[CF-metadata] New standard_names for ocean biogeochemistry

[Elodie Fernandez]

Dear all,

We would like to suggest the addition of two new standard_names for
ocean biogeochemistry:

- *mass_concentration_of_chlorophyll_a_fluorescence_in_sea_water*
unit: kg m-3
definition:
Mass concentration means mass per unit volume and is used in the
construction mass_concentration_of_X_in_Y, where X is a material
constituent of Y. A chemical species denoted by X may be described by a
single term such as 'nitrogen' or a phrase such as
'nox_expressed_as_nitrogen'. Chloropyll fluorescence is a proxy for
Chlorophyll concentration measuring re-emitted light from light
absorption. Chlorophylls are the green pigments found in most plants,
algae and cyanobacteria; their presence is essential for photosynthesis
to take place. There are several different forms of chlorophyll that
occur naturally. All contain a chlorin ring (chemical formula C20H16N4)
which gives the green pigment and a side chain whose structure varies.
The naturally occurring forms of chlorophyll contain between 35 and 55
carbon atoms.Chlorophyll fluorescence is mainly emitted from the
Chlorophyll a pigment.

I believe there are no standard_names yet for fluorescence. The
definition was built from the
mass_concentration_of_chlorophyll_a_in_sea_water definition.

- *sea_water_alkalinity_per_unit_mass*
unit: mol kg-1
definition:
sea_water_alkalinity_per_unit_mass is the total alkalinity (including
carbonate, nitrogen, silicate, and borate components).

A standard name already exists for alkalinity expressed as mol/m3,
|sea_water_alkalinity_expressed_as_mole_equivalent
<javascript:void(0)>||,||||but none exist for mol/kg.|

Best regards,

Elodie

[John Dunne - NOAA Federal]

A couple of questions...

1) Regarding the request to add Chlorophyll_a fluorescence, the proposed
unit is kg/m3, but shouldn't fluorescence have radiation units (i.e.
Watts/m2)? I was not aware that any of the proposed CMIP models treated
fluorescence explicitly, but if that were the case, it would seem like
converting to chlorophyll_a volumetric mass units would seem to me
redundant with the existing chlorophyll_a metric.

2) Regarding the request to add a variable for alkalinity in mass units to
augment the current one volumetric units, this would seem redundant for
models using the Boussinesq Assumption and thus a single reference
density. For non-Boussinesq models, one should be able to approximate this
with sea_water_potential_density (rhopoto), but I acknowledge that this
would make the global integral not exact... Are non-Boussinesq models being
planned? If so, adding alkalinity as a mass-based variable would also then
beg the question as to which tracers should be posted in both units (e.g.
DIC) - how much is the request expected to be expanded?

Cheers, John

On Mon, Dec 5, 2016 at 3:38 AM, Elodie Fernandez <

Post by Elodie Fernandez
Dear all,
We would like to suggest the addition of two new standard_names for ocean
- *mass_concentration_of_chlorophyll_a_fluorescence_in_sea_water*
unit: kg m-3
Mass concentration means mass per unit volume and is used in the
construction mass_concentration_of_X_in_Y, where X is a material
constituent of Y. A chemical species denoted by X may be described by a
single term such as 'nitrogen' or a phrase such as
'nox_expressed_as_nitrogen'. Chloropyll fluorescence is a proxy for
Chlorophyll concentration measuring re-emitted light from light absorption.
Chlorophylls are the green pigments found in most plants, algae and
cyanobacteria; their presence is essential for photosynthesis to take
place. There are several different forms of chlorophyll that occur
naturally. All contain a chlorin ring (chemical formula C20H16N4) which
gives the green pigment and a side chain whose structure varies. The
naturally occurring forms of chlorophyll contain between 35 and 55 carbon
atoms.Chlorophyll fluorescence is mainly emitted from the Chlorophyll a
pigment.
I believe there are no standard_names yet for fluorescence. The definition
was built from the mass_concentration_of_chlorophyll_a_in_sea_water
definition.
- *sea_water_alkalinity_per_unit_mass*
unit: mol kg-1
sea_water_alkalinity_per_unit_mass is the total alkalinity (including
carbonate, nitrogen, silicate, and borate components).
A standard name already exists for alkalinity expressed as mol/m3,
sea_water_alkalinity_expressed_as_mole_equivalent, but none exist for
mol/kg.
Best regards,
Elodie
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[Lowry, Roy K.]

