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. 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