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3, (Omon, 53)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 54)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
nitrogen_limitation_of_diatoms, 1, (Omon, 116)
nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
irradiance_limitation_of_diatoms, 1, (Omon, 121)
irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
iron_limitation_of_diatoms, 1, (Omon, 126)
iron_limitation_of_diazotrophs, 1, (Omon, 127)
iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
iron_limitation_of_picophytoplankton, 1, (Omon, 129)
iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-2 s-1, (Omon, 139)
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1, (Omon, 140)
ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2, (Omon, 154)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component, Pa, (Omon, 156)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component, Pa, (Omon, 157)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 170)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 172)


Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG9G0lzIu7o/edit:

mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3; Omon, 4)
mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
***

Cheers,

P

[Lowry, Roy K.]

Hi Alison,


First of all, apologies for not commenting sooner - looking at this proposal as been on my todo list, but I hadn't got around to it. However, your e-mail makes it look like you're approaching end game so I thought I'd better provide some input.


I would suggest changing the C13 and C14 definitions to:


"carbon13 is a stable isotope of carbon having six protons and seven neutrons."

"carbon14 is a radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating."


The most abundant naturally-occurring isotope of carbon is carbon12, which is also stable. There are also other radioactive isotopes such as carbon11.

Regarding (c) to me inorganic carbon and dissolved inorganic carbon are significantly different, with the inorganic carbon being the sum of dissolved inorganic carbon (CO3-- and HCO3-) and particulate inorganic carbon (primarily CaCO3).

I have often expressed my opinions about 'surface' parameter descriptions. Whilst accepting the special case of SST where measurement technologies result in different geophysical quantities as a function of the depth below the surface, I strongly feel that the parameter description should not provide a qualitative description of the z co-ordinate coverage of the measurement. If CF doesn't allow precise z co-ordinate descriptions such as '2m air temperature' then why allow imprecise z coverages such as 'surface'? sea_surface_salinity still makes me cringe whenever I see it. In my opinion, opening the flood gates here would not be a good idea. Why not have one Standard Name for the measurement no matter where the cell is located vertically in the water column?

The phytoplankton compartmentalisation definitions make me feel uneasy. Diatoms are defined taxonomically, as are (possibly) calcareous phytoplankton - presuming its a synonym for coccolithophores. However, picophytoplankton is defined as autotrophic cells in a given size range (0.2-2 microns) no matter what the taxonomy and could potentially include some diatoms and calcareous phytoplankton. Then we come to diazatrophs (cells that fix nitrogen) which may be autotrophic, but most are heterotrophic. Does it actually mean diazotrophic autotrophs? Would it be possible to engage with a domain expert to come up with more watertight definitions of each compartment that do not overlap semantically?

'Miscellaneous phytoplankton' is a moveable feast and specifically naming excluded groups may not be the best way. What happens if the next version of the model specifically identifies additional phytoplankton compartments? It's a corner I've been forced into many times in the past (other organic contaminants and the like) and so understand the problem. My current thinking is that it may be better to leave the definition more fluid, such as 'Phytoplankton that are not covered by other explicitly defined phytoplankton groupings included in the data set.'

Hope this helps.

Cheers, Roy.



Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk. Please also use this e-mail if your requirement is urgent.


________________________________
From: CF-metadata <cf-metadata-***@cgd.ucar.edu> on behalf of ***@stfc.ac.uk <***@stfc.ac.uk>
Sent: 19 October 2016 19:16
To: ***@llnl.gov; cf-***@cgd.ucar.edu
Cc: ***@noaa.gov; ***@ucar.edu
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

Dear Paul, Jim and Jonathan,

Thank you for all the proposals for OMIP biogeochemistry and chemistry names and the discussion that has already begun on these.

I have created entries for all the proposed names in the CEDA vocabulary editor, available here: http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter.
At the moment, the names themselves are all shown as originally proposed and I have added standard definition text for consistency with existing names. Please use the link to view the full list of names and definitions as it is easier than reproducing it all in an email to the list.

I think a number of the names look fine and could be published in their current form (see item 1 below). Paul and Jim, please can you check the definitions that I'm suggesting for these names and let me know if you're happy with them? (Comments from others are of course welcome).

For the groups of names where some discussion is still required my comments are in item 2.

1. Names that I think can be approved, subject to checking of the definitions.

mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1
ocean_mass_content_of_dissolved_organic_carbon, kg m-2
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2
mole_concentration_of_cfc11_in_sea_water, mol m-3
mole_concentration_of_cfc12_in_sea_water, mol m-3
surface_downward_mole_flux_of_cfc11, mol m-2 s-1
surface_downward_mole_flux_of_cfc12, mol m-2 s-1

2. Names requiring further discussion.

a. Phosphorus names
Sorry that I didn't notice it when previewing the names, but I have realized that 'phosphorus' is misspelled in the proposals, i.e., it should be 'phosphorus', not 'phosphorous'. Subject to this correction and checking of the definitions, I think the following names can be approved.
mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1

I will also correct the spelling in three further phosphorus names which remain under discussion due to other issues:
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water, mol m-3
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water, mol m-3

b. Definitions relating to new chemical species
It is usual to include a sentence in the definition when a standard name refers to a chemical species. There are three new species/isotopes in the current set of proposals. I suggest adding a single sentence to the definitions of the relevant names as follows:

carbon13: ' "carbon13" means the naturally occurring isotope of carbon having six protons and seven neutrons.'
carbon14: ' "carbon14" means the radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating.'
sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'

OK?

c. tendency_of_ocean_mole_content_of_[in]organic_carbon names

My question here refers to the following five proposals:
tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1

We have a couple of existing names for tendencies of inorganic carbon content, both of which are for dissolved_inorganic_carbon. Am I correct in thinking that your names also refer to dissolved amounts? If so, we should include it, e.g. tendency_of_ocean_mole_content_of_inorganic_carbon should be tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon, and so on.

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.

Either solution would be consistent with the proposed units and I'd be happy with either. Please let me know how you prefer to proceed.

As a final point in this section, the three proposed surface_sea_water_ph names are dimensionless, but I imagine that these too are really intended to represent the top model layer, in which case we should either drop 'surface' or change them to 'sea_surface' names too.

e. Limitation names
Jonathan has already raised the question of what 'limitation' means and also what measure of the various phytoplankton populations is being limited. This is a new concept in standard names so it's important to get the definitions right.

John Dunne replied to Jonathan:
> With respect to the limitation terms, we currently have the definitions explained in the "Resolved Comment" column as "Ratio of realizable miscellaneous other
> phytoplankton growth rate under low nitrogen stress to theoretical rate without such limitation".

So from this, my understanding is that nitrogen and iron are nutrients whose availability promotes the growth of phytoplankton, presumably by being absorbed somehow into the organic matter, while solar irradiance is clearly the energy source essential to the photosynthesis reaction. John's reply talks about growth rate, so I assume that means the growth rate of the population of a particular species (as opposed to the growth rate of individuals of that species).

Based on this I've attempted a couple of example definitions. If we can agree these, then I can go ahead and add the appropriate sentences to all the limitation names.
nitrogen_limitation_of_diatoms (canonical units: 1)
'Diatoms are single-celled phytoplankton with an external skeleton made of silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. Nitrogen is a nutrient essential to the growth of phytoplankton populations. "Nitrogen limitation" means the ratio of the growth rate of a species population in the environment (where there is a finite availability of nitrogen) to the theoretical growth rate if there were no such limit on nitrogen availability.'

N.B. For the irradiance names, I suggest we make them 'solar_irradiance' to be absolutely clear.
solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical units:1)
'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton that are not diatoms, diazotrophs, calcareous phytoplankton, picophytoplankton or other separately named components of the phytoplankton population. "Irradiance" means the power per unit area (called radiative flux in other standard names), the area being normal to the direction of flow of the radiant energy. Solar irradiance is essential to the photosynthesis reaction and its presence promotes the growth of phytoplankton populations. "Solar irradiance limitation" means the ratio of the growth rate of a species population in the environment (where the amount of sunlight reaching a location may be limited) to the theoretical growth rate if there were no such limit on solar irradiance.'

Comments and suggestions for improvement are welcome!

f. Natural/abiotic component names
Thank you for the useful discussion that has already taken place about the 22 proposed natural_component and abiotic_component names. I hadn't previously understood the details of how the OMIP experiments will be run.

Reading through the discussion, I agree with Jonathan that the natural_component names seem to be describing the forcing conditions for the model, rather than being a separate set of diagnostics that represent the effects of some process within the model. Hence I agree that it isn't necessary to define separate standard names with due_to_natural_component and I'd advocate leaving them out. Is that OK?

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?

Best wishes,
Alison

------
Alison Pamment Tel: [phone]
Centre for Environmental Data Analysis Email: ***@stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


From: Durack, Paul J. [mailto:***@llnl.gov]
Sent: 28 September 2016 19:12
To: cf-***@cgd.ucar.edu
Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu
Subject: New standard names for OMIP biogeochemistry and chemistry

Hi folks,

In preparation for the upcoming CMIP6-OMIP experiments we have a number of new standard names we'd like "blessed" for the biogeochemistry and chemistry data request.

I have appended these below. For folks interested, further information and notes are contained in the linked google sheets both indicated below. Many thanks to Alison for taking a first pass at these before sending to the mailing list.

The format below for the new names is:
standard_name_being_requested, units, (google sheet tab(s) and line number(s)).

