Hi Alison,
John's response got buried in my 'todo' pile. His 'flexible' definition almost works for me, but I would prefer to take 2um (the definition of field taxonomists) as the default, giving a definition like:
'Picophytoplankton are the smallest size class of phytoplankton with a maximum size of 2um for observational data and some models. Other models may specify the upper limit elsewhere in the range 2-5 um, in which case the actual upper limit used should be specified.'
Whether this specification should be done through the long name or a scalar co-ordinate variable as John suggests is something I'm not sure about. Anybody any preferences?
Cheers, Roy.
-----Original Message-----
From: alison.pamment at stfc.ac.uk [mailto:alison.pamment at stfc.ac.uk]
Sent: 23 April 2010 13:39
To: cf-metadata at cgd.ucar.edu; Lowry, Roy K; John.Dunne at noaa.gov; taylor13 at llnl.gov
Cc: chris.d.jones at metoffice.gov.uk; pierre.friedlingstein at lsce.ipsl.fr; doutriaux1 at llnl.gov; James.Orr at lsce.ipsl.fr; ernst.maier-reimer at zmaw.de
Subject: RE: [CF-metadata] CMIP5 ocean biogeochemistry standard names
Dear John and Roy,
Apart from the iron flux name which was discussed and agreed in the 'HAMOCC variablen' thread, there have been no further comments during the last three weeks on the ocean biogeochemistry names. There is one outstanding question regarding the definition and naming of the picophytoplankton quantities:
>
> > > > (1) I don't understand what the definition of picophytoplankton
> > > (carbon
> > > > concentration from the picophytoplankton (<2 um; < 5um)
component
> > > > alone) means Does it mean cells between 2 and 5 um in size, in
> > > which> case it should be expressed as 2-5um, or does it mean
> > > something else?
> > > >
> > >
> > > I agree that this definition doesn't make sense as it stands -
I'll
> > > check with John Dunne.
> >
> > The wishy-washiness of this definition was intended to account for
> the
> > fact that some groups make their distinction of smallest
> phytoplankton
> > class at the <2um size, while others do it at the <5um size. I
agree
> > that it would be better to have a single cut off for clarity.
> Perhaps
> > we should use the '2um' designation to be consistent with the
> > traditional definition of 'picoplankton' (where nanoplankton is the
> 2-5
> > umclass), and leave the individual participants to determine whether
> > they think their definition is consistent with this designation.
>
> >From the CF point of view, adopting a single cut off of <2um for
> picophytoplankton would certainly be clear. However, will this cause
> problems for modelling groups with different cut off sizes? I.e. will
> it make intercomparison between models difficult? As an alternative,
> we could write the definitions to cope with the vagueness, for
> example:
> "Picophytoplankton are the smallest class of phytoplankton. The
maximum
> size of picophytoplankton is in the range 2-5 um and may vary between
> models. A scalar coordinate variable should be used to specify the
> maximum size of picophytoplankton included in the data variable."
>
> This would then require the different modelling groups to specify the
> threshold they used, but would allow them all to write their data with
> the same standard name. (We could even give the coordinate variable a
> standard name such as 'plankton_size_threshold'). Would that be a
> suitable solution? Or do you still prefer to stick with the single cut
> off?
I am hoping that John will advise on which is the best approach to take with these names as I think we are close to being able to accept them.
I have temporarily removed these particular names from the attached spreadsheet.
The remaining names, including those modified in response to Roy's comments are now accepted for inclusion in the standard name table and are listed in the attached spreadsheet. To summarize, the modifications relative to the original proposals are as follows:
Row 13: correction to typo in 'concentration'
Rows 37-38: 'organic_carbon' changed to
'particulate_organic_matter_expressed_as_carbon'
Row 42: 'particulate_organic_carbon' changed to 'particulate_organic_matter_expressed_as_carbon'
Rows 51-54: 'organic_carbon' changed to
'particulate_organic_matter_expressed_as_carbon'
Rows 61-62: 'particles' changed to 'inorganic_particles'
I should also say that the clarifications to the definitions that have been suggested by both Roy and John during the discussion of these names will be included when the names are added to the table.
Best wishes,
Alison
------
Alison Pamment Tel: +44 1235 778065
NCAS/British Atmospheric Data Centre Fax: +44 1235 446314
Rutherford Appleton Laboratory Email: alison.pamment at stfc.ac.uk
Chilton, Didcot, OX11 0QX, U.K.
