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." <[email protected]> ----- > 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 > _______________________________________________ > CF-metadata mailing list > [email protected] > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > CF-metadata Info Page - mailman.cgd.ucar.edu Mailing > Lists<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > mailman.cgd.ucar.edu > This is an unmoderated list for discussions about interpretation, > clarification, and proposals for extensions or change to the CF conventions. > > > > ________________________________ > 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 ----- End forwarded message ----- _______________________________________________ CF-metadata mailing list [email protected] http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