***
160928 1105 ***@llnl.gov

Biogeochemistry see https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:

mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Oyr, 8; Omon, 63)
mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Oyr, 9; Omon, 64)
mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 13; Omon, 68)
sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Oyr, 27; Omon, 81)
sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr, 29; Omon, 83)
sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr, 30; Omon, 84)
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Oyr, 32; Omon, 86)
mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Oyr, 35; Omon, 89)
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Oyr, 37; Omon, 91)
mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 55; Omon, 108)
mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 56; Omon, 109)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr, 96; Omon, 113)
surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, mol m-3, (Omon, 7)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 8)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Omon, 10)
surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Omon, 11)
surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol m-3, (Omon, 12)
surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 13)
surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 14)
surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 15)
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 16)
surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 17)
surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 18)
surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 19)
surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 20)
surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 21)
surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 22)
surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 24)
surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 25)
surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 26)
surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3, (Omon, 27)
surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Omon, 28)
surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Omon, 30)
surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Omon, 31)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mol m-3, (Omon, 32)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Omon, 33)
surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Omon, 36)
surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3, (Omon, 37)
surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Omon, 38)
surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 39)
surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 40)
surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 41)
surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 43)
surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water, mol m-3, (Omon, 47)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 49)
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 50)
surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water, mol m-3, (Omon, 51)
surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 52)
surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3, (Omon, 53)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 54)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
nitrogen_limitation_of_diatoms, 1, (Omon, 116)
nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
irradiance_limitation_of_diatoms, 1, (Omon, 121)
irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
iron_limitation_of_diatoms, 1, (Omon, 126)
iron_limitation_of_diazotrophs, 1, (Omon, 127)
iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
iron_limitation_of_picophytoplankton, 1, (Omon, 129)
iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-2 s-1, (Omon, 139)
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1, (Omon, 140)
ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2, (Omon, 154)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component, Pa, (Omon, 156)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component, Pa, (Omon, 157)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 170)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 172)


Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG9G0lzIu7o/edit:

mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3; Omon, 4)
mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
***

Cheers,

P
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[Durack, Paul J.]

Thanks for all your extended work on this Alison and apologies for the
tardy reply.

I note that I have been more focused on the physics variable request and
so I will defer to both John and Jim (included in the To: field of this
email) to have the final say over your definition queries/suggestions
below. If there are no responses within the next week I think proceed with
your definitions and close out all the requested names that are able to be
processed.


I¹ll reply to each of your blocked: 1, 2a-f separately below.

1. Names to be approved, subject to definition check

Great, I have checked over the definitions that you have proposed and they
all look good to me.

2. Names requiring further discussion

A) Phosphorus typos: Thanks for catching the phosphorus typos - I¹ll make
these changes back in the master google sheet. I have also previewed your
definitions and they look fine to me.

B) New descriptions: It would be great to include more descriptive
definitions for the new chemical species, your suggestions are fine with
me.

C) Dissolved quantities?: I think you¹re right here (I assume the
quantities are dissolved), however I have to defer to John and Jim on this
one.

D) Surface or top model level quantities: I actually had a similar query
when putting through the request - apologies here again but I will have to
defer to John and Jim.

E) Limitation names: I¹ll have to defer again to John and Jim on this one.

F) Natural/abiotic names: I also had some queries about these names, and
think this is another John/Jim call.


Thanks again for all your efforts Alison, I¹m certainly looking forward to
getting the physics names submitted to the mailing list and getting this
OMIP standard name request finalized.

Cheers,

P

On 10/19/16, 11:16 AM, "***@stfc.ac.uk"
<***@stfc.ac.uk> wrote:

>Dear Paul, Jim and Jonathan,
>
>Thank you for all the proposals for OMIP biogeochemistry and chemistry
>names and the discussion that has already begun on these.
>
>I have created entries for all the proposed names in the CEDA vocabulary
>editor, available here:
>http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerf
>ilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter
>+and+display=Filter.
>At the moment, the names themselves are all shown as originally proposed
>and I have added standard definition text for consistency with existing
>names. Please use the link to view the full list of names and definitions
>as it is easier than reproducing it all in an email to the list.
>
>I think a number of the names look fine and could be published in their
>current form (see item 1 below). Paul and Jim, please can you check the
>definitions that I'm suggesting for these names and let me know if you're
>happy with them? (Comments from others are of course welcome).
>
>For the groups of names where some discussion is still required my
>comments are in item 2.
>
>1. Names that I think can be approved, subject to checking of the
>definitions.
>
>mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
>mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturatio
>n, mol m-3
>mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
>tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_
>carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1
>ocean_mass_content_of_dissolved_organic_carbon, kg m-2
>ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg
>m-2
>mole_concentration_of_cfc11_in_sea_water, mol m-3
>mole_concentration_of_cfc12_in_sea_water, mol m-3
>surface_downward_mole_flux_of_cfc11, mol m-2 s-1
>surface_downward_mole_flux_of_cfc12, mol m-2 s-1
>
>2. Names requiring further discussion.
>
> a. Phosphorus names
>Sorry that I didn't notice it when previewing the names, but I have
>realized that 'phosphorus' is misspelled in the proposals, i.e., it
>should be 'phosphorus', not 'phosphorous'. Subject to this correction and
>checking of the definitions, I think the following names can be approved.
>mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
>tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production
>, mol m-2 s-1
>
>I will also correct the spelling in three further phosphorus names which
>remain under discussion due to other issues:
>surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water
>, mol m-3
>surface_mole_concentration_of_particulate_organic_matter_expressed_as_phos
>phorus_in_sea_water, mol m-3
>surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea
>_water, mol m-3
>
>b. Definitions relating to new chemical species
>It is usual to include a sentence in the definition when a standard name
>refers to a chemical species. There are three new species/isotopes in the
>current set of proposals. I suggest adding a single sentence to the
>definitions of the relevant names as follows:
>
>carbon13: ' "carbon13" means the naturally occurring isotope of carbon
>having six protons and seven neutrons.'
>carbon14: ' "carbon14" means the radioactive isotope of carbon having six
>protons and eight neutrons, used in radiocarbon dating.'
>sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'
>
>OK?
>
>c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
>
>My question here refers to the following five proposals:
>tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
>tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedim
>ent_dissolution, mol m-2 s-1
>tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedim
>entation, mol m-2 s-1
>tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimen
>t_dissolution, mol m-2 s-1
>tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimen
>tation, mol m-2 s-1
>
>We have a couple of existing names for tendencies of inorganic carbon
>content, both of which are for dissolved_inorganic_carbon. Am I correct
>in thinking that your names also refer to dissolved amounts? If so, we
>should include it, e.g.
>tendency_of_ocean_mole_content_of_inorganic_carbon should be
>tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon, and so on.
>
>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.
>
>Either solution would be consistent with the proposed units and I'd be
>happy with either. Please let me know how you prefer to proceed.
>
>As a final point in this section, the three proposed surface_sea_water_ph
>names are dimensionless, but I imagine that these too are really intended
>to represent the top model layer, in which case we should either drop
>'surface' or change them to 'sea_surface' names too.
>
>e. Limitation names
>Jonathan has already raised the question of what 'limitation' means and
>also what measure of the various phytoplankton populations is being
>limited. This is a new concept in standard names so it's important to get
>the definitions right.
>
>John Dunne replied to Jonathan:
>> With respect to the limitation terms, we currently have the definitions
>>explained in the "Resolved Comment" column as "Ratio of realizable
>>miscellaneous other
>> phytoplankton growth rate under low nitrogen stress to theoretical rate
>>without such limitation".
>
>So from this, my understanding is that nitrogen and iron are nutrients
>whose availability promotes the growth of phytoplankton, presumably by
>being absorbed somehow into the organic matter, while solar irradiance is
>clearly the energy source essential to the photosynthesis reaction.
>John's reply talks about growth rate, so I assume that means the growth
>rate of the population of a particular species (as opposed to the growth
>rate of individuals of that species).
>
>Based on this I've attempted a couple of example definitions. If we can
>agree these, then I can go ahead and add the appropriate sentences to all
>the limitation names.
>nitrogen_limitation_of_diatoms (canonical units: 1)
>'Diatoms are single-celled phytoplankton with an external skeleton made
>of silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae
>that live near the water surface where there is sufficient light to
>support photosynthesis. Nitrogen is a nutrient essential to the growth of
>phytoplankton populations. "Nitrogen limitation" means the ratio of the
>growth rate of a species population in the environment (where there is a
>finite availability of nitrogen) to the theoretical growth rate if there
>were no such limit on nitrogen availability.'
>
>N.B. For the irradiance names, I suggest we make them 'solar_irradiance'
>to be absolutely clear.
>solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical
>units:1)
>'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live
>near the water surface where there is sufficient light to support
>photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton
>that are not diatoms, diazotrophs, calcareous phytoplankton,
>picophytoplankton or other separately named components of the
>phytoplankton population. "Irradiance" means the power per unit area
>(called radiative flux in other standard names), the area being normal to
>the direction of flow of the radiant energy. Solar irradiance is
>essential to the photosynthesis reaction and its presence promotes the
>growth of phytoplankton populations. "Solar irradiance limitation" means
>the ratio of the growth rate of a species population in the environment
>(where the amount of sunlight reaching a location may be limited) to the
>theoretical growth rate if there were no such limit on solar irradiance.'
>
>Comments and suggestions for improvement are welcome!
>
>f. Natural/abiotic component names
>Thank you for the useful discussion that has already taken place about
>the 22 proposed natural_component and abiotic_component names. I hadn't
>previously understood the details of how the OMIP experiments will be run.
>
>Reading through the discussion, I agree with Jonathan that the
>natural_component names seem to be describing the forcing conditions for
>the model, rather than being a separate set of diagnostics that represent
>the effects of some process within the model. Hence I agree that it isn't
>necessary to define separate standard names with due_to_natural_component
>and I'd advocate leaving them out. Is that OK?
>
>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?
>
>Best wishes,
>Alison
>
>------
>Alison Pamment Tel:
>[phone]
>Centre for Environmental Data Analysis Email:
>***@stfc.ac.uk
>STFC Rutherford Appleton Laboratory
>R25, 2.22
>Harwell Campus, Didcot, OX11 0QX, U.K.
>
>
>From: Durack, Paul J. [mailto:***@llnl.gov]
>Sent: 28 September 2016 19:12
>To: cf-***@cgd.ucar.edu
>Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James
>Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu
>Subject: New standard names for OMIP biogeochemistry and chemistry
>
>Hi folks,
>
>In preparation for the upcoming CMIP6-OMIP experiments we have a number
>of new standard names we'd like "blessed" for the biogeochemistry and
>chemistry data request.
>
>I have appended these below. For folks interested, further information
>and notes are contained in the linked google sheets both indicated below.
>Many thanks to Alison for taking a first pass at these before sending to
>the mailing list.
>
>The format below for the new names is:
>standard_name_being_requested, units, (google sheet tab(s) and line
>number(s)).
>
>***
>160928 1105 ***@llnl.gov
>
>Biogeochemistry see
>https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thi
>KaulIjfbw/edit:
>
>mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natur
>al_component, mol m-3, (Oyr, 6; Omon, 61)
>mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiot
>ic_component, mol m-3, (Oyr, 7; Omon, 62)
>mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3,
>(Oyr, 8; Omon, 63)
>mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3,
>(Oyr, 9; Omon, 64)
>mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3,
>(Oyr, 13; Omon, 68)
>sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component
>, mol m-3, (Oyr, 27; Omon, 81)
>sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr,
>29; Omon, 83)
>sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr,
>30; Omon, 84)
>mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturatio
>n, mol m-3, (Oyr, 32; Omon, 86)
>mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol
>m-3, (Oyr, 35; Omon, 89)
>mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3,
>(Oyr, 37; Omon, 91)
>mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water,
>mol m-3, (Oyr, 55; Omon, 108)
>mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water,
>mol m-3, (Oyr, 56; Omon, 109)
>mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equil
>ibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
>mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equil
>ibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
>tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_
>carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
>tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_
>carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr,
>96; Omon, 113)
>surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
>surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_na
>tural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
>surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_ab
>iotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
>surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_
>abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
>surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_
>abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
>surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water,
>mol m-3, (Omon, 7)
>surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_
>to_natural_component, mol m-3, (Omon, 8)
>surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_
>to_abiotic_component, mol m-3, (Omon, 9)
>surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water,
>mol m-3, (Omon, 10)
>surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water,
>mol m-3, (Omon, 11)
>surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol
>m-3, (Omon, 12)
>surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_wat
>er, mol m-3, (Omon, 13)
>surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water
>, mol m-3, (Omon, 14)
>surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water,
>mol m-3, (Omon, 15)
>surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_
>water, mol m-3, (Omon, 16)
>surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water,
>mol m-3, (Omon, 17)
>surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water,
>mol m-3, (Omon, 18)
>surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water,
>mol m-3, (Omon, 19)
>surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water
>, mol m-3, (Omon, 20)
>surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon
>_in_sea_water, mol m-3, (Omon, 21)
>surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea
>_water, mol m-3, (Omon, 22)
>surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_car
>bon_in_sea_water, mol m-3, (Omon, 23)
>surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_
>water, mol m-3, (Omon, 24)
>surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_w
>ater, mol m-3, (Omon, 25)
>surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbo
>n_in_sea_water, mol m-3, (Omon, 26)
>surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3,
>(Omon, 27)
>surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_c
>omponent, mol m-3, (Omon, 28)
>surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
>surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1,
>(Omon, 30)
>surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1,
>(Omon, 31)
>surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water,
>mol m-3, (Omon, 32)
>surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_s
>aturation, mol m-3, (Omon, 33)
>surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
>surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
>surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water
>, mol m-3, (Omon, 36)
>surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3,
>(Omon, 37)
>surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water,
>mol m-3, (Omon, 38)
>surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_se
>a_water, kg m-3, (Omon, 39)
>surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_wate
>r, kg m-3, (Omon, 40)
>surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_
>water, kg m-3, (Omon, 41)
>surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chloro
>phyll_in_sea_water, kg m-3, (Omon, 42)
>surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_i
>n_sea_water, kg m-3, (Omon, 43)
>surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chl
>orophyll_in_sea_water, kg m-3, (Omon, 44)
>surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitr
>ogen_in_sea_water, mol m-3, (Omon, 45)
>surface_mole_concentration_of_particulate_organic_matter_expressed_as_phos
>phorous_in_sea_water, mol m-3, (Omon, 46)
>surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron
>_in_sea_water, mol m-3, (Omon, 47)
>surface_mole_concentration_of_particulate_organic_matter_expressed_as_sili
>con_in_sea_water, mol m-3, (Omon, 48)
>surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_w
>ater, mol m-3, (Omon, 49)
>surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_se
>a_water, mol m-3, (Omon, 50)
>surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water
>, mol m-3, (Omon, 51)
>surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_wa
>ter, mol m-3, (Omon, 52)
>surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3,
>(Omon, 53)
>surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water,
>mol m-3, (Omon, 54)
>surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_d
>ue_to_natural_component, mol m-3, (Omon, 55)
>surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_d
>ue_to_abiotic_component, mol m-3, (Omon, 56)
>surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_
>in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
>surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_
>in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
>nitrogen_limitation_of_diatoms, 1, (Omon, 116)
>nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
>nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
>nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
>nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
>irradiance_limitation_of_diatoms, 1, (Omon, 121)
>irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
>irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
>irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
>irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
>iron_limitation_of_diatoms, 1, (Omon, 126)
>iron_limitation_of_diazotrophs, 1, (Omon, 127)
>iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
>iron_limitation_of_picophytoplankton, 1, (Omon, 129)
>iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
>tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production,
>mol m-2 s-1, (Omon, 139)
>tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production
>, mol m-2 s-1, (Omon, 140)
>ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
>ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg
>m-2, (Omon, 154)
>surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_com
>ponent, Pa, (Omon, 156)
>surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_com
>ponent, Pa, (Omon, 157)
>surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_a
>ir_due_to_natural_component, Pa, (Omon, 159)
>surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_a
>ir_due_to_abiotic_component, Pa, (Omon, 160)
>tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedim
>ent_dissolution, mol m-2 s-1, (Omon, 169)
>tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedim
>entation, mol m-2 s-1, (Omon, 170)
>tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimen
>t_dissolution, mol m-2 s-1, (Omon, 171)
>tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimen
>tation, mol m-2 s-1, (Omon, 172)
>
>
>Chemistry see
>https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG
>9G0lzIu7o/edit:
>
>mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3;
>Omon, 4)
>mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
>mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
>surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
>surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
>surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
>***
>
>Cheers,
>
>P