> -----Original Message-----
> From: cf-metadata-bounces at cgd.ucar.edu [mailto:cf-metadata-
> bounces at cgd.ucar.edu] On Behalf Of alison.pamment at stfc.ac.uk
> Sent: 01 April 2010 13:28
> To: cf-metadata at cgd.ucar.edu; rkl at bodc.ac.uk; John.Dunne at noaa.gov
> Cc: chris.d.jones at metoffice.gov.uk;
pierre.friedlingstein at lsce.ipsl.fr;
> doutriaux1 at llnl.gov; James.Orr at lsce.ipsl.fr;
ernst.maier-reimer at zmaw.de
> Subject: Re: [CF-metadata] CMIP5 ocean biogeochemistry standard names
>
> Dear Roy and John,
>
> Roy wrote:
>
> > The one point I think you have possibly misunderstood is the one
> about
> > 'miscellaneous'. It's not the word, so much as the possibility of
> the
> > concept having meaning that changes with time that worries me. This
> > can be addressed through the definition by a statement that
> > 'miscellaneous means phytoplankton that are not diatoms,
diazotrophs,
> > calcareous phytoplankton or picophytoplankton'. I did briefly
> consider
> > the phrase 'phytoplankton_not_diatom_diazotroph_calcareous_pico' in
> the
> > standard name, but then thought better of it.
> >
>
> Yes, I see now. I agree that the definitions should contain a
> statement such as the one you suggest. Thanks for not suggesting the
> other version of the name :)
>
> John wrote:
>
> > > > (1) I don't understand what the definition of picophytoplankton
> > > (carbon
> > > > concentration from the picophytoplankton (<2 um; < 5um)
component
> > > > alone) means Does it mean cells between 2 and 5 um in size, in
> > > which> case it should be expressed as 2-5um, or does it mean
> > > something else?
> > > >
> > >
> > > I agree that this definition doesn't make sense as it stands -
I'll
> > > check with John Dunne.
> >
> > The wishy-washiness of this definition was intended to account for
> the
> > fact that some groups make their distinction of smallest
> phytoplankton
> > class at the <2um size, while others do it at the <5um size. I
agree
> > that it would be better to have a single cut off for clarity.
> Perhaps
> > we should use the '2um' designation to be consistent with the
> > traditional definition of 'picoplankton' (where nanoplankton is the
> 2-5
> > umclass), and leave the individual participants to determine whether
> > they think their definition is consistent with this designation.
>
> >From the CF point of view, adopting a single cut off of <2um for
> picophytoplankton would certainly be clear. However, will this cause
> problems for modelling groups with different cut off sizes? I.e. will
> it make intercomparison between models difficult? As an alternative,
> we could write the definitions to cope with the vagueness, for
> example:
> "Picophytoplankton are the smallest class of phytoplankton. The
maximum
> size of picophytoplankton is in the range 2-5 um and may vary between
> models. A scalar coordinate variable should be used to specify the
> maximum size of picophytoplankton included in the data variable."
>
> This would then require the different modelling groups to specify the
> threshold they used, but would allow them all to write their data with
> the same standard name. (We could even give the coordinate variable a
> standard name such as 'plankton_size_threshold'). Would that be a
> suitable solution? Or do you still prefer to stick with the single cut
> off?
>
> John wrote:
>
> > > > (3) 'mole_concenration_of_dissolved_iron_in_sea_water'. Besides
> > the
> > > > typo (concentration), does this refer to iron in all oxidation
> > > states> (Fe2+/Fe3+) and chemical environments. If so, calling it
> > > 'total iron'
> > > > might be better.
> > >
> > > Thanks for pointing out the typo - I'll correct it. I think
> whenever
> > > the word "total" has come up in standard names proposals in the
> past
> > > that we have tried to avoid using it. Indeed, there are no
> standard
> > > names that use the term. I think "iron" essentially should be
> > > understood to mean "total iron" and if we want more specific names
> > for
> > > Fe2+, etc, we should introduce terms such as "divalent iron" in
the
> > > waythat we have done for elemental and divalent mercury in the
> > > atmosphere.Having said all that, I think it would be helpful if
> > > John could clarify the definition.
> >
> > In the geochemical literature, 'total' iron refers to the sum of
iron
> > associated with the particulate organic, particulate inorganic,
> > dissolved organic and dissolved inorganic components (both Fe2+ and
> > Fe3+). As we treat phytoplankton iron and particulate detrital iron
> > separately from dissolved, 'total' does not equal 'dissolved'. As
> > most, if not all, of the models do not distinguish between Fe2+ and
> > Fe3+,
I
> > think we could simply add a note in the definition to the effect
that
> > 'dissolved' is intended to represent both Fe2+ and Fe3+.
>
> Agreed. I'll add a sentence to the definitions.
>
> Best wishes,
> Alison
>
> ------
> Alison Pamment Tel: +44 1235 778065
> NCAS/British Atmospheric Data Centre Fax: +44 1235 446314
> Rutherford Appleton Laboratory Email:
> alison.pamment at stfc.ac.uk
> Chilton, Didcot, OX11 0QX, U.K.
>
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Received on Fri Apr 23 2010 - 07:14:53 BST
