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 +0000 > 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 +0000 > > 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:<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 > > enquir...@bodc.ac.uk. 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 > > CF-metadata@cgd.ucar.edu > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > > ----- End forwarded message ----- > _______________________________________________ > CF-metadata mailing list > CF-metadata@cgd.ucar.edu > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > ________________________________ > This message (and any attachments) is for the recipient only. NERC is subject > to the Freedom of Information Act 2000 and the contents of this email and any > reply you make may be disclosed by NERC unless it is exempt from release > under the Act. Any material supplied to NERC may be stored in an electronic > records management system. > ________________________________ ----- End forwarded message ----- _______________________________________________ CF-metadata mailing list CF-metadata@cgd.ucar.edu http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata _______________________________________________ CF-metadata mailing list CF-metadata@cgd.ucar.edu http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