[John Dunne - NOAA Federal]

Hi Alison and all,

Sorry for the delay. I have been communicating with Jim Orr and Paul
Durack about your points, and have the following responses and proposal. I
am not sure what happens know, so please advise if you want to take the
discussion offline or have me put together a new revised spreadsheet.

Thanks, John

On Wed, Oct 19, 2016 at 2:16 PM, <***@stfc.ac.uk> wrote:

> Dear Paul, Jim and Jonathan,
>
> Thank you for all the proposals for OMIP biogeochemistry and chemistry
> names and the discussion that has already begun on these.
>
> I have created entries for all the proposed names in the CEDA vocabulary
> editor, available here: http://cfeditor.ceda.ac.uk/pro
> posals/1?status=active&namefilter=&proposerfilter=Durack&
> descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP
> &filter+and+display=Filter.
> At the moment, the names themselves are all shown as originally proposed
> and I have added standard definition text for consistency with existing
> names. Please use the link to view the full list of names and definitions
> as it is easier than reproducing it all in an email to the list.
>
> I think a number of the names look fine and could be published in their
> current form (see item 1 below). Paul and Jim, please can you check the
> definitions that I'm suggesting for these names and let me know if you're
> happy with them? (Comments from others are of course welcome).
>
> For the groups of names where some discussion is still required my
> comments are in item 2.
>
> 1. Names that I think can be approved, subject to checking of the
> definitions.
>
> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation,
> mol m-3
> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
> tendency_of_mole_concentration_of_particulate_organic_
> matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton,
> mol m-3 s-1
> ocean_mass_content_of_dissolved_organic_carbon, kg m-2
> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg
> m-2
> mole_concentration_of_cfc11_in_sea_water, mol m-3
> mole_concentration_of_cfc12_in_sea_water, mol m-3
> surface_downward_mole_flux_of_cfc11, mol m-2 s-1
> surface_downward_mole_flux_of_cfc12, mol m-2 s-1
>
> 2. Names requiring further discussion.
>
> a. Phosphorus names
> Sorry that I didn't notice it when previewing the names, but I have
> realized that 'phosphorus' is misspelled in the proposals, i.e., it should
> be 'phosphorus', not 'phosphorous'. Subject to this correction and checking
> of the definitions, I think the following names can be approved.
> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
> tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production,
> mol m-2 s-1
>
> I will also correct the spelling in three further phosphorus names which
> remain under discussion due to other issues:
> surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water,
> mol m-3
> surface_mole_concentration_of_particulate_organic_matter_exp
> ressed_as_phosphorus_in_sea_water, mol m-3
> surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water,
> mol m-3
>
> b. Definitions relating to new chemical species
> It is usual to include a sentence in the definition when a standard name
> refers to a chemical species. There are three new species/isotopes in the
> current set of proposals. I suggest adding a single sentence to the
> definitions of the relevant names as follows:
>
> carbon13: ' "carbon13" means the naturally occurring isotope of carbon
> having six protons and seven neutrons.'
> carbon14: ' "carbon14" means the radioactive isotope of carbon having six
> protons and eight neutrons, used in radiocarbon dating.'
> sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'
>
> OK?
>

OK

>
> c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
>
> My question here refers to the following five proposals:
> tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_
> runoff_and_sediment_dissolution, mol m-2 s-1
> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation,
> mol m-2 s-1
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_
> runoff_and_sediment_dissolution, mol m-2 s-1
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation,
> mol m-2 s-1
>
> We have a couple of existing names for tendencies of inorganic carbon
> content, both of which are for dissolved_inorganic_carbon. Am I correct in
> thinking that your names also refer to dissolved amounts? If so, we should
> include it, e.g. tendency_of_ocean_mole_content_of_inorganic_carbon
> should be tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon,
> and so on.
>

These terms are intended to allow users to construct a complete carbon
budget, and were not intended to distinguish between particulate and
dissolved. Should we restrict the definitions and add more terms? add
"total" to the name before "inorganic"? Please note that the names listed
above with "sedimentation" are incorrect. As they are intended to
represent loss from the ocean, they should not have "runoff_and". Like in
Paul's spreadsheet, they should just be "tendency_of_ocean_mole_content
_of_inorganic_carbon_due_to_sedimentation" and
"tendency_of_ocean_mole_content_of_organic_carbon_due_to_sedimentation".
These are effectively both "particulate" since they just represent pelagic
sinking in current models to my knowledge, though it is possible that
models might include insitu benthic organic production and/or inorganic
precipitation which could be represented as a dissolved loss. Of course,
"sediment dissolution" would be just dissolved, but runoff could be either
particulate or dissolved... did you want to distinguish between them?


