Re: [CF-metadata] Fw: Standard Names to support Trac ticket 99

[Lowry, Roy K.]

Thanks Alison,


Think biological_taxon_lsid is the preferred option.


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  on behalf of Alison 
Pamment - UKRI STFC 
Sent: 27 April 2018 13:38
To: CF-metadata (cf-metadata@cgd.ucar.edu)
Subject: Re: [CF-metadata] Fw: Standard Names to support Trac ticket 99

Dear Roy et al,

Thank you for the standard name proposals relating to Trac ticket 99 and the 
discussion of these. I have added all the proposals to the standard names 
editor: 
http://cfeditor.ceda.ac.uk/proposals/1?status=active==Lowry99+and+display=Filter.
 Initially I made entries for both biological_taxon_lsid and 
biological_taxon_identifier and added a note that only one of these will be 
chosen for publication. The discussion seems to be leaning towards choosing 
biological_taxon_lsid so I have now marked biological_taxon_identifier as 
"rejected" and it no longer appears among the active list of proposals. 
However, I can revive it if necessary. As has been discussed, we can add 
further standard names in the future if there is a need to support other 
identifiers besides lsid.

1. 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/;.'

Is this okay? Can we regard this as agreed?

Regarding the other proposals, apart from minor adjustments to make the 
definitions consistent with those of existing names, e.g. the text for "number 
concentration" and for "chlorophyll" I think they are very clear and could be 
accepted pretty much in the form Roy proposed them. I haven't marked them as 
accepted in the editor as yet, because that would cause them to be 
automatically included in the next standard name table update, and I think we 
should wait until Trac ticket 99 is formally agreed before actually putting the 
names in the table. However, I think we can regard them as "agreed". For 
convenience I've listed them in full below.

2. biological_taxon_name
"A plain text 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."

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

3. number_concentration_of_biological_taxon_in_sea_water (m-3)
' "Number concentration" means the number of particles or other specified 
objects per unit volume. It 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".'

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

4. mass_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water (kg 
m-3)
'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.'

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

5. mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water 
(kg m-3)
'Mass concentration means mass per unit volume and is used in the construction 

Re: [CF-metadata] Fw: Standard Names to support Trac ticket 99

[Alison Pamment - UKRI STFC]

Dear Roy et al,

Thank you for the standard name proposals relating to Trac ticket 99 and the 
discussion of these. I have added all the proposals to the standard names 
editor: 
http://cfeditor.ceda.ac.uk/proposals/1?status=active==Lowry99+and+display=Filter.
 Initially I made entries for both biological_taxon_lsid and 
biological_taxon_identifier and added a note that only one of these will be 
chosen for publication. The discussion seems to be leaning towards choosing 
biological_taxon_lsid so I have now marked biological_taxon_identifier as 
"rejected" and it no longer appears among the active list of proposals. 
However, I can revive it if necessary. As has been discussed, we can add 
further standard names in the future if there is a need to support other 
identifiers besides lsid.

1. 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/;.'

Is this okay? Can we regard this as agreed?

Regarding the other proposals, apart from minor adjustments to make the 
definitions consistent with those of existing names, e.g. the text for "number 
concentration" and for "chlorophyll" I think they are very clear and could be 
accepted pretty much in the form Roy proposed them. I haven't marked them as 
accepted in the editor as yet, because that would cause them to be 
automatically included in the next standard name table update, and I think we 
should wait until Trac ticket 99 is formally agreed before actually putting the 
names in the table. However, I think we can regard them as "agreed". For 
convenience I've listed them in full below.

2. biological_taxon_name
"A plain text 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."

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

3. number_concentration_of_biological_taxon_in_sea_water (m-3)
' "Number concentration" means the number of particles or other specified 
objects per unit volume. It 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".'

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

4. mass_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water (kg 
m-3)
'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.'

This name is agreed and will be accepted for publication, pending agreement of 
CF Trac ticket #99.

5. mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water 
(kg m-3)
'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. Chlorophylls are the green pigments found in 
most plants, algae and cyanobacteria; their presence is essential for 
photosynthesis to take place. There are several different forms of 

Re: [CF-metadata] Standard Names to support Trac ticket 99

[Lowry, Roy K.]

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  on behalf of Jonathan 
Gregory 
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."  -

> Date: Fri, 13 Apr 2018 14:02:59 +
> From: "Lowry, Roy K." 
> To: "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
>
> 

Re: [CF-metadata] use of integral_wrt_depth_of_sea_water_practical_salinity

[Alison Pamment - UKRI STFC]

Dear Sebastien, All,

I have just been reading through this thread and it raises some interesting 
points. 

