Dear Jonathan,
The extra text that I am preparing in the Trac ticket for addition to the CF Conventions. I was hoping your familiarity with these could recommend a suitable section for amendment. Cheers, Roy. I have now retired but will continue to be active through an Emeritus Fellowship using this e-mail address. ________________________________ From: CF-metadata <[email protected]> on behalf of Jonathan Gregory <[email protected]> Sent: 12 July 2018 16:36 To: [email protected] Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 Dear Roy That's good news. Thanks for your patience. I like this new proposal, but I'm not sure what you're asking me. Which extra text? Best wishes Jonathan ----- Forwarded message from "Lowry, Roy K." <[email protected]> ----- > Date: Thu, 12 Jul 2018 11:54:57 +0000 > From: "Lowry, Roy K." <[email protected]> > To: Jonathan Gregory <[email protected]>, "[email protected]" > <[email protected]> > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > Dear Jonathan, > > > Getting back to this now I've had some feedback. 'organisms_in_taxon' is fine > and a remodelled proposal on this basis is given below. I'll try and get to > your comments on the trac proposal in the coming week. To save me a lot of > reading would you have a recommendation on where I should look to add the > extra text? > > > Cheers, Roy. > > biological_taxon_name > biological_taxon_lsid > number_concentration_of_organisms_in_taxon_in_sea_water > mass_concentration_of_organisms_in_taxon_expressed_as_carbon_in_sea_water > mass_concentration_of_organisms_in_taxon_expressed_as_chlorophyll_in_sea_water > mass_concentration_of_organisms_in_taxon_expressed_as_nitrogen_in_sea_water > mole_concentration_of_organisms_in_taxon_expressed_as_carbon_in_sea_water > mole_concentration_of_organisms_in_taxon_expressed_as_nitrogen_in_sea_water > > > biological_taxon_name > > A plaintext human-readable label, usually a Latin binomial such as Calanus > finmarchicus, applied to a biological taxon. Biological taxon is a name or > other label identifying an organism or a group of organisms as belonging to a > unit of classification in a hierarchical taxonomy. > > dimensionless > > biological_taxon_lsid > > The Life Science Identifier (LSID) is a standard URI for a biological taxon. > Biological taxon is a name or other label identifying an organism or a group > of organisms as belonging to a unit of classification in a hierarchical > taxonomy. The LSID is a URN with the syntax > ‘urn:lsid:<Authority>:<Namespace>:<ObjectID>[:<Version>]’. 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). These URNs may be > converted to URLs delivering RDF by prefixing with 'http://lsid.tdwg.org/'. > > dimensionless > > number_concentration_of_organisms_in_taxon_in_sea_water > > Number concentration means the count of an entity per unit volume and is used > in the construction ‘number_concentration_of_X_in_Y’, where X is a material > constituent of Y.. Biological taxon is a name or other label identifying an > organism or a group of organisms as belonging to a unit of classification in > a hierarchical taxonomy. Number concentration of biota is also referred to as > abundance. > > m-3 > > mass_concentration_of_organisms_in_taxon_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. Mass concentration of biota expressed as carbon is also > referred to as carbon biomass. Biological taxon is a name or other label > identifying an organism or a group of organisms as belonging to a unit of > classification in a hierarchical taxonomy. > > kg m-3 > > mass_concentration_of_organisms_in_taxon_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 contained in A, neglecting all other chemical > constituents of A. Chlorophyll means all naturally occurring pigments of the > chlorophyll group. Biological taxon is a name or other label identifying an > organism or a group of organisms as belonging to a unit of classification in > a hierarchical taxonomy. > > kg m-3 > > mass_concentration_of_organisms_in_taxon_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. Mass concentration of biota expressed as nitrogen is also > referred to as nitrogen biomass. Biological taxon is a name or other label > identifying an organism or a group of organisms as belonging to a unit of > classification in a hierarchical taxonomy. > > kg m-3 > > mole_concentration_of_organisms_in_taxon_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 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. Biological taxon is a name or other label identifying an > organism or a group of organisms as belonging to a unit of classification in > a hierarchical taxonomy. > > mol m-3 > > mole_concentration_of_organisms_in_taxon_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 solely > with respect to the B contained in A, neglecting all other chemical > constituents of A. Biological taxon is a name or other label identifying an > organism or a group of organisms as belonging to a unit of classification in > a hierarchical taxonomy. > > mol m-3 > > > > I have now retired but will continue to be active through an Emeritus > Fellowship using this e-mail address. > > > ________________________________ > From: CF-metadata <[email protected]> on behalf of Jonathan > Gregory <[email protected]> > Sent: 21 May 2018 16:37 > To: [email protected] > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > Dear Roy and Martin > > I think taxonomic_category might be a little better than taxon, but it still > seems obscure to me. Can you see something wrong with organisms_in_taxon (or > _from_ or _belonging_to_) for instance? It is the organisms we mean. > > Best wishes > > Jonathan > > ----- Forwarded message from "Lowry, Roy K." <[email protected]> ----- > > > Date: Mon, 21 May 2018 08:02:05 +0000 > > From: "Lowry, Roy K." <[email protected]> > > To: Martin Juckes - UKRI STFC <[email protected]>, > > "[email