> 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_dissolve
> d_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.
>
> Either solution would be consistent with the proposed units and I'd be
> happy with either. Please let me know how you prefer to proceed.
>
> As a final point in this section, the three proposed surface_sea_water_ph
> names are dimensionless, but I imagine that these too are really intended
> to represent the top model layer, in which case we should either drop
> 'surface' or change them to 'sea_surface' names too.
>

While we are sensitive to your and Jonathan's point that it leads to
proliferation of variable names, we prefer the second option, particularly
in light of the variables that we are requesting daily as 2D sea surface
and monthly full 3D. If we are going to go this route, should these names
be
"sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water",
or just
"sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll"


> e. Limitation names
> Jonathan has already raised the question of what 'limitation' means and
> also what measure of the various phytoplankton populations is being
> limited. This is a new concept in standard names so it's important to get
> the definitions right.
>
> John Dunne replied to Jonathan:
> > With respect to the limitation terms, we currently have the definitions
> explained in the "Resolved Comment" column as "Ratio of realizable
> miscellaneous other
> > phytoplankton growth rate under low nitrogen stress to theoretical rate
> without such limitation".
>
> So from this, my understanding is that nitrogen and iron are nutrients
> whose availability promotes the growth of phytoplankton, presumably by
> being absorbed somehow into the organic matter, while solar irradiance is
> clearly the energy source essential to the photosynthesis reaction. John's
> reply talks about growth rate, so I assume that means the growth rate of
> the population of a particular species (as opposed to the growth rate of
> individuals of that species).
>

Yes, it is a population-level metric.


>
> Based on this I've attempted a couple of example definitions. If we can
> agree these, then I can go ahead and add the appropriate sentences to all
> the limitation names.
> nitrogen_limitation_of_diatoms (canonical units: 1)
> 'Diatoms are single-celled phytoplankton with an external skeleton made of
> silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae that
> live near the water surface where there is sufficient light to support
> photosynthesis. Nitrogen is a nutrient essential to the growth of
> phytoplankton populations. "Nitrogen limitation" means the ratio of the
> growth rate of a species population in the environment (where there is a
> finite availability of nitrogen) to the theoretical growth rate if there
> were no such limit on nitrogen availability.'
>



>
> N.B. For the irradiance names, I suggest we make them 'solar_irradiance'
> to be absolutely clear.
> solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical
> units:1)
> 'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live
> near the water surface where there is sufficient light to support
> photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton
> that are not diatoms, diazotrophs, calcareous phytoplankton,
> picophytoplankton or other separately named components of the phytoplankton
> population. "Irradiance" means the power per unit area (called radiative
> flux in other standard names), the area being normal to the direction of
> flow of the radiant energy. Solar irradiance is essential to the
> photosynthesis reaction and its presence promotes the growth of
> phytoplankton populations. "Solar irradiance limitation" means the ratio of
> the growth rate of a species population in the environment (where the
> amount of sunlight reaching a location may be limited) to the theoretical
> growth rate if there were no such limit on solar irradiance.'
>
>

If you think this level of detail is necessary, I am fine with it, though
I'm not sure where it is being proposed the be entered (the comment?) it
seems inconsistent with the lack of detail on most variables. Editorially,
I think adding the fact that they are "single celled", and "prokaryotic or
eukaryotic" seem superfluous (e.g. the models intend to
represent diazotrophs, diatoms, and others groups even when they form
chains)", and "live near the water surface" would probably be better as
simply "grow".


> Comments and suggestions for improvement are welcome!
>
> f. Natural/abiotic component names
> Thank you for the useful discussion that has already taken place about the
> 22 proposed natural_component and abiotic_component names. I hadn't
> previously understood the details of how the OMIP experiments will be run.
>
> Reading through the discussion, I agree with Jonathan that the
> natural_component names seem to be describing the forcing conditions for
> the model, rather than being a separate set of diagnostics that represent
> the effects of some process within the model. Hence I agree that it isn't
> necessary to define separate standard names with due_to_natural_component
> and I'd advocate leaving them out. Is that OK?
>

I agree that the "due_to_natural_component" reference is potentially
misleading. In the simplest models it is envisioned as a separate tracer
in the same run - in the more complex BGC models where the biological
interactions are pH and/or saturation sensitive - such a tracer is an
approximation (analogue) of what one would get in a full control run, thus
give the moniker of the "natural"

>
> 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?
>

Like for "natural", this is only an analogue of what would otherwise be a
solubility-driven tracer. To identify these as separate tracers more
clearly, I propose changing the comment and standard names to the following:

"Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration natural analogue
forced by preindustrial atmospheric xCO2"
mole_concentration_of_dissolved_inorganic_carbon_
natural_analogue_in_sea_water

"Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration abiotic analogue
ignoring biological effects on carbon and alkalinity"
mole_concentration_of_dissolved_inorganic_carbon_
abiotic_analogue_in_sea_water

Does that make more sense?


>
> Best wishes,
> Alison
>
> ------
> Alison Pamment Tel: +44
> 1235 778065
> Centre for Environmental Data Analysis Email:
> ***@stfc.ac.uk
> STFC Rutherford Appleton Laboratory
> R25, 2.22
> Harwell Campus, Didcot, OX11 0QX, U.K.
>
>
> From: Durack, Paul J. [mailto:***@llnl.gov]
> Sent: 28 September 2016 19:12
> To: cf-***@cgd.ucar.edu
> Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James
> Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu
> Subject: New standard names for OMIP biogeochemistry and chemistry
>
> Hi folks,
>
> In preparation for the upcoming CMIP6-OMIP experiments we have a number of
> new standard names we'd like "blessed" for the biogeochemistry and
> chemistry data request.
>
> I have appended these below. For folks interested, further information and
> notes are contained in the linked google sheets both indicated below. Many
> thanks to Alison for taking a first pass at these before sending to the
> mailing list.
>
> The format below for the new names is:
> standard_name_being_requested, units, (google sheet tab(s) and line
> number(s)).
>
> ***
> 160928 1105 ***@llnl.gov
>
> Biogeochemistry see https://docs.google.com/spread
> sheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:
>
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_
> water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
> mole_concentration_of_dissolved_inorganic_carbon_in_sea_
> water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
> mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3,
> (Oyr, 8; Omon, 63)
> mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3,
> (Oyr, 9; Omon, 64)
> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3,
> (Oyr, 13; Omon, 68)
> sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component,
> mol m-3, (Oyr, 27; Omon, 81)
> sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr,
> 29; Omon, 83)
> sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr,
> 30; Omon, 84)
> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation,
> mol m-3, (Oyr, 32; Omon, 86)
> mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol
> m-3, (Oyr, 35; Omon, 89)
> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3,
> (Oyr, 37; Omon, 91)
> mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water,
> mol m-3, (Oyr, 55; Omon, 108)
> mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water,
> mol m-3, (Oyr, 56; Omon, 109)
> mole_concentration_of_carbonate_expressed_as_carbon_for_sea_
> water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
> mole_concentration_of_carbonate_expressed_as_carbon_for_sea_
> water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
> tendency_of_mole_concentration_of_particulate_organic_
> matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3
> s-1, (Oyr, 75)
> tendency_of_mole_concentration_of_particulate_organic_
> matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton,
> mol m-3 s-1, (Oyr, 96; Omon, 113)
> surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
> surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component,
> kg m-2 s-1, (Oyr, 101; Omon, 163)
> surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component,
> kg m-2 s-1, (Oyr, 102; Omon, 164)
> surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_
> carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
> surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_
> carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water,
> mol m-3, (Omon, 7)
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_
> sea_water_due_to_natural_component, mol m-3, (Omon, 8)
> surface_mole_concentration_of_dissolved_inorganic_carbon_in_
> sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
> surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water,
> mol m-3, (Omon, 10)
> surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water,
> mol m-3, (Omon, 11)
> surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol
> m-3, (Omon, 12)
> surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 13)
> surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 14)
> surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 15)
> surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 16)
> surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 17)
> surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 18)
> surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 19)
> surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 20)
> surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 21)
> surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 22)
> surface_mole_concentration_of_miscellaneous_phytoplankton_ex
> pressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
> surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 24)
> surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 25)
> surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 26)
> surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3,
> (Omon, 27)
> surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component,
> mol m-3, (Omon, 28)
> surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
> surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1,
> (Omon, 30)
> surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1,
> (Omon, 31)
> surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water,
> mol m-3, (Omon, 32)
> surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation,
> mol m-3, (Omon, 33)
> surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
> surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
> surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water,
> mol m-3, (Omon, 36)
> surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3,
> (Omon, 37)
> surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water,
> mol m-3, (Omon, 38)
> surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water,
> kg m-3, (Omon, 39)
> surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water,
> kg m-3, (Omon, 40)
> surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water,
> kg m-3, (Omon, 41)
> surface_mass_concentration_of_calcareous_phytoplankton_expre
> ssed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
> surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water,
> kg m-3, (Omon, 43)
> surface_mass_concentration_of_miscellaneous_phytoplankton_ex
> pressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
> surface_mole_concentration_of_particulate_organic_matter_exp
> ressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
> surface_mole_concentration_of_particulate_organic_matter_exp
> ressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
> surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water,
> mol m-3, (Omon, 47)
> surface_mole_concentration_of_particulate_organic_matter_exp
> ressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
> surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water,
> mol m-3, (Omon, 49)
> surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water,
> mol m-3, (Omon, 50)
> surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water,
> mol m-3, (Omon, 51)
> surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water,
> mol m-3, (Omon, 52)
> surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3,
> (Omon, 53)
> surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water,
> mol m-3, (Omon, 54)
> surface_mole_concentration_of_carbonate_expressed_as_carbon_
> in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
> surface_mole_concentration_of_carbonate_expressed_as_carbon_
> in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
> surface_mole_concentration_of_carbonate_expressed_as_carbon_
> for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
> surface_mole_concentration_of_carbonate_expressed_as_carbon_
> for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
> nitrogen_limitation_of_diatoms, 1, (Omon, 116)
> nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
> nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
> nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
> nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
> irradiance_limitation_of_diatoms, 1, (Omon, 121)
> irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
> irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
> irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
> irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
> iron_limitation_of_diatoms, 1, (Omon, 126)
> iron_limitation_of_diazotrophs, 1, (Omon, 127)
> iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
> iron_limitation_of_picophytoplankton, 1, (Omon, 129)
> iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
> tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production,
> mol m-2 s-1, (Omon, 139)
> tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production,
> mol m-2 s-1, (Omon, 140)
> ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg
> m-2, (Omon, 154)
> surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component,
> Pa, (Omon, 156)
> surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component,
> Pa, (Omon, 157)
> surface_carbon_dioxide_partial_pressure_difference_between_
> sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
> surface_carbon_dioxide_partial_pressure_difference_between_
> sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_
> runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation,
> mol m-2 s-1, (Omon, 170)
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_
> runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation,
> mol m-2 s-1, (Omon, 172)
>
>
> Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6
> Y8oIxx9APLOlCG9G0lzIu7o/edit:
>
> mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3;
> Omon, 4)
> mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
> mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
> surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
> surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
> surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
> ***
>
> Cheers,
>
> P
>

