Dear Martin, Roy, Jim, John,
Many thanks to Martin for pointing out the potential confusion between the definitions of silicate/phosphate and dissolved inorganic silicon/phosphorus. Thanks also to Roy, Jim and John for answering the question.
The following changes to existing standard names have been agreed. The changes will be implemented in the standard name table update on Monday (24th April).
mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water (mol m-3)
'Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". "Dissolved inorganic phosphorus" means the sum of all dissolved inorganic phosphorus in solution (including phosphate, hydrogen phosphate, dihydrogen phosphate, and phosphoric acid).'
The change here is to replace the final sentence in the definition which previously read '"Dissolved inorganic phosphorus" means phosphate ions in solution.'
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water (mol m-3)
'Mole concentration means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". "Dissolved inorganic silicon" means the sum of all dissolved silicon in solution (including silicic acid and its first dissociated anion SiO(OH)3-).'
The change here is to replace the final sentence in the definition which previously read '"Dissolved inorganic silicon" means silicate ions in solution.'
During the discussion it was agreed to retain the existing standard names mole_concentration_of_phosphate_in_sea_water and mole_concentration_of_silicate_in_sea_water without change. They should not be made into aliases of the dissolved inorganic phosphate/silicate names.
Best wishes,
Alison
------
Alison Pamment Tel: +44 1235 778065
Centre for Environmental Data Analysis Email: alison.pamment at stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Campus, Didcot, OX11 0QX, U.K.
From: Lowry, Roy K. [mailto:rkl at bodc.ac.uk]
Sent: 28 March 2017 09:01
To: James Orr
Cc: John Dunne - NOAA Federal; Juckes, Martin (STFC,RAL,RALSP); Pamment, Alison (STFC,RAL,RALSP); cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon
Hi James,
I've no problem with that change or to having the chemical formula included in the definition. My real concern is to retain the generic 'silicate' and 'phosphate' as accepted Standard Names.
My sea-going oceanography was from 1984 to 1999 and so there is a risk of my getting a little out of date!
Cheers, Roy.
Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to enquiries at bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
________________________________________
From: James Orr <James.Orr at lsce.ipsl.fr>
Sent: 27 March 2017 12:23
To: Lowry, Roy K.
Cc: John Dunne - NOAA Federal; <martin.juckes at stfc.ac.uk>; Alison Pamment; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon
?
Hi Roy,
There has been a trend as you suggest, although it started a few decades
ago, e.g., "silicic acid" is used instead of "silicate" in the
following:
Gordon, L. I., Jennings Jr, J. C., Ross, A. A., & Krest, J. M. (1993). A
suggested protocol for continuous flow automated analysis of seawater
nutrients (phosphate, nitrate, nitrite and silicic acid) in the WOCE
Hydrographic Program and the Joint Global Ocean Fluxes Study. WOCE
Operations Manual, Part, 3(3), 91-1.
Knap, A. H., Michaels, A., Close, A. R., Ducklow, H., & Dickson, A. G.
(1996). Protocols for the joint global ocean flux study (JGOFS) core
measurements.
For our purposes though, both terms can be used synonymously.? To avoid
confusion, would you agree to the following 2nd correction to the CF
Standard Name List:
(2) '"Dissolved inorganic silicon" means the sum of all dissolved
silicon in solution (including silicic acid and its first dissociated
anion SiO(OH)3-)'
i.e., for the definition of
mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
I've just now replaced 'silicate' with 'its first dissociated anion
SiO(OH)3-' to keep the more general sense of silicate intact. For
simplicity, we may want to remove the chemical formula after the
word 'anion'.
Your thoughts?
Jim
On Mon, 27 Mar 2017, Lowry, Roy K. wrote:
>
> Many thanks James,
>
>
> I like it. I had visions of tens of thousands of files needing to be edited - we're bringing in semantically
> aware compliance checkers that require action if?deprecated terms are used.
>
>
> Interesting, in?36 years I have never heard an oceanographer refer to silicic acid - it's always been
> 'silicate' referring to the measurement made by the standard colorometric analytical technique.?
>
>
> Out of curiosity I'll sound out my own organisation (UK National Oceanography Centre) on the usage of DIP and
> DISi to see if there is any change in the viewpoint in the younger oceanographers.
>
>
> Cheers, Roy.
>
> _____________________________________________________________________________________________________________
> From: James Orr <James.Orr at lsce.ipsl.fr>
> Sent: 25 March 2017 14:21
> To: Lowry, Roy K.