protected]" <[email protected]>, > > "[email protected]" <[email protected]> > > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > > > Dear Jonathan, > > > > > > Getting back to Trac 99. I prefer Martin's suggestion here. Are you happy > > with that? > > > > > > Cheers, Roy. > > > > > > I am retiring on 31/05/2018 but will continue to be active through an > > Emeritus Fellowship using this e-mail address. > > > > > > ________________________________ > > From: Martin Juckes - UKRI STFC <[email protected]> > > Sent: 02 May 2018 08:47 > > To: [email protected]; [email protected]; Lowry, Roy K. > > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > > > Dear Roy, Jonathan, > > > > > > I understand the cause of Jonathan's concern: wikipedia suggests a broader > > interpretation of "taxon" which would be consistent with using the word to > > refer to the organisms from a biological taxon, but the Encyclopedia > > Britannica has a narrower and perhaps more scientifically precise > > definition in which "taxon" refers to the name, not the organisms matching > > the name (https://www.britannica.com/science/taxon ). The article uses the > > phrase "taxonomic category" which could be used as an alternative to > > Jonathan's suggestion: > > > > mass_concentration_of_taxonomic_category_expressed_as_carbon_in_sea_water > > > > > > regards, > > > > Martin > > > > > > ________________________________ > > From: CF-metadata <[email protected]> on behalf of Jonathan > > Gregory <[email protected]> > > Sent: 01 May 2018 17:08 > > To: [email protected] > > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > > > Dear Roy > > > > I agree that the confusion is unlikely. Maybe I shouldn't have given that > > example, because it's distracting. My discomfort is just that "taxon" > > doesn't > > mean "organisms" but "name of type of organisms" e.g. in > > mass_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water > > you can substitute your proposed definition of taxon, to get > > > > mass_concentration_of_name_identifying_an_organism_as_belonging_to_a_unit_of_classification_expressed_as_carbon_in_sea_water > > I think you mean > > > > mass_concentration_of_organisms_from_biological_taxon_expressed_as_carbon_in_sea_water > > That's a bit longer, but feels more comfortable to me. > > > > Best wishes > > > > Jonathan > > > > > > ----- Forwarded message from "Lowry, Roy K." <[email protected]> ----- > > > > > Date: Fri, 27 Apr 2018 11:55:26 +0000 > > > From: "Lowry, Roy K." <[email protected]> > > > To: "[email protected]" <[email protected]>, > > > "[email protected]" <[email protected]> > > > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > > > > > Dear Jonathon, > > > > > > > > > I realised that I hadn't replied to this. Think we're all agreed on > > > biological_taxon_lsid. > > > > > > > > > I can't think of an alternative to cover your second comment, but feel > > > that 'number_concentration_of_biological_taxon' with 'concentration' and > > > taxon in the singular is clearly different from > > > 'number_of_biological_taxa', or more likely 'count_of_biological_taxa' > > > and so feel that there is not a significant risk of confusion. > > > > > > > > > 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 > > > [email protected]. Please also use this e-mail if your requirement is > > > urgent. > > > > > > > > > ________________________________ > > > From: CF-metadata <[email protected]> on behalf of > > > Jonathan Gregory <[email protected]> > > > Sent: 16 April 2018 19:19 > > > To: [email protected] > > > Subject: [CF-metadata] Standard Names to support Trac ticket 99 > > > > > > Dear Roy > > > > > > Thanks for this. It looks sensible and well-constructed to me. I have two > > > comments. > > > > > > * In response to your question, I think biological_taxon_lsid is better, > > > since > > > you propose that's what we use. The more generic version would be > > > suitable if > > > we offered a choice about which sort of ID to use, but it would present a > > > difficulty if you wanted to provide more than one kind of ID; this would > > > need > > > more than one coord var, and it would be helpful to give them different > > > standard names. > > > > > > * In the concentration names, I think "biological taxon" means "organisms > > > of biological taxon", doesn't it? I suggest it would be better to spell > > > this > > > out in some way in the standard name. For example, > > > number_concentration_of_biological_taxon_in_sea_water > > > might (surprisingly) be interpreted as meaning how many species there are > > > per unit volume. > > > > > > Best wishes > > > > > > Jonathan > > > > > > > > > ----- Forwarded message from "Lowry, Roy K." <[email protected]> ----- > > > > > > > Date: Fri, 13 Apr 2018 14:02:59 +0000 > > > > From: "Lowry, Roy K." <[email protected]> > > > > To: "[email protected]" <[email protected]> > > > > Subject: [CF-metadata] Standard Names to support Trac ticket 99 > > > > > > > > Dear All, > > > > > > > > > > > > Here is an initial batch of 8 Standard Names to support the CF taxon > > > > dimension. Two are dimension labels whilst the other six are > > > > measurements to which the taxon is a co-ordinate. Five of these are to > > > > cover Daniel's proposal that prompted the resurrection of Ticket 99. > > > > > > > > > > > > I've presented a summary list followed by a full list with units and > > > > definitions. I have one uncertainty in my mind (biological_taxon_label > > > > versus biological_taxon_lsid) where I would really appreciate input. > > > > > > > > > > > > Cheers, Roy. > > > > > > > > biological_taxon_name > > > > biological_taxon_identifier or biological_taxon_lsid – any > > > > preferences???? > > > > number_concentration_of_biological_taxon_in_sea_water > > > > mass_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water > > > > mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water > > > > mass_concentration_of_biological_taxon_expressed_as_nitrogen_in_sea_water > > > > mole_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water > > > > mole_concentration_of_biological_taxon_expressed_as_nitrogen_in_sea_water > > > > > > > > > > > > biological_taxon_name > > > > > > > > A plaintext human-readable label, usually a Latin binomial such as > > > > Calanus finmarchicus, applied to a biological taxon. Biological taxon > > > > is a name or other label identifying an organism or a group of > > > > organisms as belonging to a unit of classification in a hierarchical > > > > taxonomy. > > > > > > > > dimensionless > > > > > > > > biological_taxon_identifier > > > > > > > > An opaque label, most usefully a URI that resolves to an authoritative > > > > information source, applied to a biological taxon. Biological taxon is > > > > a name or other label identifying an organism or a group of organisms > > > > as belonging to a unit of classification in a hierarchical taxonomy. > > > > The identifier adopted for CF is the Life Science Identifier (LSID), a > > > > URN with the syntax > > > > ‘urn:lsid:<Authority>:<Namespace>:<ObjectID>[:<Version>]’. 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). These URNs may be > > > > converted to URLs delivering RDF by prefixing with > > > > 'http://lsid.tdwg.org/'. > > > > > > > > dimensionless > > > > > > > > OR > > > > > > > > biological_taxon_lsid > > > > > > > > The Life Science Identifier (LSID) is a standard URI for a biological > > > > taxon. Biological taxon is a name or other label identifying an > > > > organism or a group of organisms as belonging to a unit of > > > > classification in a hierarchical taxonomy. The LSID is a URN with the > > > > syntax ‘urn:lsid:<Authority>:<Namespace>:<ObjectID>[:<Version>]’. 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). These URNs may be > > > > converted to URLs delivering RDF by prefixing with > > > > 'http://lsid.tdwg.org/'. > > > > > > > > dimensionless > > > > > > > > number_concentration_of_biological_taxon_in_sea_water > > > > > > > > Number concentration means the count of an entity per unit volume and > > > > is used in the construction ‘number_concentration_of_X_in_Y’, where X > > > > is a material constituent of Y.. Biological taxon is a name or other > > > > label identifying an organism or a group of organisms as belonging to a > > > > unit of classification in a hierarchical taxonomy. Number concentration > > > > of biota is also referred to as abundance. > > > > > > > > m-3 > > > > > > > > mass_concentration_of_biological_taxon_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. Mass concentration of biota expressed > > > > as carbon is also referred to as carbon biomass. Biological taxon is a > > > > name or other label identifying an organism or a group of organisms as > > > > belonging to a unit of classification in a hierarchical taxonomy. > > > > > > > > kg m-3 > > > > > > > > > > > > mass_concentration_of_biological_taxon_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 contained in A, neglecting all > > > > other chemical constituents of A. Chlorophyll means all naturally > > > > occurring pigments of the chlorophyll group. Biological taxon is a name > > > > or other label identifying an organism or a group of organisms as > > > > belonging to a unit of classification in a hierarchical taxonomy. > > > > > > > > kg m-3 > > > > > > > > > > > > mass_concentration_of_biological_taxon_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. Mass concentration of biota expressed > > > > as nitrogen is also referred to as nitrogen biomass. Biological taxon > > > > is a name or other label identifying an organism or a group of > > > > organisms as belonging to a unit of classification in a hierarchical > > > > taxonomy. > > > > > > > > kg m-3 > > > > > > > > mole_concentration_of_biological_taxon_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 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. > > > > Biological taxon is a name or other label identifying an organism or a > > > > group of organisms as belonging to a unit of classification in a > > > > hierarchical taxonomy. > > > > > > > > mol m-3 > > > > > > > > mole_concentration_of_biological_taxon_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 solely with respect to the > > > > B contained in A, neglecting all other chemical constituents of A. > > > > Biological taxon is a name or other label identifying an organism or a > > > > group of organisms as belonging to a unit of classification in a > > > > hierarchical taxonomy. > > > > > > > > mol m-3 > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > ________________________________ > > > > 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 > > > ________________________________ > > > 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. > > > ________________________________ > > > > ----- End forwarded message ----- > > _______________________________________________ > > CF-metadata mailing list > > [email protected] > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > ________________________________ > > 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. > > ________________________________ > > ----- End forwarded message ----- > _______________________________________________ > CF-metadata mailing list > [email protected] > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > ________________________________ > 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. > ________________________________ ----- End forwarded message ----- _______________________________________________ CF-metadata mailing list [email protected] http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata ________________________________ 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. ________________________________
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