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: +44 1235 778065
Centre for Environmental Data Analysis Email: alison.pamment at stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.
From: Durack, Paul J. [mailto:durack1 at llnl.gov]
Sent: 28 September 2016 19:12
To: cf-metadata at cgd.ucar.edu
Cc: Pamment, Alison (STFC,RAL,RALSP); John Dunne - NOAA Federal; James Orr; Stephen Griffies - NOAA Federal; gokhan at 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 durack at 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
Received on Wed Oct 19 2016 - 12:16:22 BST
