Dear All,
Many thanks to all those who have commented in this discussion. I think we have reached, or are very close to reaching, agreement on many of the names. In this posting I have not addressed the "sea_surface" names which are proving to be the only contentious issue - I will deal with them in a separate message (to follow shortly). We need to raise the profile of that discussion in order to reach a fair and timely decision.
The link to the full list of names with their units and definitions is
http://cfeditor.ceda.ac.uk/proposals/1?status=active&namefilter=&proposerfilter=Durack&descfilter=&unitfilter=&yearfilter=&commentfilter=OMIP&filter+and+display=Filter. The list has been updated to show the latest status of the names. The next update to the published standard name table will take place on 15th November when all names marked as 'Accepted' will be added. Any names that are accepted before that date will be included in the update. Another update will take place in December.
The numbering of the sections below refers to my previous summary:
1. The following names are now accepted for inclusion in the standard name table.
> 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, kgm-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
2a. Phosporus names
The following names are now accepted for inclusion in the standard name table.
> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, mol m-3
> tendency_of_ocean_mole_content_of_phosphorus_due_to_biological_production, mol m-2 s-1
In addition, the spelling has now been corrected in all 'phosphorus' names.
2b. Definitions relating to new chemical species
I agree with Roy's amendments to my suggested carbon13 and carbon14 definitions. The new chemical species definitions for carbon13, carbon 14 and sulfur_hexafluoride have been added to the appropriate names and the following four names are now accepted for inclusion in the standard name table:
mole_concentration_of_dissolved_inorganic_carbon13_in_sea_water, mol m-3
mole_concentration_of_dissolved_inorganic_carbon14_in_sea_water, mol m-3
mole_concentration_of_sulfur_hexafluoride_in_sea_water, mol m-3
surface_downward_mole_flux_of_sulfur_hexafluoride, mol m-3
Looking at the carbon 13 and 14 names again, I suggest a slight amendment to the following two proposals:
surface_downward_mass_flux_of_carbon13_dioxide_expressed_as_carbon_due_to_abiotic_component
surface_downward_mass_flux_of_carbon14_dioxide_expressed_as_carbon_due_to_abiotic_component.
I think these should be, respectively, expressed_as_carbon13 and expressed_as_carbon14 rather than simply expressed_as_carbon. Is that right? Up to now we have always used the generic term 'expressed_as_carbon' in standard names which makes no distinction between isotopes but is that precise enough for these names?
2c. tendency_of_ocean_mole_content_of_[in]organic_carbon names
I wrote:
>
> 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.
John wrote:
> 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?
OK, thank you for the clarification. Since you intend to include both particulate and dissolved carbon, the names are in fact fine (I just wanted to check). In CF, an unqualified term is always interpreted as a 'total' amount and if only a component is intended, e.g. dissolved, particulate, it should be included in the name.
Existing sedimentation names do not specify 'particulate' but it is included in the definition using the following sentence: ' "Sedimentation" is the sinking of particulate matter to the floor of a body of water.' Is that adequate? If we included an additional sentence 'Some models may also include insitu benthic organic production and/or inorganic precipitation', would that be useful or would it just confuse people?
You say that some of the names themselves are listed incorrectly, so again just to clarify, is the following correct?
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_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_sedimentation, mol m-2 s-1
2e. Limitation names
Jonathan has suggested that we include the term 'growth' in these names, to which John has agreed. Also, Jonathan is suggesting the use of our well established "due_to" syntax for the solar irradiance names e.g., growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance. I think this is clear. So the names would then be as follows:
growth_limitation_of_picophytoplankton_due_to_solar_irradiance (canonical units: 1)
growth_limitation_of_calcareous_phytoplankton_due_to_solar_irradiance (canonical units: 1)
growth_limitation_of_diazotrophs_due_to_solar_irradiance (canonical units: 1)
growth_limitation_of_diatoms_due_to_solar_irradiance (canonical units: 1)
growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance (canonical units: 1)
nitrogen_growth_limitation_of_picophytoplankton (canonical units: 1)
nitrogen_growth_limitation_of_calcareous_phytoplankton (canonical units: 1)
nitrogen_growth_limitation_of_diazotrophs (canonical units: 1)
nitrogen_growth_limitation_of_diatoms (canonical units: 1)
nitrogen_growth_limitation_of_miscellaneous_phytoplankton (canonical units: 1)
iron_growth_limitation_of_picophytoplankton (canonical units: 1)
iron_growth_limitation_of_calcareous_phytoplankton (canonical units: 1)
iron_growth_limitation_of_diazotrophs (canonical units: 1)
iron_growth_limitation_of_diatoms (canonical units: 1)
iron_growth_limitation_of_miscellaneous_phytoplankton (canonical units: 1)
OK?
John asked a question about where the definition text should go - the answer is that it resides in the published standard name table:
http://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html (click on a name to see its definition). (Almost) all standard names have definitions but they don't need to be reproduced in the data files. Those wishing to access the information can obtain it from a number of sources, namely the html table, the xml version (which is actually the 'master' copy of standard names)
http://cfconventions.org/Data/cf-standard-names/current/src/cf-standard-name-table.xml or the NERC vocabulary server which is developed and maintained by the British Oceanographic Data Centre
http://vocab.nerc.ac.uk/collection/P07/current/.
