search

cf-convention / vocabularies

Issues and source files for CF controlled vocabularies
3 stars 0 forks source link

Standard names in support of conventions issue #218 - biological taxa #110

Closed japamment closed 4 years ago

japamment commented 4 years ago

Original proposer: Roy Lowry Original proposal date: 13 April 2018 Original CF mailing list discussion: http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2018/019979.html

These names relate to cf-convention/cf-conventions issue #218 (Taxon Names and Identifiers) which was previously discussed in cf trac ticket #99.

Conventions issue cf-convention/vocabularies#35 has been formally accepted and the proposed changes will be included in CF 1.8.

Four names are proposed in issue cf-convention/vocabularies#35, as detailed below.

  1. biological_taxon_name (string valued) ' "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 quantity with standard name biological_taxon_name is the human-readable label for the taxon such as Calanus finmarchicus. The label should be registered in either WoRMS (http://www.marinespecies.org) or ITIS (https://www.itis.gov/) and spelled exactly as registered. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  2. biological_taxon_identifier (string valued) ' "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 quantity with standard name biological_taxon_identifier is the machine-readable identifier for the taxon registration in either WoRMS (the AphiaID) or ITIS (the taxonomic serial number or TSN), including namespace. The namespace strings are 'aphia:' or 'tsn:'. For example, Calanus finmarchicus is encoded as either 'aphia:104464' or 'tsn:85272'. For the marine domain WoRMS has more complete coverage and so aphia Ids are preferred. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  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. "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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  4. colony_forming_unit_number_concentration_of_biological_taxon_in_sea_water (m-3) ' "Colony forming unit" means an estimate of the viable bacterial or fungal numbers determined by counting colonies grown from a sample. "Number concentration" means the number of particles or other specified objects per unit volume. "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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

The names themselves differ slightly from the original mailing list discussion but are consistent with the latest version of issue cf-convention/vocabularies#35. I have added some additional text to the definitions (taken from the mailing list discussion) to define "biological taxon" and added a reference to the new section of the conventions document. @roy-lowry please could you check through and let me know if you are happy with these - if so I think they can be accepted for publication in the standard name table.

In the mailing list discussion a further five names were discussed and agreed in principle, pending the original trac ticket being finalised. I have reworked the definitions a little to be consistent with the wording of names 1-4 above and the recent cf-convention/discuss issues #24 and #25 regarding removing "biological species" from the text. Again, @roy-lowry please could you check and let me know if these are okay - if so they can be accepted for publication in the standard name table.

  1. 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 or biological group 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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  2. 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 species or biological group 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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables. 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 chlorophyll that occur naturally. All contain a chlorin ring (chemical formula C20H16N4) which gives the green pigment and a side chain whose structure varies. The naturally occurring forms of chlorophyll contain between 35 and 55 carbon atoms.'

  3. mass_concentration_of_biological_taxon_expressed_as_nitrogen_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 or biological group 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". There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  4. mole_concentration_of_biological_taxon_expressed_as_carbon_in_sea_water (mol m-3) ' "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 or biological group 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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

  5. mole_concentration_of_biological_taxon_expressed_as_nitrogen_in_sea_water (mol m-3) ' "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 or biological group 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. There must be an auxiliary coordinate variable with standard name biological_taxon_name to identify the taxon in human readable format and optionally an auxiliary coordinate variable with standard name biological_taxon_identifier to provide a machine-readable identifier. See Section 6.1.2 of the CF convention (version 1.8 or later) for information about biological taxon auxiliary coordinate variables.'

roy-lowry commented 4 years ago

Excellent job that looks good to go to me. Many thanks.

japamment commented 4 years ago

@roy-lowry many thanks - these names are now accepted for publication in the standard name table and will be added in the 3rd February update.

feggleton commented 4 years ago

These changes have been published in version 71 of the standard name table.