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[CF-metadata] Proposing new names for marine biogeochemical modeling

From: Daniel Neumann <daniel.neumann>
Date: Thu, 29 Mar 2018 20:20:29 +0200

Dear Roy, Dear Jonathan,

Thank you for the feedback.


> First, the correct spelling is 'flagellate', not 'flaggelate'.

Thanks for the correction. I should re-read the names before posting
them ...


> Secondly, this proposal causes me concerns because it is adding more
> biological names [...], which raises the spectre of Trac ticket 99 [...]
> where we proposed normalising out biological labels rather than
> including them explicitly in Standard Names.

The ticket sounds quite reasonable. It is a much better option than
creating individual standard names.

To summarize the status of the ticket in my on words (whether I
understand it correctly):
 ?- there needs to be made a decision on whether one reference database
for machine-readable taxon IDs should be predefined; and if yes, which
database
 ?- someone needs to revise the text of the original ticket as first
draft for adding it to CF1.8


My request/need is not urgent in the sense that I would need standard
names for an official data publication until a specific date. Because
the suggestion in the tickets seems to be a good solution for my
situation, I am happy with discarding my suggested new standard names.


Regards,
Daniel


On 29.03.2018 18:46, Jonathan Gregory wrote:
> Dear Roy
>
> Yes, it was ticket 99 https://cf-trac.llnl.gov/trac/ticket/99
>
> I still accept the conclusion we reached there re biological taxa and I support
> the ticket. As you know, I am not an expert on this, but I will try to
> contribute if you revitalise the ticket. I hope that it can be made to meet
> Daniel's needs.
>
> Best wishes
>
> Jonathan
>
> ----- Forwarded message from "Lowry, Roy K." <rkl at bodc.ac.uk> -----
>
>> Date: Thu, 29 Mar 2018 16:12:50 +0000
>> From: "Lowry, Roy K." <rkl at bodc.ac.uk>
>> To: Daniel Neumann <daniel.neumann at io-warnemuende.de>, CF Metadata Mail List
>> <cf-metadata at cgd.ucar.edu>
>> Subject: Re: [CF-metadata] Proposing new names for marine biogeochemical
>> modeling
>>
>> Dear All,
>>
>>
>> First, the correct spelling is 'flagellate', not 'flaggelate'.
>>
>>
>> Secondly, this proposal causes me concerns because it is adding more biological names (not species but taxonomic phyla, although Flagellate in an unaccepted synonym for Discomitochondria<http://www.marinespecies.org/aphia.php?p=taxdetails&id=146221> - see http://www.marinespecies.org/aphia.php?p=taxdetails&id=146222), which raises the spectre of Trac ticket 99 (I think I've got the number right) where we proposed normalising out biological labels rather than including them explicitly in Standard Names.
>>
>>
>> I think we got to the stage with this ticket of agreeing that normalisation would be a good idea, but without coming up with firm details of how the taxon label should be incorporated into the CF Parameter attributes to qualify a Standard Name such as 'mass_concentration_expressed_as_carbon_in_sea_water'. I would start the ball rolling by pushing WoRMS as the authoritative taxonomic reference and the the label should include both human-readable information an the AphiaID (which can be used as the basis for a WoRMS URL). Other suggestions or ideas on how this information should be encoded syntactically welcome!
>>
>>
>> I think Daniels' proposal forces the issue. Either the Trac ticket is taken to completion - presumably by somebody writing a section for the CF1.8 document - or we give up the idea and allow explicit taxon labels with the Standard Names.
>>
>>
>> I would favour the former approach, but appreciate that work needs to be done and needs to be done quickly if we are not to block Daniel's work. I can put some time in, but would need some assistance. Any volunteers?
>>
>>
>> Cheers, Roy.
>>
>> WoRMS - World Register of Marine Species - Flagellates<http://www.marinespecies.org/aphia.php?p=taxdetails&id=146222>
>> www.marinespecies.org
>> basis of record Margulis, L.; Schwartz, K.V. (1998). Five Kingdoms: an illustrated guide to the Phyla of life on earth. 3rd edition. Freeman: New York, NY (USA).
>>
>>
>>
>>
>> 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 Daniel Neumann <daniel.neumann at io-warnemuende.de>
>> Sent: 29 March 2018 12:36
>> To: CF Metadata Mail List
>> Subject: [CF-metadata] Proposing new names for marine biogeochemical modeling
>>
>> Dear List,
>>
>> I would like to propose 10 new standard names for cyanobacteria and
>> flagellates (five each). Similar names exist already for diatoms. The
>> descriptions are copied except for the species-specific part. There is
>> no urgency in processing this proposal but it produces considerably less
>> work than my other one.
>>
>> We only need six of them (three per species). But, by suggesting these
>> ten names, each diatom standard name has a corresponding cyanobacteria
>> and flagellate name.
>>
>> The standard names are:
>>
>> mass_concentration_of_cyanobacteria_expressed_as_carbon_in_sea_water
>> mass_concentration_of_cyanobacteria_expressed_as_chlorophyll_in_sea_water
>> mass_concentration_of_cyanobacteria_expressed_as_nitrogen_in_sea_water
>> mole_concentration_of_cyanobacteria_expressed_as_carbon_in_sea_water
>> mole_concentration_of_cyanobacteria_expressed_as_nitrogen_in_sea_water
>> mass_concentration_of_flaggelates_expressed_as_carbon_in_sea_water
>> mass_concentration_of_flaggelates_expressed_as_chlorophyll_in_sea_water
