After mulling it over, I'd suggest restricting the picoplankton definition to <2, and having a separate definition for nanoplankton, if necessary. I think there is at least one model that has explicit nanoplankton, but not mine, so I'm not sure if it's necessary.
----- Original Message ----- From: "Lowry, Roy K" <[email protected]> Date: Friday, April 23, 2010 9:14 am Subject: RE: [CF-metadata] CMIP5 ocean biogeochemistry standard names > 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: [email protected] [mailto:[email protected]] > Sent: 23 April 2010 13:39 > To: [email protected]; Lowry, Roy K; [email protected]; > [email protected]: [email protected]; > [email protected]; [email protected]; > [email protected]; [email protected] > 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: > [email protected], Didcot, OX11 0QX, U.K. > > > > -----Original Message----- > > From: [email protected] [mailto:cf-metadata- > > [email protected]] On Behalf Of [email protected] > > Sent: 01 April 2010 13:28 > > To: [email protected]; [email protected]; [email protected] > > Cc: [email protected]; > [email protected]; > > [email protected]; [email protected]; > [email protected] > > 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: > > [email protected] > > Chilton, Didcot, OX11 0QX, U.K. > > > > -- > > Scanned by iCritical. > > _______________________________________________ > > CF-metadata mailing list > > [email protected] > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > -- > Scanned by iCritical. > > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > _______________________________________________ CF-metadata mailing list [email protected] http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
