Re: [CF-metadata] Standard Names to support Trac ticket 99
Many thanks, I'll have a look at Section 6 and get back to you if I've any further queries or issues. I wasn't sure how much had changed since 1.5 and consequently whether you're previous comments were still valid. Cheers, Roy. I have now retired but will continue to be active through an Emeritus Fellowship using this e-mail address. From: CF-metadata on behalf of Jonathan Gregory Sent: 12 July 2018 17:48 To: cf-metadata@cgd.ucar.edu Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 Dear Roy Ah, OK. Thanks. Having thought about that, I went to look at ticket 99, and found that I'd said the same thing five years ago in comment 1. As you see, I'm bit-reproducible. I propose that we should tidy the CF document by promoting 6.1.1 on "Geographic regions" to 6.3 (i.e. remove it from 6.1), and adding yours as 6.4. Then 6.1 and 6.2 will describe mechanisms in CF, and 6.3 and 6.4 applications of these mechanisms. Does that seem OK? Jonathan - Forwarded message from "Lowry, Roy K." - > Date: Thu, 12 Jul 2018 16:04:07 + > From: "Lowry, Roy K." > To: "cf-metadata@cgd.ucar.edu" , > "j.m.greg...@reading.ac.uk" > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > 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 on behalf of Jonathan > Gregory > Sent: 12 July 2018 16:36 > To: cf-metadata@cgd.ucar.edu > 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." - > > > Date: Thu, 12 Jul 2018 11:54:57 + > > From: "Lowry, Roy K." > > To: Jonathan Gregory , "cf-metadata@cgd.ucar.edu" > > > > 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:::[:]’. 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 cons
Re: [CF-metadata] Standard Names to support Trac ticket 99
Dear Roy Ah, OK. Thanks. Having thought about that, I went to look at ticket 99, and found that I'd said the same thing five years ago in comment 1. As you see, I'm bit-reproducible. I propose that we should tidy the CF document by promoting 6.1.1 on "Geographic regions" to 6.3 (i.e. remove it from 6.1), and adding yours as 6.4. Then 6.1 and 6.2 will describe mechanisms in CF, and 6.3 and 6.4 applications of these mechanisms. Does that seem OK? Jonathan - Forwarded message from "Lowry, Roy K." - > Date: Thu, 12 Jul 2018 16:04:07 + > From: "Lowry, Roy K." > To: "cf-metadata@cgd.ucar.edu" , > "j.m.greg...@reading.ac.uk" > Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99 > > 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 on behalf of Jonathan > Gregory > Sent: 12 July 2018 16:36 > To: cf-metadata@cgd.ucar.edu > 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." - > > > Date: Thu, 12 Jul 2018 11:54:57 + > > From: "Lowry, Roy K." > > To: Jonathan Gregory , "cf-metadata@cgd.ucar.edu" > > > > 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:::[:]’. 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’, whe
Re: [CF-metadata] Standard Names to support Trac ticket 99
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 on behalf of Jonathan Gregory Sent: 12 July 2018 16:36 To: cf-metadata@cgd.ucar.edu 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." - > Date: Thu, 12 Jul 2018 11:54:57 + > From: "Lowry, Roy K." > To: Jonathan Gregory , "cf-metadata@cgd.ucar.edu" > > 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:::[:]’. 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 chemica
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." - > Date: Thu, 12 Jul 2018 11:54:57 + > From: "Lowry, Roy K." > To: Jonathan Gregory , "cf-metadata@cgd.ucar.edu" > > 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:::[:]’. 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_concentrati
Re: [CF-metadata] Standard Names to support Trac ticket 99
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 on behalf of Jonathan Gregory Sent: 21 May 2018 16:37 To: cf-metadata@cgd.ucar.edu 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." - > Date: Mon, 21 May 2018 08:02:05 + > From: "Lowry, Roy K." > To: Martin Juckes - UKRI STFC , >"cf-metadata@cgd.ucar.edu" , >"j.m.greg...@reading.ac.uk" > 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 > Sent: 02 May 2018 08:47 > To: cf-metadata@cgd.ucar.edu; j.m.greg...@reading.ac.uk; 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 on behalf of Jonathan > Gregory > Sent: 01 May 2018 17:08 > To: cf-metadata@cgd.ucar.edu > 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 > > > ---
Re: [CF-metadata] Standard Names to support Trac ticket 99
Dear Jonathan, I'll go back to the biological experts and see what they think. They were recommending 'biological entity', but I thought that might cause issues because it would bring into scope morphological classifications and bits of organisms such as 'cod liver' for which there is no (to my knowledge) governance in place like there is with taxon. 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: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan Gregory <j.m.greg...@reading.ac.uk> Sent: 21 May 2018 16:37 To: cf-metadata@cgd.ucar.edu 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." <r...@bodc.ac.uk> - > Date: Mon, 21 May 2018 08:02:05 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: Martin Juckes - UKRI STFC <martin.juc...@stfc.ac.uk>, >"cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > "j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > 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 <martin.juc...@stfc.ac.uk> > Sent: 02 May 2018 08:47 > To: cf-metadata@cgd.ucar.edu; j.m.greg...@reading.ac.uk; 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 <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > Gregory <j.m.greg...@reading.ac.uk> > Sent: 01 May 2018 17:08 > To: cf-metadata@cgd.ucar.edu > 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." <r...@bodc.ac.uk> - > > > Date: Fri, 27 Apr 2018 11:55:26 + > > From: "Lowry, Roy K." <r...@bodc.ac.uk> > > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > >"j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > > 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 th
