Hi,
reg. the chlorophyll fluorescence, I would recommend against a new
standard name if the scientific interest is in fact the mass
fraction/concentration of chlorophyll. In that case, use one of the
existing standard names relating to mass fraction or concentration (if I
search for "chlorophyll" in the online table, 9 standard names pop up).
You can explain in the "comments" or some other metadata field that the
data is derived from fluorescence values, and annotate it with an
uncertainty.
If the model actually simulates fluorescence e.g. based on different
plankton species composition and the property of interest is in fact the
fluorescence, then by all means, we should create a new standard name
for that. There are two approaches to this: one is specific to the
wavelengths of chlorophyll A, and the standard name could be something
like "chlorophyll_a_fluorescence_expressed_as_mass_concentration_of...".
However, this could escalate into many new standard names if we decide
we also want names for other substances (CDOM, rhodamine,
tryptophan, ...). The other option is to define an entirely new
fluorescence standard name with arbitrary exciting and response wave
lengths. This will need to have two auxiliary coordinates (incoming and
outgoing wavelength) much like this existing name (has one wavelength):
surface_downwelling_spherical_irradiance_per_unit_wavelength_in_sea_water
The unit of the fluorescence thing would have to be something like the
energy ratio out/in, or an outgoing irradiance assuming a normalized
input irradiance. This requires some thinking.
Matthias
On Tue, 2016-12-06 at 03:17 -0700, cf-metadata-request at cgd.ucar.edu
wrote:
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> Today's Topics:
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> 1. Re: New standard_names for ocean biogeochemistry
> (John Dunne - NOAA Federal)
> 2. Re: New standard_names for ocean biogeochemistry (Lowry, Roy K.)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Dec 2016 15:45:00 -0500
> From: John Dunne - NOAA Federal <john.dunne at noaa.gov>
> To: Elodie Fernandez <elodie.fernandez at mercator-ocean.fr>
> Cc: cf-metadata at cgd.ucar.edu, Fernando Manzano Mu?oz
> <fmanzano at puertos.es>
> Subject: Re: [CF-metadata] New standard_names for ocean
> biogeochemistry
> Message-ID:
> <CAPqsCaG3B04eVqYmvfTAE2X0-3okRV+Nb2cMNt_9F2_v5uAQGg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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 <
> elodie.fernandez at 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
> >
> > _______________________________________________
> > CF-metadata mailing list
> > CF-metadata at cgd.ucar.edu
> > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Tue, 6 Dec 2016 10:17:29 +0000
> From: "Lowry, Roy K." <rkl at bodc.ac.uk>
> To: John Dunne - NOAA Federal <john.dunne at noaa.gov>, Elodie Fernandez
> <elodie.fernandez at mercator-ocean.fr>
> Cc: "cf-metadata at cgd.ucar.edu" <cf-metadata at cgd.ucar.edu>, Fernando
> Manzano Mu?oz <fmanzano at puertos.es>
> Subject: Re: [CF-metadata] New standard_names for ocean
> biogeochemistry
> Message-ID:
> <DB6PR0601MB26142BDC8F9E458D3A2D74D599820 at DB6PR0601MB2614.eurprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="utf-8"
>
> 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-bounces at cgd.ucar.edu] On Behalf Of John Dunne - NOAA Federal
> Sent: 05 December 2016 20:45
> To: Elodie Fernandez <elodie.fernandez at mercator-ocean.fr>
> Cc: cf-metadata at cgd.ucar.edu; Fernando Manzano Mu?oz <fmanzano at 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 <elodie.fernandez at mercator-ocean.fr<mailto:elodie.fernandez at 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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--
_______________________________________
Dr. Matthias Lankhorst
Scripps Institution of Oceanography
9500 Gilman Drive, Mail Code 0230
La Jolla, CA 92093-0230
USA
Phone: +1 858 822 5013
Fax: +1 858 534 9820
E-Mail: mlankhorst at ucsd.edu
http://pordlabs.ucsd.edu/mlankhorst/
Received on Tue Dec 06 2016 - 12:47:40 GMT