When I made my original comments back in 2016 (that 
ocean_integral_wrt_depth_of_sea_water_practical_salinity (i.e. integral over 
the whole depth from sea floor to surface) is a special case of 
integral_wrt_depth_of_sea_water_practical_salinity) I don't think I had fully 
thought through how one would go about specifying the limits for the full depth 
case.  I see now that we don't really have an agreed mechanism for doing this, 
although a number of ideas have been put forward. I agree with Martin's comment 
that one would expect to look at the coordinates and coordinate bounds for the 
limits of an integral - certainly that's what we do for cases where the limits 
define a layer and I think it's preferable  to treat the full depth case 
similarly.

Jonathan suggested making the existing in_atmosphere_layer/in_ocean_layer names 
aliases of the full depth atmosphere/ocean names and stating in the definition 
that if coordinate bounds are not specified it means the entire vertical extent 
of the atmosphere/ocean. The question that Sebastien has raised is concerned 
specifically with how to state the limits on the integral_wrt_Y_of_X names and 
I do think we can solve the problem by modifying the definitions along the 
lines Jonathan suggests. Currently the definitions all say 'The phrase 
"integral_wrt_X_of_Y" means int Y dX. The data variable should have an axis for 
X specifying the limits of the integral as bounds.' We could modify this to 
read 'The phrase "integral_wrt_X_of_Y" means int Y dX. To specify the limits of 
the integral the data variable should have an axis for X and associated 
coordinate bounds. If no axis for X is associated with the data variable, or no 
coordinate bounds are specified, it is assumed that the integral is calculated 
over the entire vertical extent of the medium, e.g, if the medium is air the 
integral is assumed to be calculated over the full depth of the atmosphere.'

If we take this approach then Sebastien could use the existing 
integral_wrt_depth_of_sea_water_practical_salinity name and it would cover all 
use cases. Do others agree? If so, then I will modify the definitions of all 
387 existing integral names in the next update. This will create some 
housekeeping work for the standard name table, but it avoids the need to modify 
the conventions which would be necessary for some of the other ideas that have 
been discussed in this thread.

As to whether we should make layer names into aliases, e.g. 
mass_content_of_cloud_ice_in_atmosphere_layer becoming an alias of 
atmosphere_mass_content_of_cloud_ice, we could certainly do this by taking a 
similar approach regarding  bounds in the definitions, but strictly speaking, 
it's not necessary to do this to address Sebastien's question. Also, if we are 
trying to be completely consistent about integrals and layers, it raises the 
question of whether atmosphere_mass_content, atmosphere_mole_content, etc,  
names should all be changed to integral names. For example, should both the 
existing mass_content_of_cloud_ice names be turned into aliases of a new name 
integral_wrt_height_of_mass_of_cloud_ice_in_air? Personally, I don't feel it 
would make the names any clearer so I'm not keen on following that idea. I 
think it's preferable to stick with fixing the integral definitions to cope 
with all bounds possibilities.

Best wishes,
Alison

--
Alison Pamment Tel: +44 1235 778065
NCAS/Centre for Environmental Data ArchivalEmail: alison.pamm...@stfc.ac.uk
STFC Rutherford Appleton Laboratory 
R25, 2.22
Harwell Oxford, Didcot, OX11 0QX, U.K.


-Original Message-
From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of 
Jonathan Gregory
Sent: 16 April 2018 19:53
To: cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] use of 
integral_wrt_depth_of_sea_water_practical_salinity

Dear Sebastien et al.

It's allowed to put "depth: mean" in cell_methods even if there is no depth 
coordinate variable (and no bounds). This is described in sect 7.3.4 of the 
convention. It's allowed by the "first" case described there, because depth is 
a standard name. We could suit your case better if we explicitly allowed the 
"second" case of 7.3.4 to apply to the vertical coordinate, meaning the range 
over the complete vertical extent where the quantity is defined i.e.
from the sea surface to the sea floor for an ocean quantity. Would this be a 
good solution?

Since some more general issues have been raised, I'd like to comment on them.

First, there are a number of pairs of standard names, where one of the pair is 
for the whole vertical extent of the atmosphere or the ocean, and the other is 
for a layer within it e.g.
  atmosphere_mass_content_of_cloud_ice
  mass_content_of_cloud_ice_in_atmosphere_layer
This is my fault or choice, I believe, but from a *long* time ago