John suggested some refinements to the wording of the definitions, so taking these into account, my two examples would now be as follows.
growth_limitation_of_miscellaneous_phytoplankton_due_to_solar_irradiance
'Phytoplankton are algae that live near the grow 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. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. "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. "Growth limitation due to solar irradiance" 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.'
nitrogen_growth_limitation_of_diatoms
'Diatoms are phytoplankton with an external skeleton made of silica. Phytoplankton are algae that grow where there is sufficient light to support photosynthesis. Nitrogen is a nutrient essential to the growth of phytoplankton populations. "Nitrogen growth 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.'
Are these OK?
John, Jim and Paul, if you are happy with these names and sample definitions then I think the limitation names can all be accepted for publication. I will then construct definitions for them all, consistent with the examples.
One final note about these phytoplankton names: Roy queried whether we have the best classification system for the different types of phytoplankton, i.e. we are currently mixing size and species as ways of delineating sections of the population. All I can say is that this is the system that was first proposed for CMIP5 and is being used again in CMIP6. Nothing else has ever been proposed. I agree that if new categories are ever proposed we will need to take account of the existing names, and in particular we may then need to think hard about the definition of 'miscellaneous phytoplankton'. However, in the time honoured tradition of CF, I propose to defer this discussion until such time as there is a clear need to change what we are doing. I hope that's OK.
2f. Natural/abiotic component names
I confess that I have struggled somewhat to understand these names, although it's becoming gradually clearer. I do see now that we need both sets of names and that the "natural analogue" names are model diagnostics rather than forcing conditions.
In John's most recent posting he suggests names and definitions of the form:
mole_concentration_of_dissolved_inorganic_carbon_natural_analogue_in_sea_water
Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration natural analogue forced by preindustrial atmospheric xCO2
mole_concentration_of_dissolved_inorganic_carbon_abiotic_analogue_in_sea_water
Dissolved inorganic carbon (CO3+HCO3+H2CO3) concentration abiotic analogue ignoring biological effects on carbon and alkalinity
Certainly I think these names are a lot better and the terminology "natural analogue" and "abiotic analogue" is useful. We need to think about how this, or a similar, syntax will work in a standardised way with all the proposed natural and abiotic names. For example, how would we rewrite surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_due_to_natural_component? Perhaps we could replace the "due_to_X" in the current proposals with "X_analogue" at the end of the name or we could prepend it with "X_analogue_of". This would mean that the new names are consistent with many existing ones and would simply contain an additional qualification, e.g.
[sea_]surface_mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water_natural_analogue
or
natural_analogue_of_[sea_]surface_ mole_concentration_of_carbonate_expressed_as_carbon_in_sea_water.
How does that sound? If we can settle on a syntax, then the definitions shouldn't be too difficult to sort out. We'd need some explanatory words for the analogues, which should include some information about when these names might be used (for the benefit of the many CF users who will be totally unfamiliar with the OMIP experiments). Based on John's text I'd suggest the following:
natural_analogue
'In ocean biogeochemistry models, a "natural analogue" is used to simulate the effect on a modelled variable of imposing preindustrial atmospheric carbon dioxide concentrations, even when the model as a whole may be subjected to varying forcings.'
abiotic_analogue
'In ocean biogeochemistry models, an "abiotic analogue" is used to simulate the effect on a modelled variable when biological effects on ocean carbon concentration and alkalinity are ignored.'
Based on the above, an example of a full definition would then be something like:
surface_carbon_dioxide_partial_pressure_difference_between_sea_water_and_air_natural_analogue
'The surface called "surface" means the lower boundary of the atmosphere. The partial pressure of a gaseous constituent of air is the pressure which it alone would exert with unchanged temperature and number of moles per unit volume. The chemical formula for carbon dioxide is CO2. In ocean biogeochemistry models, a "natural analogue" is used to simulate the effect on a modelled variable of imposing preindustrial atmospheric carbon dioxide concentrations, even when the model as a whole may be subjected to varying forcings.'
Any good?
Best wishes,
Alison
> -----Original Message-----
> From: CF-metadata [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of
> alison.pamment at stfc.ac.uk
> Sent: 19 October 2016 19:16
> To: durack1 at llnl.gov; cf-metadata at cgd.ucar.edu
> Cc: stephen.griffies at noaa.gov; gokhan at 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=&proposerfilt
> er=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_saturat
> ion, mol m-3
> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water, mol m-3
> tendency_of_mole_concentration_of_particulate_organic_matter_expressed_a
> s_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_product
> ion, 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_wat
> er, mol m-3
> surface_mole_concentration_of_particulate_organic_matter_expressed_as_ph
> osphorus_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_s
> ediment_dissolution, mol m-2 s-1
> tendency_of_ocean_mole_content_of_inorganic_carbon_due_to_runoff_and_s
> edimentation, mol m-2 s-1
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sed
> iment_dissolution, mol m-2 s-1
> tendency_of_ocean_mole_content_of_organic_carbon_due_to_runoff_and_sed
> imentation, 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.
Received on Thu Nov 10 2016 - 10:00:17 GMT