>> mass_concentration_of_flaggelates_expressed_as_nitrogen_in_sea_water
>> mole_concentration_of_flaggelates_expressed_as_carbon_in_sea_water
>> mole_concentration_of_flaggelates_expressed_as_nitrogen_in_sea_water
>>
>> Please find the descriptions and units further below in this email.
>>
>> Further I would like to propose two minor and one major changes in the
>> descriptions of the existing diatom standard names. I will describe the
>> change, print first the old description, and then print the new description.
>>
>> Regards,
>> Daniel
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~
>>
>> NEW NAMES
>>
>> mass_concentration_of_cyanobacteria_expressed_as_carbon_in_sea_water
>>
>> 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. Cyanobacteria in this context are
>> dinitrogen-fixing bacteria (diazotrophs), which perform photosynthesis
>> and produce oxygen.
>>
>> kg m-3
>>
>>
>> mass_concentration_of_cyanobacteria_expressed_as_chlorophyll_in_sea_water
>>
>> 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 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B containedin A, neglecting all other
>> chemical constituents of A. 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. Cyanobacteria in this context are
>> dinitrogen-fixing bacteria (diazotrophs), which perform photosynthesis
>> and produce oxygen.
>>
>> kg m-3
>>
>>
>> mass_concentration_of_cyanobacteria_expressed_as_nitrogen_in_sea_water
>>
>> 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. Cyanobacteria in this context are
>> dinitrogen-fixing bacteria (diazotrophs), which perform photosynthesis
>> and produce oxygen.
>>
>> kg m-3
>>
>>
>> mole_concentration_of_cyanobacteria_expressed_as_carbon_in_sea_water
>>
>> 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'.The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. Cyanobacteria in this context are
>> dinitrogen-fixing bacteria (diazotrophs), which perform photosynthesis
>> and produce oxygen.
>>
>> mol m-3
>>
>>
>> mole_concentration_of_cyanobacteria_expressed_as_nitrogen_in_sea_water
>>
>> 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 species denoted by X may be described by a single term such as
>> 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. The phrase
>> 'expressed_as' is used in the construction A_expressed_as_B, where B is
>> a chemical constituent of A. It means that the quantity indicated by the
>> standard name is calculated in terms of B alone, neglecting all other
>> chemical constituents of A. Cyanobacteria in this context are
>> dinitrogen-fixing bacteria (diazotrophs), which perform photosynthesis
>> and produce oxygen.
>>
>> mol m-3
>>
>>
>> mass_concentration_of_flaggelates_expressed_as_carbon_in_sea_water
>>
>> 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. 'Flagellates' describes a group of plankton,
>> which have in common whip-like appendages (flagella) that they use for
>> their locomotion. Flagellates are a diverse group of organisms, some are
>> photoautotrophs, many are mixotrophs. In most models, flagellates are
>> considered small (smaller than diatoms) and photoautotrophic. A comment
>> should indicate whether this variable describes all flagellates or only
>> the photoautotrophic flagellates.
>>
>> kg m-3
>>
>>
>> mass_concentration_of_flaggelates_expressed_as_chlorophyll_in_sea_water
>>
>> 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 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B containedin A, neglecting all other
>> chemical constituents of A. Chlorophylls are the green pigments found in
>> most plants, algae and flaggelates; 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. 'Flagellates' describes a group of
>> plankton, which have in common whip-like appendages (flagella) that they
>> use for their locomotion. Flagellates are a diverse group of organisms,
>> some are photoautotrophs, many are mixotrophs. In most models,
>> flagellates are considered small (smaller than diatoms) and
>> photoautotrophic. A comment should indicate whether this variable
>> describes all flagellates or only the photoautotrophic flagellates.
>>
>> kg m-3
>>
>>
>> mass_concentration_of_flaggelates_expressed_as_nitrogen_in_sea_water
>>
>> 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. 'Flagellates' describes a group of plankton,
>> which have in common whip-like appendages (flagella) that they use for
>> their locomotion. Flagellates are a diverse group of organisms, some are
>> photoautotrophs, many are mixotrophs. In most models, flagellates are
>> considered small (smaller than diatoms) and photoautotrophic. A comment
>> should indicate whether this variable describes all flagellates or only
>> the photoautotrophic flagellates.
>>
>> kg m-3
>>
>>
>> mole_concentration_of_flaggelates_expressed_as_carbon_in_sea_water
>>
>> 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'.The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. 'Flagellates' describes a group of plankton,
>> which have in common whip-like appendages (flagella) that they use for
>> their locomotion. Flagellates are a diverse group of organisms, some are
>> photoautotrophs, many are mixotrophs. In most models, flagellates are
>> considered small (smaller than diatoms) and photoautotrophic. A comment
>> should indicate whether this variable describes all flagellates or only
>> the photoautotrophic flagellates.
>>
>> mol m-3
>>
>>
>> mole_concentration_of_flaggelates_expressed_as_nitrogen_in_sea_water
>>
>> 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 species denoted by X may be described by a single term such as
