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 enquiries at bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
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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 enquiries at bodc.ac.uk. Please also use this e-mail if your requirement is urgent.
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From: Daniel Neumann <daniel.neumann at 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 enquiries at bodc.ac.uk<mailto:enquiries at bodc.ac.uk>. Please also use this e-mail if your requirement is urgent.
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Physical Oceanography and Instrumentation
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