[Lowry, Roy K.]

Dear John,


Following these comments, I now wonder a little more about your previous comment on differences in dimensionality between your surface concentrations and concentrations at depth. Could you clarify what the units of measure are for your 2D simulations? Are they concentrations per unit area (e.g. mg/m2) where the value represents an integration over depth or concentrations per unit volume (e.g. mg/m3) where the value represents the concentration in the surface water layer?


If it's the former then separate Standard Names are certainly required, but I would say the wording would need tweaking to reflect the fact such as the addition of 'integrated' or 'integral'.


Cheers, Roy.


Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk. Please also use this e-mail if your requirement is urgent.


________________________________
From: CF-metadata <cf-metadata-***@cgd.ucar.edu> on behalf of John Dunne - NOAA Federal <***@noaa.gov>
Sent: 04 November 2016 00:09
To: ***@stfc.ac.uk
Cc: cf-***@cgd.ucar.edu; Stephen Griffies; ***@ucar.edu; Durack, Paul J.
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

Hi Alison and all,

Sorry for the delay. I have been communicating with Jim Orr and Paul Durack about your points, and have the following responses and proposal. I am not sure what happens know, so please advise if you want to take the discussion offline or have me put together a new revised spreadsheet.

Thanks, John

On Wed, Oct 19, 2016 at 2:16 PM, <***@stfc.ac.uk<mailto:***@stfc.ac.uk>> wrote:
Dear Paul, Jim and Jonathan,

Thank you for all the proposals for OMIP biogeochemistry and chemistry names and the discussion that has already begun on these.

I have created entries for all the proposed names in the CEDA vocabulary editor, available here: http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter.
At the moment, the names themselves are all shown as originally proposed and I have added standard definition text for consistency with existing names. Please use the link to view the full list of names and definitions as it is easier than reproducing it all in an email to the list.

I think a number of the names look fine and could be published in their current form (see item 1 below). Paul and Jim, please can you check the definitions that I'm suggesting for these names and let me know if you're happy with them? (Comments from others are of course welcome).

For the groups of names where some discussion is still required my comments are in item 2.

1. Names that I think can be approved, subject to checking of the definitions.

mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1
ocean_mass_content_of_dissolved_organic_carbon, kg m-2
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2
mole_concentration_of_cfc11_in_sea_water, mol m-3
mole_concentration_of_cfc12_in_sea_water, mol m-3
surface_downward_mole_flux_of_cfc11, mol m-2 s-1
surface_downward_mole_flux_of_cfc12, mol m-2 s-1

2. Names requiring further discussion.

a. Phosphorus names
Sorry that I didn't notice it when previewing the names, but I have realized that 'phosphorus' is misspelled in the proposals, i.e., it should be 'phosphorus', not 'phosphorous'. Subject to this correction and checking of the definitions, I think the following names can be approved.
mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1

I will also correct the spelling in three further phosphorus names which remain under discussion due to other issues:
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water, mol m-3
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water, mol m-3

b. Definitions relating to new chemical species
It is usual to include a sentence in the definition when a standard name refers to a chemical species. There are three new species/isotopes in the current set of proposals. I suggest adding a single sentence to the definitions of the relevant names as follows:

carbon13: ' "carbon13" means the naturally occurring isotope of carbon having six protons and seven neutrons.'
carbon14: ' "carbon14" means the radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating.'
sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'

OK?

OK

c. tendency_of_ocean_mole_content_of_[in]organic_carbon names

My question here refers to the following five proposals:
tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1

We have a couple of existing names for tendencies of inorganic carbon content, both of which are for dissolved_inorganic_carbon. Am I correct in thinking that your names also refer to dissolved amounts? If so, we should include it, e.g. tendency_of_ocean_mole_content_of_inorganic_carbon should be tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon, and so on.

These terms are intended to allow users to construct a complete carbon budget, and were not intended to distinguish between particulate and dissolved. Should we restrict the definitions and add more terms? add "total" to the name before "inorganic"? Please note that the names listed above with "sedimentation" are incorrect. As they are intended to represent loss from the ocean, they should not have "runoff_and". Like in Paul's spreadsheet, they should just be "tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_sedimentation" and "tendency_of_ocean_mole_content_of_organic_carbon_due_to_sedimentation". These are effectively both "particulate" since they just represent pelagic sinking in current models to my knowledge, though it is possible that models might include insitu benthic organic production and/or inorganic precipitation which could be represented as a dissolved loss. Of course, "sediment dissolution" would be just dissolved, but runoff could be either particulate or dissolved... did you want to distinguish between them?


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.

Either solution would be consistent with the proposed units and I'd be happy with either. Please let me know how you prefer to proceed.

As a final point in this section, the three proposed surface_sea_water_ph names are dimensionless, but I imagine that these too are really intended to represent the top model layer, in which case we should either drop 'surface' or change them to 'sea_surface' names too.

While we are sensitive to your and Jonathan's point that it leads to proliferation of variable names, we prefer the second option, particularly in light of the variables that we are requesting daily as 2D sea surface and monthly full 3D. If we are going to go this route, should these names be "sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water", or just "sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll"


e. Limitation names
Jonathan has already raised the question of what 'limitation' means and also what measure of the various phytoplankton populations is being limited. This is a new concept in standard names so it's important to get the definitions right.

John Dunne replied to Jonathan:
> With respect to the limitation terms, we currently have the definitions explained in the "Resolved Comment" column as "Ratio of realizable miscellaneous other
> phytoplankton growth rate under low nitrogen stress to theoretical rate without such limitation".

So from this, my understanding is that nitrogen and iron are nutrients whose availability promotes the growth of phytoplankton, presumably by being absorbed somehow into the organic matter, while solar irradiance is clearly the energy source essential to the photosynthesis reaction. John's reply talks about growth rate, so I assume that means the growth rate of the population of a particular species (as opposed to the growth rate of individuals of that species).

Yes, it is a population-level metric.


Based on this I've attempted a couple of example definitions. If we can agree these, then I can go ahead and add the appropriate sentences to all the limitation names.
nitrogen_limitation_of_diatoms (canonical units: 1)
'Diatoms are single-celled phytoplankton with an external skeleton made of silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. Nitrogen is a nutrient essential to the growth of phytoplankton populations. "Nitrogen limitation" means the ratio of the growth rate of a species population in the environment (where there is a finite availability of nitrogen) to the theoretical growth rate if there were no such limit on nitrogen availability.'



N.B. For the irradiance names, I suggest we make them 'solar_irradiance' to be absolutely clear.
solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical units:1)
'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton that are not diatoms, diazotrophs, calcareous phytoplankton, picophytoplankton or other separately named components of the phytoplankton population. "Irradiance" means the power per unit area (called radiative flux in other standard names), the area being normal to the direction of flow of the radiant energy. Solar irradiance is essential to the photosynthesis reaction and its presence promotes the growth of phytoplankton populations. "Solar irradiance limitation" means the ratio of the growth rate of a species population in the environment (where the amount of sunlight reaching a location may be limited) to the theoretical growth rate if there were no such limit on solar irradiance.'



If you think this level of detail is necessary, I am fine with it, though I'm not sure where it is being proposed the be entered (the comment?) it seems inconsistent with the lack of detail on most variables. Editorially, I think adding the fact that they are "single celled", and "prokaryotic or eukaryotic" seem superfluous (e.g. the models intend to represent diazotrophs, diatoms, and others groups even when they form chains)", and "live near the water surface" would probably be better as simply "grow".

Comments and suggestions for improvement are welcome!

f. Natural/abiotic component names
Thank you for the useful discussion that has already taken place about the 22 proposed natural_component and abiotic_component names. I hadn't previously understood the details of how the OMIP experiments will be run.

