Date: Thu, 29 Mar 2018 16:12:50 +0000
From: "Lowry, Roy K." <[email protected]>
To: Daniel Neumann <[email protected]>, CF Metadata Mail List
<[email protected]>
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 [email protected].
Please also use this e-mail if your requirement is urgent.
________________________________
From: CF-metadata <[email protected]> on behalf of Daniel Neumann
<[email protected]>
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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