Many thanks Jonathan,
I've just re-read Trac 99 and it looks like it was a lot closer to getting completed than I remembered, with agreement on an outline design based on the principle of a 'taxon' dimension with a mandatory human-readable taxon name and at least one taxon identifier from a source recognised by CF. There is no upper limit on the number of taxon identifiers. I proposed two sources CF should recognise initially:
AphiaID from World Register for Marine Species
TSN (Taxonomic Serial Number) from Integrated Taxonomic Information System
John Graybeal made the point that this is restrictive and that we should allow for the possibility of other sources such as the Catalog of Life LSID (Life Science Identifier). LSIDs are multiple-namespace URNs that can be encoded to include either AphiaIDs or TSNs. For example, the copepod Calocalanus pavo may be represented by LSIDs urn:lsid:marinespecies.org:taxname:104669 (based on WoRMS) and urn:lsid:itis.gov:itis_tsn:85335 (based on ITIS) and possibly others from sources unknown to me. These URNs may be converted to URLs delivering RDF by prefixing with '
http://lsid.tdwg.org/'.
So, we could get by with a 'taxon' dimension containing two character arrays, one for the taxon and and the other for the LSID without any need for any other integer identifiers. I could live with this approach, could you? Does anybody else on the list find this objectionable?
If this proves acceptable, then I'll put in a Standard Name proposal covering generic forms of abundance, Daniel's biomass expressions (e.g. mass_concentration_of_taxon_expressed_as_carbon_in_sea_water), the taxon name and the taxon identifier. Whilst that is being considered I'll prepare a CDL example and draft text for CF1.8 and update the Trac ticket.
How does that sound?
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 Jonathan Gregory <jonathan.gregory at ncas.ac.uk>
Sent: 29 March 2018 17:46
To: cf-metadata at cgd.ucar.edu
Subject: [CF-metadata] Proposing new names for marine biogeochemical modeling
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<http://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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>
>
>
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