Reading through the discussion, I agree with Jonathan that the natural_component names seem to be describing the forcing conditions for the model, rather than being a separate set of diagnostics that represent the effects of some process within the model. Hence I agree that it isn't necessary to define separate standard names with due_to_natural_component and I'd advocate leaving them out. Is that OK?

I agree that the "due_to_natural_component" reference is potentially misleading. In the simplest models it is envisioned as a separate tracer in the same run - in the more complex BGC models where the biological interactions are pH and/or saturation sensitive - such a tracer is an approximation (analogue) of what one would get in a full control run, thus give the moniker of the "natural"

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?

Like for "natural", this is only an analogue of what would otherwise be a solubility-driven tracer. To identify these as separate tracers more clearly, I propose changing the comment and standard names to the following:

"Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration natural analogue forced by preindustrial atmospheric xCO2"
mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water

"Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration abiotic analogue ignoring biological effects on carbon and alkalinity"
mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water

Does that make more sense?


Best wishes,
Alison

------
Alison Pamment Tel: [phone]<tel:%2B44%201235%20778065>
Centre for Environmental Data Analysis Email: ***@stfc.ac.uk<mailto:***@stfc.ac.uk>
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.


From: Durack, Paul J. [mailto:***@llnl.gov<mailto:***@llnl.gov>]
Sent: 28 September 2016 19:12
To: cf-***@cgd.ucar.edu<mailto:cf-***@cgd.ucar.edu>
Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu<mailto:***@ucar.edu>
Subject: New standard names for OMIP biogeochemistry and chemistry

Hi folks,

In preparation for the upcoming CMIP6-OMIP experiments we have a number of new standard names we'd like "blessed" for the biogeochemistry and chemistry data request.

I have appended these below. For folks interested, further information and notes are contained in the linked google sheets both indicated below. Many thanks to Alison for taking a first pass at these before sending to the mailing list.

The format below for the new names is:
standard_name_being_requested, units, (google sheet tab(s) and line number(s)).

***
160928 1105 ***@llnl.gov<mailto:***@llnl.gov>

Biogeochemistry see https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:

mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Oyr, 8; Omon, 63)
mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Oyr, 9; Omon, 64)
mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 13; Omon, 68)
sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Oyr, 27; Omon, 81)
sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr, 29; Omon, 83)
sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr, 30; Omon, 84)
mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Oyr, 32; Omon, 86)
mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Oyr, 35; Omon, 89)
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Oyr, 37; Omon, 91)
mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 55; Omon, 108)
mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 56; Omon, 109)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr, 96; Omon, 113)
surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, mol m-3, (Omon, 7)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 8)
surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Omon, 10)
surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Omon, 11)
surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol m-3, (Omon, 12)
surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 13)
surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 14)
surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 15)
surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 16)
surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 17)
surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 18)
surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 19)
surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 20)
surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 21)
surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 22)
surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 24)
surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 25)
surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 26)
surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3, (Omon, 27)
surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Omon, 28)
surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Omon, 30)
surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Omon, 31)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mol m-3, (Omon, 32)
surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Omon, 33)
surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Omon, 36)
surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3, (Omon, 37)
surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Omon, 38)
surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 39)
surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 40)
surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 41)
surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 43)
surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water, mol m-3, (Omon, 47)
surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 49)
surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 50)
surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water, mol m-3, (Omon, 51)
surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 52)
surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3, (Omon, 53)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 54)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
nitrogen_limitation_of_diatoms, 1, (Omon, 116)
nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
irradiance_limitation_of_diatoms, 1, (Omon, 121)
irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
iron_limitation_of_diatoms, 1, (Omon, 126)
iron_limitation_of_diazotrophs, 1, (Omon, 127)
iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
iron_limitation_of_picophytoplankton, 1, (Omon, 129)
iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-2 s-1, (Omon, 139)
tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1, (Omon, 140)
ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2, (Omon, 154)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component, Pa, (Omon, 156)
surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component, Pa, (Omon, 157)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 170)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 172)


Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG9G0lzIu7o/edit:

mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3; Omon, 4)
mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
***

Cheers,

P

________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
________________________________

[John Dunne]

"Sea_surface_mole_concentration..." is a concentration (mol m-3).