> Cc: John Dunne - NOAA Federal; <martin.juckes at stfc.ac.uk>; Alison Pamment; cf-metadata at cgd.ucar.edu
> Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon ?
> Hi Roy,
>
> I understand your concern and would agree that it would be fine to keep
> the standard names but to explain what we mean by them in the
> definitions.
>
> So in response to Martin's questions, I would suggest the following
> corrections in the CF Standard Name List:
>
> (1) '"Dissolved inorganic phosphorus" means the sum of all dissolved
> inorganic phosphorus in solution (including phosphate, hydrogen
> phosphate, dihydrogen phosphate, and phosphoric acid)' for the
> definition of
> mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, and
>
> (2) '"Dissolved inorganic silicon" means the sum of all dissolved
> silicon in solution (including silicic acid and silicate)' for the
> definition of
> mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
>
> By the way, although many oceanographers refer only to silicate as you
> mention, many others refer only to silicic acid.? In both cases though
> what is meant is the sum of both.
>
> Best regards,
>
> Jim
>
> On Fri, 24 Mar 2017, Lowry, Roy K. wrote:
>
> >
> > Dear All,
> >
> >
> > That would make no sense at all for the observational oceanographic community who have referred to silicate
> > and phosphate for decades because all the various types of phosphate and silicate?react to the?standard
> > colorometric reagents in exactly the same way. Replacing?terminology in common usage with more pedantic
> > synonyms can only result in confusion.
> >
> >
> > So, the situation we have is that we have a technically precise Standard Names and?Standard Names that
> > reflect terminology in common usage. ?One solution might be to leave all four Standard Names in place but
> to
> > clarify the definitions. In our server the pairs could be mapped as synonyms if Alison requests it.
> >
> >
> > Cheers, Roy.
> >
> >
> > Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and can only
> > guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be sent to
> > enquiries at bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
> >
> >
> >
> >____________________________________________________________________________________________________________
> _
> > From: John Dunne - NOAA Federal <john.dunne at noaa.gov>
> > Sent: 24 March 2017 17:14
> > To: <martin.juckes at stfc.ac.uk>
> > Cc: James Orr; Lowry, Roy K.; Alison Pamment; cf-metadata at cgd.ucar.edu
> > Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon ?
> > Is the plan also to demote the "silicate" and "phosphate" names?? That would seem to make sense to me,
> > consistent with Jim's points.
> >
> > On Fri, Mar 24, 2017 at 12:13 PM, <martin.juckes at stfc.ac.uk> wrote:
> >?????? Dear Jim,
> >
> >?????? thanks. I think that means that we need a corrections to the statements, from the CF Standard
> >?????? Name list, that:
> >
> >?????? (1) '"Dissolved inorganic phosphorus" means phosphate ions in solution' in the CF Standard Name
> >?????? definition for mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water, and
> >?????? (2) '"Dissolved inorganic silicon" means silicate ions in solution' in the definition of
> >?????? mole_concentration_of_dissolved_inorganic_silicon_in_sea_water
> >
> >?????? regards,
> >?????? Martin
> >?????? ________________________________________
> >?????? From: James Orr [James.Orr at lsce.ipsl.fr]
> >?????? Sent: 24 March 2017 15:46
> >?????? To: Lowry, Roy K.
> >?????? Cc: Juckes, Martin (STFC,RAL,RALSP); cf-metadata at cgd.ucar.edu
> >?????? Subject: Re: [CF-metadata] Silicate vs. dissolved inorganic silicon
> >
> >?????? Dissolved inorganic phosphorus in seawater takes several forms, with
> >?????? phosphate (P043-) being only one of them. Furthermore, PO43- is not
> >?????? even the most abundant form at normal seawater pH. Rather it is HPO42-
> >?????? (hydrogen phosphate). Oceanographers do often refer to phosphate but
> >?????? what they really taking about is total dissolved inorganic phosphorus
> >?????? (the sum of all inorganic forms).
> >
> >?????? The seawater system for dissolved inorganic silicon is simpler because
> >?????? we only need to consider two forms: silicic acid (Si(OH)4) and silicate
> >?????? (SiO(OH)3-). The former is more abundant than the latter in seawater.
> >
> >?????? It is best then to refer to
> >?????? - total dissolved inorganic phosphorus rather than phosphate and
> >?????? - total dissolved inorganic silicon rather than silicate.
