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 +0000 > 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 +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 > ________________________________ > 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