> On Nov 4, 2016, at 5:18 AM, Lowry, Roy K. <***@bodc.ac.uk> wrote:
>
> Dear John,
>
>
> Following these comments, I now wonder a little more about your previous comment on differences in dimensionality between your surface concentrations and concentrations at depth. Could you clarify what the units of measure are for your 2D simulations? Are they concentrations per unit area (e.g. mg/m2) where the value represents an integration over depth or concentrations per unit volume (e.g. mg/m3) where the value represents the concentration in the surface water layer?
>
>
> If it's the former then separate Standard Names are certainly required, but I would say the wording would need tweaking to reflect the fact such as the addition of 'integrated' or 'integral'.
>
>
> Cheers, Roy.
>
>
> Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
>
>
>
>
> From: CF-metadata <cf-metadata-***@cgd.ucar.edu> on behalf of John Dunne - NOAA Federal <***@noaa.gov>
> Sent: 04 November 2016 00:09
> To: ***@stfc.ac.uk
> Cc: cf-***@cgd.ucar.edu; Stephen Griffies; ***@ucar.edu; Durack, Paul J.
> Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry
>
> Hi Alison and all,
>
> Sorry for the delay. I have been communicating with Jim Orr and Paul Durack about your points, and have the following responses and proposal. I am not sure what happens know, so please advise if you want to take the discussion offline or have me put together a new revised spreadsheet.
>
> Thanks, John
>
>> On Wed, Oct 19, 2016 at 2:16 PM, <***@stfc.ac.uk> wrote:
>> Dear Paul, Jim and Jonathan,
>>
>> Thank you for all the proposals for OMIP biogeochemistry and chemistry names and the discussion that has already begun on these.
>>
>> I have created entries for all the proposed names in the CEDA vocabulary editor, available here: http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter.
>> At the moment, the names themselves are all shown as originally proposed and I have added standard definition text for consistency with existing names. Please use the link to view the full list of names and definitions as it is easier than reproducing it all in an email to the list.
>>
>> I think a number of the names look fine and could be published in their current form (see item 1 below). Paul and Jim, please can you check the definitions that I'm suggesting for these names and let me know if you're happy with them? (Comments from others are of course welcome).
>>
>> For the groups of names where some discussion is still required my comments are in item 2.
>>
>> 1. Names that I think can be approved, subject to checking of the definitions.
>>
>> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3
>> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3
>> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
>> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1
>> ocean_mass_content_of_dissolved_organic_carbon, kg m-2
>> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2
>> mole_concentration_of_cfc11_in_sea_water, mol m-3
>> mole_concentration_of_cfc12_in_sea_water, mol m-3
>> surface_downward_mole_flux_of_cfc11, mol m-2 s-1
>> surface_downward_mole_flux_of_cfc12, mol m-2 s-1
>>
>> 2. Names requiring further discussion.
>>
>> a. Phosphorus names
>> Sorry that I didn't notice it when previewing the names, but I have realized that 'phosphorus' is misspelled in the proposals, i.e., it should be 'phosphorus', not 'phosphorous'. Subject to this correction and checking of the definitions, I think the following names can be approved.
>> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
>> tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1
>>
>> I will also correct the spelling in three further phosphorus names which remain under discussion due to other issues:
>> surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3
>> surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorus_in_sea_water, mol m-3
>> surface_mole_concentration_of_phytoplankton_expressed_as_phosphorus_in_sea_water, mol m-3
>>
>> b. Definitions relating to new chemical species
>> It is usual to include a sentence in the definition when a standard name refers to a chemical species. There are three new species/isotopes in the current set of proposals. I suggest adding a single sentence to the definitions of the relevant names as follows:
>>
>> carbon13: ' "carbon13" means the naturally occurring isotope of carbon having six protons and seven neutrons.'
>> carbon14: ' "carbon14" means the radioactive isotope of carbon having six protons and eight neutrons, used in radiocarbon dating.'
>> sulfur_hexafluoride: 'The chemical formula of sulfur hexafluoride is SF6.'
>>
>> OK?
>
> OK
>>
>> c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
>>
>> My question here refers to the following five proposals:
>> tendency_of_ocean_mole_content_of_inorganic_carbon, mol m-2 s-1
>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1
>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1
>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1
>>
>> We have a couple of existing names for tendencies of inorganic carbon content, both of which are for dissolved_inorganic_carbon. Am I correct in thinking that your names also refer to dissolved amounts? If so, we should include it, e.g. tendency_of_ocean_mole_content_of_inorganic_carbon should be tendency_of_ocean_mole_content_of_dissolved_inorganic_carbon, and so on.
>
> These terms are intended to allow users to construct a complete carbon budget, and were not intended to distinguish between particulate and dissolved. Should we restrict the definitions and add more terms? add "total" to the name before "inorganic"? Please note that the names listed above with "sedimentation" are incorrect. As they are intended to represent loss from the ocean, they should not have "runoff_and". Like in Paul's spreadsheet, they should just be "tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_sedimentation" and "tendency_of_ocean_mole_content_of_organic_carbon_due_to_sedimentation". These are effectively both "particulate" since they just represent pelagic sinking in current models to my knowledge, though it is possible that models might include insitu benthic organic production and/or inorganic precipitation which could be represented as a dissolved loss. Of course, "sediment dissolution" would be just dissolved, but runoff could be either particulate or dissolved... did you want to distinguish between them?
>
>>
>> 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.
>>
>> Either solution would be consistent with the proposed units and I'd be happy with either. Please let me know how you prefer to proceed.
>>
>> As a final point in this section, the three proposed surface_sea_water_ph names are dimensionless, but I imagine that these too are really intended to represent the top model layer, in which case we should either drop 'surface' or change them to 'sea_surface' names too.
>
> While we are sensitive to your and Jonathan's point that it leads to proliferation of variable names, we prefer the second option, particularly in light of the variables that we are requesting daily as 2D sea surface and monthly full 3D. If we are going to go this route, should these names be "sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water", or just "sea_surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll"
>
>>
>> e. Limitation names
>> Jonathan has already raised the question of what 'limitation' means and also what measure of the various phytoplankton populations is being limited. This is a new concept in standard names so it's important to get the definitions right.
>>
>> John Dunne replied to Jonathan:
>> > With respect to the limitation terms, we currently have the definitions explained in the "Resolved Comment" column as "Ratio of realizable miscellaneous other
>> > phytoplankton growth rate under low nitrogen stress to theoretical rate without such limitation".
>>
>> So from this, my understanding is that nitrogen and iron are nutrients whose availability promotes the growth of phytoplankton, presumably by being absorbed somehow into the organic matter, while solar irradiance is clearly the energy source essential to the photosynthesis reaction. John's reply talks about growth rate, so I assume that means the growth rate of the population of a particular species (as opposed to the growth rate of individuals of that species).
>
> Yes, it is a population-level metric.
>
>>
>> Based on this I've attempted a couple of example definitions. If we can agree these, then I can go ahead and add the appropriate sentences to all the limitation names.
>> nitrogen_limitation_of_diatoms (canonical units: 1)
>> 'Diatoms are single-celled phytoplankton with an external skeleton made of silica. Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. Nitrogen is a nutrient essential to the growth of phytoplankton populations. "Nitrogen limitation" means the ratio of the growth rate of a species population in the environment (where there is a finite availability of nitrogen) to the theoretical growth rate if there were no such limit on nitrogen availability.'
>
>
>>
>> N.B. For the irradiance names, I suggest we make them 'solar_irradiance' to be absolutely clear.
>> solar_irradiance_limitation_of_miscellaneous_phytoplankton (canonical units:1)
>> 'Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live near the water surface where there is sufficient light to support photosynthesis. "Miscellaneous phytoplankton" are all those phytoplankton that are not diatoms, diazotrophs, calcareous phytoplankton, picophytoplankton or other separately named components of the phytoplankton population. "Irradiance" means the power per unit area (called radiative flux in other standard names), the area being normal to the direction of flow of the radiant energy. Solar irradiance is essential to the photosynthesis reaction and its presence promotes the growth of phytoplankton populations. "Solar irradiance limitation" means the ratio of the growth rate of a species population in the environment (where the amount of sunlight reaching a location may be limited) to the theoretical growth rate if there were no such limit on solar irradiance.'
>>
>
>
> If you think this level of detail is necessary, I am fine with it, though I'm not sure where it is being proposed the be entered (the comment?) it seems inconsistent with the lack of detail on most variables. Editorially, I think adding the fact that they are "single celled", and "prokaryotic or eukaryotic" seem superfluous (e.g. the models intend to represent diazotrophs, diatoms, and others groups even when they form chains)", and "live near the water surface" would probably be better as simply "grow".
>
>> Comments and suggestions for improvement are welcome!
>>
>> f. Natural/abiotic component names
>> Thank you for the useful discussion that has already taken place about the 22 proposed natural_component and abiotic_component names. I hadn't previously understood the details of how the OMIP experiments will be run.
>>
>> Reading through the discussion, I agree with Jonathan that the natural_component names seem to be describing the forcing conditions for the model, rather than being a separate set of diagnostics that represent the effects of some process within the model. Hence I agree that it isn't necessary to define separate standard names with due_to_natural_component and I'd advocate leaving them out. Is that OK?
>
> I agree that the "due_to_natural_component" reference is potentially misleading. In the simplest models it is envisioned as a separate tracer in the same run - in the more complex BGC models where the biological interactions are pH and/or saturation sensitive - such a tracer is an approximation (analogue) of what one would get in a full control run, thus give the moniker of the "natural"
>>
>> 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?
>
> Like for "natural", this is only an analogue of what would otherwise be a solubility-driven tracer. To identify these as separate tracers more clearly, I propose changing the comment and standard names to the following:
>
> "Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration natural analogue forced by preindustrial atmospheric xCO2"
> mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water
>
> "Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration abiotic analogue ignoring biological effects on carbon and alkalinity"
> mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water
>
> Does that make more sense?
>
>>
>> Best wishes,
>> Alison
>>
>> ------
>> Alison Pamment Tel: [phone]
>> Centre for Environmental Data Analysis Email: ***@stfc.ac.uk
>> STFC Rutherford Appleton Laboratory
>> R25, 2.22
>> Harwell Campus, Didcot, OX11 0QX, U.K.
>>
>>
>> From: Durack, Paul J. [mailto:***@llnl.gov]
>> Sent: 28 September 2016 19:12
>> To: cf-***@cgd.ucar.edu
>> Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James Orr; Stephen Griffies - NOAA Federal; ***@ucar.edu
>> Subject: New standard names for OMIP biogeochemistry and chemistry
>>
>> Hi folks,
>>
>> In preparation for the upcoming CMIP6-OMIP experiments we have a number of new standard names we'd like "blessed" for the biogeochemistry and chemistry data request.
>>
>> I have appended these below. For folks interested, further information and notes are contained in the linked google sheets both indicated below. Many thanks to Alison for taking a first pass at these before sending to the mailing list.
>>
>> The format below for the new names is:
>> standard_name_being_requested, units, (google sheet tab(s) and line number(s)).
>>
>> ***
>> 160928 1105 ***@llnl.gov
>>
>> Biogeochemistry see https://docs.google.com/spreadsheets/d/1HFYLi9mEypLdos7IG07Rv5XqBLyQ9r_thiKaulIjfbw/edit:
>>
>> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Oyr, 6; Omon, 61)
>> mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Oyr, 7; Omon, 62)
>> mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Oyr, 8; Omon, 63)
>> mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Oyr, 9; Omon, 64)
>> mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 13; Omon, 68)
>> sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Oyr, 27; Omon, 81)
>> sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Oyr, 29; Omon, 83)
>> sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Oyr, 30; Omon, 84)
>> mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Oyr, 32; Omon, 86)
>> mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Oyr, 35; Omon, 89)
>> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Oyr, 37; Omon, 91)
>> mole_concentration_of_natural_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 55; Omon, 108)
>> mole_concentration_of_abiotic_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Oyr, 56; Omon, 109)
>> mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Oyr, 57; Omon, 110)
>> mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Oyr, 58; Omon, 111)
>> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_remineralization, mol m-3 s-1, (Oyr, 75)
>> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_as_carbon_in_sea_water_due_to_grazing_of_phytoplankton, mol m-3 s-1, (Oyr, 96; Omon, 113)
>> surface_downward_mass_flux_of_carbon_dioxide, kg m-2 s-1, (Oyr, 100)
>> surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_natural_component, kg m-2 s-1, (Oyr, 101; Omon, 163)
>> surface_downward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 102; Omon, 164)
>> surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 103; Omon, 165)
>> surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component, kg m-2 s-1, (Oyr, 104; Omon, 166)
>> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water, mol m-3, (Omon, 7)
>> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 8)
>> surface_mole_concentration_of_dissolved_inorganic_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 9)
>> surface_mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3, (Omon, 10)
>> surface_mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3, (Omon, 11)
>> surface_mole_concentration_of_dissolved_organic_carbon_in_sea_water, mol m-3, (Omon, 12)
>> surface_mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 13)
>> surface_mole_concentration_of_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 14)
>> surface_mole_concentration_of_bacteria_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 15)
>> surface_mole_concentration_of_organic_detritus_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 16)
>> surface_mole_concentration_of_calcite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 17)
>> surface_mole_concentration_of_aragonite_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 18)
>> surface_mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 19)
>> surface_mole_concentration_of_diazotrophs_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 20)
>> surface_mole_concentration_of_calcareous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 21)
>> surface_mole_concentration_of_picophytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 22)
>> surface_mole_concentration_of_miscellaneous_phytoplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 23)
>> surface_mole_concentration_of_microzooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 24)
>> surface_mole_concentration_of_mesozooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 25)
>> surface_mole_concentration_of_miscellaneous_zooplankton_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 26)
>> surface_sea_water_alkalinity_expressed_as_mole_equivalent, mol m-3, (Omon, 27)
>> surface_sea_water_alkalinity_expressed_as_mole_equivalent_due_to_natural_component, mol m-3, (Omon, 28)
>> surface_sea_water_ph_reported_on_total_scale, 1, (Omon, 29)
>> surface_sea_water_ph_reported_on_total_scale_due_to_natural_component, 1, (Omon, 30)
>> surface_sea_water_ph_reported_on_total_scale_due_to_abiotic_component, 1, (Omon, 31)
>> surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mol m-3, (Omon, 32)
>> surface_mole_concentration_of_dissolved_molecular_oxygen_in_sea_water_at_saturation, mol m-3, (Omon, 33)
>> surface_mole_concentration_of_nitrate_in_sea_water, mol m-3, (Omon, 34)
>> surface_mole_concentration_of_ammonium_in_sea_water, mol m-3, (Omon, 35)
>> surface_mole_concentration_of_dissolved_inorganic_phosphorous_in_sea_water, mol m-3, (Omon, 36)
>> surface_mole_concentration_of_dissolved_iron_in_sea_water, mol m-3, (Omon, 37)
>> surface_mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3, (Omon, 38)
>> surface_mass_concentration_of_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 39)
>> surface_mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 40)
>> surface_mass_concentration_of_diazotrophs_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 41)
>> surface_mass_concentration_of_calcareous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 42)
>> surface_mass_concentration_of_picophytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 43)
>> surface_mass_concentration_of_miscellaneous_phytoplankton_expressed_as_chlorophyll_in_sea_water, kg m-3, (Omon, 44)
>> surface_mole_concentration_of_particulate_organic_matter_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 45)
>> surface_mole_concentration_of_particulate_organic_matter_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 46)
>> surface_mole_concentration_of_particulate_organic_matter_expressed_as_iron_in_sea_water, mol m-3, (Omon, 47)
>> surface_mole_concentration_of_particulate_organic_matter_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 48)
>> surface_mole_concentration_of_phytoplankton_expressed_as_nitrogen_in_sea_water, mol m-3, (Omon, 49)
>> surface_mole_concentration_of_phytoplankton_expressed_as_phosphorous_in_sea_water, mol m-3, (Omon, 50)
>> surface_mole_concentration_of_phytoplankton_expressed_as_iron_in_sea_water, mol m-3, (Omon, 51)
>> surface_mole_concentration_of_phytoplankton_expressed_as_silicon_in_sea_water, mol m-3, (Omon, 52)
>> surface_mole_concentration_of_dimethyl_sulfide_in_sea_water, mol m-3, (Omon, 53)
>> surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water, mol m-3, (Omon, 54)
>> surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component, mol m-3, (Omon, 55)
>> surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_abiotic_component, mol m-3, (Omon, 56)
>> surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_calcite, mol m-3, (Omon, 57)
>> surface_mole_concentration_of_carbonate_expressed_as_carbon_for_sea_water_in_equilibrium_with_pure_aragonite, mol m-3, (Omon, 58)
>> nitrogen_limitation_of_diatoms, 1, (Omon, 116)
>> nitrogen_limitation_of_diazotrophs, 1, (Omon, 117)
>> nitrogen_limitation_of_calcareous_phytoplankton, 1, (Omon, 118)
>> nitrogen_limitation_of_picophytoplankton, 1, (Omon, 119)
>> nitrogen_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 120)
>> irradiance_limitation_of_diatoms, 1, (Omon, 121)
>> irradiance_limitation_of_diazotrophs, 1, (Omon, 122)
>> irradiance_limitation_of_calcareous_phytoplankton, 1, (Omon, 123)
>> irradiance_limitation_of_picophytoplankton, 1, (Omon, 124)
>> irradiance_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 125)
>> iron_limitation_of_diatoms, 1, (Omon, 126)
>> iron_limitation_of_diazotrophs, 1, (Omon, 127)
>> iron_limitation_of_calcareous_phytoplankton, 1, (Omon, 128)
>> iron_limitation_of_picophytoplankton, 1, (Omon, 129)
>> iron_limitation_of_miscellaneous_phytoplankton, 1, (Omon, 130)
>> tendency_of_ocean_mole_content_of_nitrogen_due_to_biological_production, mol m-2 s-1, (Omon, 139)
>> tendency_of_ocean_mole_content_of_phosphorous_due_to_biological_production, mol m-2 s-1, (Omon, 140)
>> ocean_mass_content_of_dissolved_organic_carbon, kg m-2, (Omon, 153)
>> ocean_mass_content_of_particulate_organic_matter_expressed_as_carbon, kg m-2, (Omon, 154)
>> surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_natural_component, Pa, (Omon, 156)
>> surface_partial_pressure_of_carbon_dioxide_in_sea_water_due_to_abiotic_component, Pa, (Omon, 157)
>> surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_natural_component, Pa, (Omon, 159)
>> surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_due_to_abiotic_component, Pa, (Omon, 160)
>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 169)
>> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 170)
>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sediment_dissolution, mol m-2 s-1, (Omon, 171)
>> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sedimentation, mol m-2 s-1, (Omon, 172)
>>
>>
>> Chemistry see https://docs.google.com/spreadsheets/d/1SfxHKASSwLbPM6xBDjZ6Y8oIxx9APLOlCG9G0lzIu7o/edit:
>>
>> mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3, (Oyr, 3; Omon, 4)
>> mole_concentration_of_cfc11_in_sea_water, mol m-3, (Oyr, 4; Omon, 5)
>> mole_concentration_of_cfc12_in_sea_water, mol m-3, (Oyr, 5; Omon, 6)
>> surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-2 s-1, (Omon, 9)
>> surface_downward_mole_flux_of_cfc11, mol m-2 s-1, (Omon, 10)
>> surface_downward_mole_flux_of_cfc12, mol m-2 s-1, (Omon, 11)
>> ***
>>
>> Cheers,
>>
>> P
>
> This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.