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." <r...@bodc.ac.uk> - > Date: Mon, 21 May 2018 08:02:05 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: Martin Juckes - UKRI STFC <martin.juc...@stfc.ac.uk>, > "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > "j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > 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 <martin.juc...@stfc.ac.uk> > Sent: 02 May 2018 08:47 > To: cf-metadata@cgd.ucar.edu; j.m.greg...@reading.ac.uk; 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 <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > Gregory <j.m.greg...@reading.ac.uk> > Sent: 01 May 2018 17:08 > To: cf-metadata@cgd.ucar.edu > 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." <r...@bodc.ac.uk> - > > > Date: Fri, 27 Apr 2018 11:55:26 + > > From: "Lowry, Roy K." <r...@bodc.ac.uk> > > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > >"j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > > 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 > > enquir...@bodc.ac.uk. Please also use this e-mail if your requirement is > > urgent. > > > > > > > > From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > > Gregory <jonathan.greg...@ncas.ac.uk> > > Sent: 16 April 2018 19:19 > > To: cf-metadata@cgd.ucar.edu > &g
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 <martin.juc...@stfc.ac.uk> Sent: 02 May 2018 08:47 To: cf-metadata@cgd.ucar.edu; j.m.greg...@reading.ac.uk; 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 <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan Gregory <j.m.greg...@reading.ac.uk> Sent: 01 May 2018 17:08 To: cf-metadata@cgd.ucar.edu 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." <r...@bodc.ac.uk> - > Date: Fri, 27 Apr 2018 11:55:26 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, >"j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > 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 enquir...@bodc.ac.uk. > Please also use this e-mail if your requirement is urgent. > > > ____________ > From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > Gregory <jonathan.greg...@ncas.ac.uk> > Sent: 16 April 2018 19:19 > To: cf-metadata@cgd.ucar.edu > 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." <r...@bodc.ac.uk> - > > > Date: Fri, 13 Apr 2018 14:02:59 + > > From: "Lowry, Roy K." <r...@bodc.ac.uk> > >
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 <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan Gregory <j.m.greg...@reading.ac.uk> Sent: 01 May 2018 17:08 To: cf-metadata@cgd.ucar.edu 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." <r...@bodc.ac.uk> - > Date: Fri, 27 Apr 2018 11:55:26 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > "j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > 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 enquir...@bodc.ac.uk. > Please also use this e-mail if your requirement is urgent. > > > ________ > From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > Gregory <jonathan.greg...@ncas.ac.uk> > Sent: 16 April 2018 19:19 > To: cf-metadata@cgd.ucar.edu > 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." <r...@bodc.ac.uk> - > > > Date: Fri, 13 Apr 2018 14:02:59 + > > From: "Lowry, Roy K." <r...@bodc.ac.uk> > > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu> > > 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 > > pro
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." <r...@bodc.ac.uk> - > Date: Fri, 27 Apr 2018 11:55:26 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu>, > "j.m.greg...@reading.ac.uk" <j.m.greg...@reading.ac.uk> > 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 enquir...@bodc.ac.uk. > Please also use this e-mail if your requirement is urgent. > > > > From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan > Gregory <jonathan.greg...@ncas.ac.uk> > Sent: 16 April 2018 19:19 > To: cf-metadata@cgd.ucar.edu > 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." <r...@bodc.ac.uk> - > > > Date: Fri, 13 Apr 2018 14:02:59 + > > From: "Lowry, Roy K." <r...@bodc.ac.uk> > > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu> > > 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 > > > > > &
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 enquir...@bodc.ac.uk. Please also use this e-mail if your requirement is urgent. From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan Gregory <jonathan.greg...@ncas.ac.uk> Sent: 16 April 2018 19:19 To: cf-metadata@cgd.ucar.edu 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." <r...@bodc.ac.uk> - > Date: Fri, 13 Apr 2018 14:02:59 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu> > 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:::[:]’. 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:::[:]’. For example, the > copepod Caloca
[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." <r...@bodc.ac.uk> - > Date: Fri, 13 Apr 2018 14:02:59 + > From: "Lowry, Roy K." <r...@bodc.ac.uk> > To: "cf-metadata@cgd.ucar.edu" <cf-metadata@cgd.ucar.edu> > 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:::[:]’. 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:::[:]’. 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
[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:::[:]’. 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:::[:]’. 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