>> 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. The phrase
>> 'expressed_as' is used in the construction A_expressed_as_B, where B is
>> a chemical constituent of A. It means that the quantity indicated by the
>> standard name is calculated in terms of B alone, neglecting all other
>> chemical constituents of A. 'Flagellates' describes a group of plankton,
>> which have in common whip-like appendages (flagella) that they use for
>> their locomotion. Flagellates are a diverse group of organisms, some are
>> photoautotrophs, many are mixotrophs. In most models, flagellates are
>> considered small (smaller than diatoms) and photoautotrophic. A comment
>> should indicate whether this variable describes all flagellates or only
>> the photoautotrophic flagellates.
>>
>> mol m-3
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~
>>
>> CHANGES
>>
>> mass_concentration_of_diatoms_expressed_as_chlorophyll_in_sea_water
>>
>> CHANGE:
>> Remove quotation marks around 'Mass concentration' because it is only
>> done in this description.
>>
>> OLD:
>> '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 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B containedin A, neglecting all other
>> chemical constituents of A. 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. Diatoms are single-celled phytoplankton
>> with an external skeleton made of silica. Phytoplankton are autotrophic
>> prokaryotic or eukaryotic algae that live near the water surface where
>> there is sufficient light to support photosynthesis.
>>
>> NEW:
>> 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 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'. The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B containedin A, neglecting all other
>> chemical constituents of A. 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. Diatoms are single-celled phytoplankton
>> with an external skeleton made of silica. Phytoplankton are autotrophic
>> prokaryotic or eukaryotic algae that live near the water surface where
>> there is sufficient light to support photosynthesis.
>>
>>
>> mole_concentration_of_diatoms_expressed_as_carbon_in_sea_water
>>
>> CHANGE:
>> A missing space.
>>
>> OLD:
>> 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'.The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. Diatoms are single-celled phytoplankton with
>> an external skeleton made of silica.Phytoplankton are autotrophic
>> prokaryotic or eukaryotic algae that live near the water surface where
>> there is sufficient light to support photosynthesis.
>>
>> NEW:
>> 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'.The phrase 'expressed_as' is used in the
>> construction A_expressed_as_B, where B is a chemical constituent of A.
>> It means that the quantity indicated by the standard name is calculated
>> solely with respect to the B contained in A, neglecting all other
>> chemical constituents of A. Diatoms are single-celled phytoplankton with
>> an external skeleton made of silica. Phytoplankton are autotrophic
>> prokaryotic or eukaryotic algae that live near the water surface where
>> there is sufficient light to support photosynthesis.
>>
>>
>> mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_water
>>
>> CHANGE:
>> Some part of the description was missing in the end (copied from other
>> descriptions).
>>
>> OLD:
>> 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 species denoted by X may be described by a single term such as
>> 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. The phrase
>> 'expressed_as' is used in the construction A_expressed_as_B, where B is
>> a chemical constituent of A. It means that the quantity indicated by the
>> standard name is calculated in terms of B alone, neglecting all other
>> chemical constituents of A.
>>
>> NEW:
>> 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 species denoted by X may be described by a single term such as
>> 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. The phrase
>> 'expressed_as' is used in the construction A_expressed_as_B, where B is
>> a chemical constituent of A. It means that the quantity indicated by the
>> standard name is calculated in terms of B alone, neglecting all other
>> chemical constituents of A. It means that the quantity indicated by the
>> standard name is calculated solely with respect to the B contained in A,
>> neglecting all other chemical constituents of A. Diatoms are
>> single-celled phytoplankton with an external skeleton made of silica.
>> Phytoplankton are autotrophic prokaryotic or eukaryotic algae that live
>> near the water surface where there is sufficient light to support
>> photosynthesis.
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~
>>
>> THE END
>> _______________________________________________
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>> This is an unmoderated list for discussions about interpretation, clarification, and proposals for extensions or change to the CF conventions.
>>
>>
>>
>> ________________________________
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>
> ----- End forwarded message -----
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-- 
Daniel Neumann
Leibniz Institute for Baltic Sea Research Warnemuende
Physical Oceanography and Instrumentation
Seestrasse 15
18119 Rostock
Germany
phone:  +49-381-5197-287
fax:    +49-381-5197-114 or 440
e-mail: daniel.neumann at io-warnemuende.de
Received on Thu Mar 29 2018 - 12:20:29 BST

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