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