> >
> >?????? For more insight see the last figure in the OMIP-BGC protocols paper
> >?????? in the CMIP6 special issue at
> >
> >?????? http://www.geosci-model-dev-discuss.net/gmd-2016-155/
GMDD - Biogeochemical protocols and diagnostics for the ...
www.geosci-model-dev-discuss.net
Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)
> GMDD - Biogeochemical protocols and diagnostics for the ...
> www.geosci-model-dev-discuss.net
GMDD - Recent
www.geosci-model-dev-discuss.net
Daniel J. Lunt, Matthew Huber, Eleni Anagnostou, Michiel L. J. Baatsen, Rodrigo Caballero, Rob DeConto, Henk A. Dijkstra, Yannick Donnadieu, David Evans, Ran Feng ...
> Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)
>
>
> >
> >?????? Cheers,
> >
> >?????? Jim
> >
> >?????? On Fri, 24 Mar 2017, Lowry, Roy K. wrote:
> >
> >?????? > Dear All,
> >?????? >
> >?????? >
> >?????? > If one makes the assumption that all the silicon and phosphorus atoms not associated with
> >?????? organic ligands are
> >?????? > in a single chemical form associated with oxygen in solution then what Martin says is correct.
> >?????? In my
> >?????? > experience I have never known anybody challenge this assumption and I cannot think of any other
> >?????? anions
> >?????? > incorporating P and Si. Consequently, I would agree that whilst there is a theoretical semantic
> >?????? difference
> >?????? > between the members of each Standard Name pair I would agree that this could be ignored and
> >?????? they could be
> >?????? > considered synonyms.
> >?????? >
> >?????? >
> >?????? > Note, this only holds true as these are MOLE concentrations. The MASS concentration of
> >?????? inorganic phosphorus
> >?????? > is very different from the MASS concentration of phosphate as the oxygen atoms have mass.
> >?????? >
> >?????? >
> >?????? > If the decision is taken to take action on this then I would recommend that the
> >?????? 'inorganic_silicon' and
> >?????? > 'inorganic_phosphorus' names be than ones to be converted to aliases. This is based on common
> >?????? terminology
> >?????? > usage in the oceanographic community.
> >?????? >
> >?????? >
> >?????? > Cheers, Roy.
> >?????? >
> >?????? >
> >?????? > Please note that I partially retired on 01/11/2015. I am now only working 7.5 hours a week and
> >?????? can only
> >?????? > guarantee e-mail response on Wednesdays, my day in the office. All vocabulary queries should be
> >?????? sent to
> >?????? > enquiries at bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
> >?????? >
> >?????? >
> >?????? >
> >??????>___________________________________________________________________________________________________________
> _
> >?????? _
> >?????? > From: CF-metadata <cf-metadata-bounces at cgd.ucar.edu> on behalf of martin.juckes at stfc.ac.uk
> >?????? > <martin.juckes at stfc.ac.uk>
> >?????? > Sent: 24 March 2017 08:48
> >?????? > To: cf-metadata at cgd.ucar.edu
> >?????? > Subject: [CF-metadata] Silicate vs. dissolved inorganic silicon
> >?????? > Hello Alison, others,
> >?????? >
> >?????? > the standard name list includes both
> >?????? > (1) mole_concentration_of_dissolved_inorganic_silicon_in_sea_water and (2)
> >?????? > mole_concentration_of_silicate_in_sea_water
> >?????? >
> >?????? > The definition of the first says that "dissolved inorganic silicon" means silicate ions in
> >?????? solution. Both
> >?????? > have units of "mol m-3". It looks to me as though they are describing the same thing. If this
> >?????? is true, should
> >?????? > one be demoted to the alias of the other? If they are different, what is the difference?
> >?????? >
> >?????? > The same question applies to mole_concentration_of_dissolved_inorganic_phosphorus_in_sea_water
> >?????? and
> >?????? > mole_concentration_of_phosphate_in_sea_water.
> >?????? >
> >?????? > regards,
> >?????? > Martin
> >?????? >
> >?????? > _______________________________________________
> >?????? > CF-metadata mailing list
> >?????? > CF-metadata at cgd.ucar.edu
> >?????? > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
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> >?????? >
> >
> >?????? --
> >?????? LSCE/IPSL, Laboratoire des Sciences du Climat et de l'Environnement
> >?????? CEA-CNRS-UVSQ
> >
> >?????? LSCE/IPSL, CEA Saclay http://www.ipsl.jussieu.fr/~jomce
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> --
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