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 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
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’, 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
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 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
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_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 >
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_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