Dear All,

Some additional information on 'chorophyll-a fluorescence' in observational oceanography. As John says, strictly speaking fluorescence is the amount of radiation within a given waveband resulting from excitation. It could also be expressed as a dimensionless parameter that is the ratio of the radiation generated over the amount of excitation energy (sometimes called fluorescence yield).

Over the years, I have come across many types of in-situ fluorometers used to estimate chlorophyll-a in seawater. Many of these deliver a parameter called 'chlorophyll-a fluorescence'. Over the years I have encountered this manifesting itself as raw voltages or ADC counts but these days these raw measurements have some sort of internal algorithm applied to produce a measurement that is linearly related to the chlorophyll-a concentration in units such as ug/l. I think this is what Elodie wishes to describe semantically in CF. If so, one solution would be to use existing chlorophyll-a concentration Standard Names with a qualification that it is an uncalibrated measurement in the long name. Any other suggestions?

As for alkalinity, whilst John's viewpoint holds from a modelling perspective there is a strong voice in the observational marine science community for alkalinity measurements having units of Equivalents per kilogram (dimensionality mol/kg) which cannot be interconverted with sufficient precision to mol/m3 using factors based on in-situ density (other factors come into play such as temperature of measurement etc.). Consequently, I support Elodie's request.

The current standard name with dimensionality mol/m3 is sea_water_alkalinity_expressed_as_mole_equivalent, so the new name would be better as sea_water_alkalinity_per_unit_mass_expressed_as_mole_equivalent rather than just sea_water_alkalinity_per_unit mass.

Cheers, Roy

From: CF-metadata [mailto:cf-metadata-***@cgd.ucar.edu] On Behalf Of John Dunne - NOAA Federal
Sent: 05 December 2016 20:45
To: Elodie Fernandez <***@mercator-ocean.fr>
Cc: cf-***@cgd.ucar.edu; Fernando Manzano Muñoz <***@puertos.es>
Subject: Re: [CF-metadata] New standard_names for ocean biogeochemistry

A couple of questions...

1) Regarding the request to add Chlorophyll_a fluorescence, the proposed unit is kg/m3, but shouldn't fluorescence have radiation units (i.e. Watts/m2)? I was not aware that any of the proposed CMIP models treated fluorescence explicitly, but if that were the case, it would seem like converting to chlorophyll_a volumetric mass units would seem to me redundant with the existing chlorophyll_a metric.
2) Regarding the request to add a variable for alkalinity in mass units to augment the current one volumetric units, this would seem redundant for models using the Boussinesq Assumption and thus a single reference density. For non-Boussinesq models, one should be able to approximate this with sea_water_potential_density (rhopoto), but I acknowledge that this would make the global integral not exact... Are non-Boussinesq models being planned? If so, adding alkalinity as a mass-based variable would also then beg the question as to which tracers should be posted in both units (e.g. DIC) - how much is the request expected to be expanded?

Cheers, John

On Mon, Dec 5, 2016 at 3:38 AM, Elodie Fernandez <***@mercator-ocean.fr<mailto:***@mercator-ocean.fr>> wrote:

Dear all,

We would like to suggest the addition of two new standard_names for ocean biogeochemistry:

- mass_concentration_of_chlorophyll_a_fluorescence_in_sea_water
unit: kg m-3
definition:
Mass concentration means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Chloropyll fluorescence is a proxy for Chlorophyll concentration measuring re-emitted light from light absorption. Chlorophylls are the green pigments found in most plants, algae and cyanobacteria; their presence is essential for photosynthesis to take place. There are several different forms of chlorophyll that occur naturally. All contain a chlorin ring (chemical formula C20H16N4) which gives the green pigment and a side chain whose structure varies. The naturally occurring forms of chlorophyll contain between 35 and 55 carbon atoms.Chlorophyll fluorescence is mainly emitted from the Chlorophyll a pigment.

I believe there are no standard_names yet for fluorescence. The definition was built from the mass_concentration_of_chlorophyll_a_in_sea_water definition.

- sea_water_alkalinity_per_unit_mass
unit: mol kg-1
definition:
sea_water_alkalinity_per_unit_mass is the total alkalinity (including carbonate, nitrogen, silicate, and borate components).

A standard name already exists for alkalinity expressed as mol/m3, sea_water_alkalinity_expressed_as_mole_equivalent, but none exist for mol/kg.

Best regards,
Elodie

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