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. ________________________________
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