[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.

[John Dunne - NOAA Federal]

The attempt to as sea surface - SS prefixes was only to follow the
convention as my understanding was that the convention could not handle two
variables with the same name but different dimensions. If that is not
truly a problem on your end, then perhaps it is a non issue.

On Thu, Oct 20, 2016 at 12:55 PM, Jonathan Gregory <
***@reading.ac.uk> wrote:

> 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.
> _______________________________________________
> CF-metadata mailing list
> CF-***@cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>

[Lowry, Roy K.]

Hello John,


I'm getting a little confused here. Why is the dimensionality of the surface measurement different? I would have expected it to be something like mol m-3 for concentrations at any depth. Or am I misunderstanding what you wish to describe?


Cheers, Roy.


Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk. Please also use this e-mail if your requirement is urgent.


________________________________
From: CF-metadata <cf-metadata-***@cgd.ucar.edu> on behalf of John Dunne - NOAA Federal <***@noaa.gov>
Sent: 20 October 2016 18:20
To: Jonathan Gregory
Cc: cf-***@cgd.ucar.edu
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

The attempt to as sea surface - SS prefixes was only to follow the convention as my understanding was that the convention could not handle two variables with the same name but different dimensions. If that is not truly a problem on your end, then perhaps it is a non issue.

On Thu, Oct 20, 2016 at 12:55 PM, Jonathan Gregory <***@reading.ac.uk<mailto:***@reading.ac.uk>> wrote:
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.
_______________________________________________
CF-metadata mailing list
CF-***@cgd.ucar.edu<mailto:CF-***@cgd.ucar.edu>
http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata

________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
________________________________

[John Dunne - NOAA Federal]

Units are the same. It's like Jonathan and Allison said, we wanted to
request both the topmost layer values in 2D as well as the full 3D values
as a lower priority, and tried to use the "so" versus "sos" implementation
as a template.

On Fri, Oct 21, 2016 at 5:12 AM, Lowry, Roy K. <***@bodc.ac.uk> wrote:

> Hello John,
>
>
> I'm getting a little confused here. Why is the dimensionality of the
> surface measurement different? I would have expected it to be something
> like mol m-3 for concentrations at any depth. Or am I misunderstanding what
> you wish to describe?
>
>
> Cheers, Roy.
>
>
> Please note that I partially retired on 01/11/2015. I am now only working
> 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my
> day in the office. All vocabulary queries should be sent to
> ***@bodc.ac.uk. Please also use this e-mail if your requirement is
> urgent.
>
>
> ------------------------------
> *From:* CF-metadata <cf-metadata-***@cgd.ucar.edu> on behalf of John
> Dunne - NOAA Federal <***@noaa.gov>
> *Sent:* 20 October 2016 18:20
> *To:* Jonathan Gregory
> *Cc:* cf-***@cgd.ucar.edu
> *Subject:* Re: [CF-metadata] New standard names for OMIP biogeochemistry
> and chemistry
>
> The attempt to as sea surface - SS prefixes was only to follow the
> convention as my understanding was that the convention could not handle two
> variables with the same name but different dimensions. If that is not
> truly a problem on your end, then perhaps it is a non issue.
>
> On Thu, Oct 20, 2016 at 12:55 PM, Jonathan Gregory <
> ***@reading.ac.uk> wrote:
>
>> 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_dissolve
>> d_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.
>> _______________________________________________
>> CF-metadata mailing list
>> CF-***@cgd.ucar.edu
>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>>
>
> ------------------------------
> This message (and any attachments) is for the recipient only. NERC is
> subject to the Freedom of Information Act 2000 and the contents of this
> email and any reply you make may be disclosed by NERC unless it is exempt
> from release under the Act. Any material supplied to NERC may be stored in
> an electronic records management system.
> ------------------------------
>

[Lowry, Roy K.]

Hi John,


Thanks for the clarification.


Cheers, Roy.


Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk. Please also use this e-mail if your requirement is urgent.


________________________________
From: John Dunne - NOAA Federal <***@noaa.gov>
Sent: 21 October 2016 20:31
To: Lowry, Roy K.
Cc: Jonathan Gregory; cf-***@cgd.ucar.edu
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

Units are the same. It's like Jonathan and Allison said, we wanted to request both the topmost layer values in 2D as well as the full 3D values as a lower priority, and tried to use the "so" versus "sos" implementation as a template.

On Fri, Oct 21, 2016 at 5:12 AM, Lowry, Roy K. <***@bodc.ac.uk<mailto:***@bodc.ac.uk>> wrote:

Hello John,


I'm getting a little confused here. Why is the dimensionality of the surface measurement different? I would have expected it to be something like mol m-3 for concentrations at any depth. Or am I misunderstanding what you wish to describe?


Cheers, Roy.


Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to ***@bodc.ac.uk<mailto:***@bodc.ac.uk>. Please also use this e-mail if your requirement is urgent.


________________________________
From: CF-metadata <cf-metadata-***@cgd.ucar.edu<mailto:cf-metadata-***@cgd.ucar.edu>> on behalf of John Dunne - NOAA Federal <***@noaa.gov<mailto:***@noaa.gov>>
Sent: 20 October 2016 18:20
To: Jonathan Gregory
Cc: cf-***@cgd.ucar.edu<mailto:cf-***@cgd.ucar.edu>
Subject: Re: [CF-metadata] New standard names for OMIP biogeochemistry and chemistry

The attempt to as sea surface - SS prefixes was only to follow the convention as my understanding was that the convention could not handle two variables with the same name but different dimensions. If that is not truly a problem on your end, then perhaps it is a non issue.

On Thu, Oct 20, 2016 at 12:55 PM, Jonathan Gregory <***@reading.ac.uk<mailto:***@reading.ac.uk>> wrote:
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.
_______________________________________________
CF-metadata mailing list
CF-***@cgd.ucar.edu<mailto:CF-***@cgd.ucar.edu>
http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata

________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
________________________________

________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
________________________________

[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

[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 <***@reading.ac.uk
> 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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