Forgot to do reply all....

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: Lowry, Roy K.
Sent: 16 April 2018 11:09
To: Daniel Neumann
Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99


Thanks Daniel,


To clarify LSID isn't a database, it's an identifier for an organism that 
neatly brings together multiple taxonomies under the single umbrella of the 
Catalogue of Life project. It also resolves, actually in multiple ways, into a 
URL that then provides access into a database providing information on that 
organism.


We came to the conclusion that we should use LSIDs in CF in the first round of 
discussions on Trac 99. My quandary is not whether we should use them, but 
whether the Standard Name should specify 'lsid' or just 'identifier'.  
'Identifier' is what we discussed, but 'lsid' opens the door for future 
Standard Names based on other governances should there be a need to deal with 
entities not covered by lsids. I'm aware of one possible issue related to 
coccoliths plus the possibility of dealing with organism parts (e.g. cod 
livers).


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: Daniel Neumann <daniel.neum...@io-warnemuende.de>
Sent: 16 April 2018 10:44
To: Lowry, Roy K.
Subject: Re: [CF-metadata] Standard Names to support Trac ticket 99

Dear Roy,

Thank you for bringing this topic forward!

I contacted the responsible person for our institute's data publishing und 
metadata policy and will talk to her about the choice of the LSID database. She 
is more into that topic than I am. It may take some days.

Cheers,
Daniel


On 13.04.2018 16:02, Lowry, Roy K. wrote:

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<mailto: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 
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the Act. Any material supplied to NERC may be stored in an electronic records 
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Daniel Neumann

Leibniz Institute for Baltic Sea Research Warnemuende
Physical Oceanography and Instrumentation
Seestrasse 15
18119 Rostock
Germany

phone:  +49-381-5197-287
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