[CF-metadata] Proposed standard names for biological model outputs

[Michael Godin]

Hi Roy,

It seems that a majority of biologists here agree with your biologists
and would prefer to use "concentration" to express moles/volume, as the
usual units for biomass involve mass.  However, since the CF-Metadata
uses both "concentration" and "mass_conentation" to represent
mass/volume, it is probably appropriate to specify "mole_concentration"
to express moles/volume (which is roughly equivalent to using
"mole_fraction" to express moles/moles).

I also concur with Jonathan's earlier recommendation to use the
"expressed_as" modifier. So, my revised list of proposed standard names
is as follows (all units are mol m-3):

Prefix to all descriptions: Mole concentration means moles (amount of
substance) per unit volume and is used in the construction
mole_concentration_of_X_in_Y, where X is a material constituent of Y. 

mole_concentration_of_organic_detritus_in_sea_water_expressed_as_nitrogen
Description: Organic detritus are particles of debris from decaying
plants and animals. The construction expressed_as_nitrogen indicates
that the indicated mole concentration is of nitrogen atoms due to the
organic detritus.

mole_concentration_of_organic_detritus_in_sea_water_expressed_as_silica
Description: Organic detritus are particles of debris from decaying
plants and animals. The construction expressed_as_silica indicates that
the indicated mole concentration is of silica atoms due to the organic
detritus.

mole_concentration_of_diatoms_in_sea_water_expressed_as_nitrogen
Description: Diatoms are single-celled phytoplankton with an external
skeleton made of silica. The construction expressed_as_nitrogen
indicates that the indicated mole concentration is of nitrogen atoms due
to the diatoms.

mole_concentration_of_mesozooplankton_in_sea_water_expressed_as_nitrogen
Description: Mesozooplankton are large protozoans (single-celled
organisms) and small metazoans (multi-celled organisms) sized between
2x10-4 m and 2x10-2 m that feed on other plankton and telonemia. The
construction expressed_as_nitrogen indicates that the indicated mole
concentration is of nitrogen atoms due to the mesozooplankton.

mole_concentration_of_microzooplankton_in_sea_water_expressed_as_nitrogen
Description: Microzooplankton are protozoans (single-celled organisms)
sized between 2x10-5 m and 2x10-4 m that feed on other plankton and
telonemia. The construction expressed_as_nitrogen indicates that the
indicated mole concentration is of nitrogen atoms due to the
microzooplankton.

mole_concentration_of_phytoplankton_in_sea_water_expressed_as_nitrogen
Description: Phytoplankton are autotrophic prokaryotic or eukaryotic
algae that live near the water surface where there is sufficient light
to support photosynthesis. The construction expressed_as_nitrogen
indicates that the indicated mole concentration is of nitrogen atoms due
to the phytoplankton.

mole_concentration_of_ammonium_in_sea_water

mole_concentration_of_nitrate_in_sea_water

mole_concentration_of_silicate_in_sea_water 

Regards,
Mike

> -----Original Message----- 
> From: cf-metadata-bounces at cgd.ucar.edu
> [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Roy Lowry 
> Sent: Friday, December 22, 2006 12:06 AM 
> To: cf-metadata at cgd.ucar.edu 
> Subject: RE: [CF-metadata] Proposed standard names for biological
> model outputs
> 
> Michael,
> 
> This discussion seems to have stalled and it would be nice to get your
> proposed standard names into the system.  As regards the 'biomass'
> versus 'molar concentration' issue further talks with biological
> colleagues indicate that the association of the units 'moles' with
> biomass is a totall alien concept.  To them canonical units biomass
> are kg/m3 (usually expressed as mg/m2 or ug/l).  So, how about if we
> go with your initial suggestions and reserve the term 'biomass' for
> the inevitable future request?
> 
> Cheers, Roy.
> 
> >>> "Godin, Michael" <Godin at mbari.org> 12/6/2006 4:42 pm >>> 
> Ron,
> 
> The small group of biological oceanographers I have spoken with thus
> far fall into two camps: those who use ecosystem model outputs, and
> those who don't (I'm still waiting to talk with more of each).  Of
> those who use ecosystem model outputs (and publish papers in the
> field), the term to describe moles of X per unit volume water due to Y
> is simply "concentration" (with no "molar" or "amount-of-substance"
> prefix).  Those who don't use biological models call it
> "biomass" (even those who use physical models).  
> 
> I also asked about terms for moles per kilogram, and was told that
> such a measure is rarely used by biologists, as it is too akin to the
> chemist's concepts of molality and molinity, which tend to imply a
> dissolved solution.  Similarly, it appears that oceanographers avoid
> expressing "mass of X per unit volume water," as it is non-trivial to
> measure the dry mass of biological samples; and the resulting quantity
> would have to be called "density", which could be confused with water
> density.
> 
> Mike
> 
> -----Original Message----- 
> From: cf-metadata-bounces at cgd.ucar.edu
> [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Roy Lowry 
> Sent: Wednesday, December 06, 2006 12:50 AM 
> To: cf-metadata at cgd.ucar.edu 
> Subject: Re: [CF-metadata] Proposed standard names for biological
> model outputs
> 
> Hello Jonathan,
> 
> Let's see what Mike turns up when he talks to his MBARI colleagues
> about the best way to describe substance held in biological material.
> A straw poll of four biologists in BODC indicated that biomass was the
> better understood term in this context.
> 
> I agree with you about molality.  I again asked around the BODC data
> scientists and nobody could give me a definition of molality -
> including a couple of people with chemical oceanography PhDs.
> 
> Longer term we need to 'get smart' and provide the technology to
> manage synonyms operationally.
> 
> Cheers, Roy. 
> 
> >>> Jonathan Gregory <j.m.gregory at reading.ac.uk> 12/05/06 6:27 PM >>> 
> Dear Roy
> 
> > I can see a future request for
> 'Nitrogen_molar_biomass_of_phytoplankton' and nobody realising that it
> is the same thing as the pre-existing
> 'molar_concentration_of_nitrogen_in_sea_water_due_to_phytoplankton'.
> 
> This kind of thing is certainly a problem but I don't think we can
> avoid it. 
> When people approach things from different backgrounds they have
> different expectations. We just have to point that the quantity exists
> under a different name already. This has happened before.
> 
> Of course, we can minimise it by using familiar terms, and that is one
> reason for doing so. However, I somewhat disagree with Steve's
> preference for the technical terms of specialised fields, as often
> these terms are unclear and confused - at least, I have got that
> impression from previous exercises to devise new standard names. In
> their own fields they are jargon which is understood, and the
> background is known, but to outsiders they can seem unintuitive and
> unclear. Obviously this is not always the case. We have to take each
> case on its merits.
> 
> Best wishes
> 
> Jonathan 
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